peptideshaker: peptide_shaker.xml annotate

annotate peptide_shaker.xml @ 48:b72821cab1d7 draft

"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"

author	galaxyp
date	Fri, 15 Jan 2021 14:05:46 +0000
parents	5da80a2c0ef9
children	f2f4695ad996

rev	line source
48 b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	1 <tool id="peptide_shaker" name="Peptide Shaker" version="@PEPTIDESHAKER_VERSION@+galaxy@PEPTIDESHAKER_VERSION_SUFFIX@">
0 a9e90cdcb97a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty galaxyp parents: diff changeset	2 <description>
a9e90cdcb97a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty galaxyp parents: diff changeset	3 Perform protein identification using various search engines based on results from SearchGUI
a9e90cdcb97a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty galaxyp parents: diff changeset	4 </description>
3 8d6c1807c5a5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit d369c3451aaf7bfc8cc4f6f1dc52f6ea604e66bc-dirty iracooke parents: 1 diff changeset	5 <macros>
48 b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	6 <import>macros_basic.xml</import>
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	7 <import>macros_modifications.xml</import>
3 8d6c1807c5a5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit d369c3451aaf7bfc8cc4f6f1dc52f6ea604e66bc-dirty iracooke parents: 1 diff changeset	8 </macros>
0 a9e90cdcb97a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty galaxyp parents: diff changeset	9 <requirements>
42 80ed6522192c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6e846f7195a9e939047ac975c6523e8cf99da6b4 galaxyp parents: 39 diff changeset	10 <requirement type="package" version="@PEPTIDESHAKER_VERSION@">peptide-shaker</requirement>
48 b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	11 <requirement type="package">unzip</requirement>
0 a9e90cdcb97a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty galaxyp parents: diff changeset	12 </requirements>
a9e90cdcb97a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty galaxyp parents: diff changeset	13 <expand macro="stdio" />
42 80ed6522192c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6e846f7195a9e939047ac975c6523e8cf99da6b4 galaxyp parents: 39 diff changeset	14
80ed6522192c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6e846f7195a9e939047ac975c6523e8cf99da6b4 galaxyp parents: 39 diff changeset	15 <command><![CDATA[
80ed6522192c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6e846f7195a9e939047ac975c6523e8cf99da6b4 galaxyp parents: 39 diff changeset	16 ## When supporting more advanced Galaxy versions: command use_shared_home="false"
0 a9e90cdcb97a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty galaxyp parents: diff changeset	17 #from datetime import datetime
a9e90cdcb97a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty galaxyp parents: diff changeset	18 #set $exp_str = "Galaxy_Experiment_%s" % datetime.now().strftime("%Y%m%d%H%M%s")
a9e90cdcb97a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty galaxyp parents: diff changeset	19 #set $samp_str = "Sample_%s" % datetime.now().strftime("%Y%m%d%H%M%s")
a9e90cdcb97a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty galaxyp parents: diff changeset	20 #set $temp_stderr = "peptideshaker_stderr"
18 ffed32e397cb Uploaded galaxyp parents: 17 diff changeset	21 #set $bin_dir = "bin"
48 b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	22 #set $exporting_followup_boolean = False
12 d298e0b6fd72 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 464dc333f2e8d359265e1574b01386c4e7e9d840 iracooke parents: 10 diff changeset	23
42 80ed6522192c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6e846f7195a9e939047ac975c6523e8cf99da6b4 galaxyp parents: 39 diff changeset	24 mkdir output_reports &&
80ed6522192c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6e846f7195a9e939047ac975c6523e8cf99da6b4 galaxyp parents: 39 diff changeset	25 cwd=`pwd` &&
80ed6522192c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6e846f7195a9e939047ac975c6523e8cf99da6b4 galaxyp parents: 39 diff changeset	26 export HOME=\$cwd &&
80ed6522192c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6e846f7195a9e939047ac975c6523e8cf99da6b4 galaxyp parents: 39 diff changeset	27
80ed6522192c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6e846f7195a9e939047ac975c6523e8cf99da6b4 galaxyp parents: 39 diff changeset	28 echo "" > $temp_stderr &&
0 a9e90cdcb97a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty galaxyp parents: diff changeset	29
a9e90cdcb97a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty galaxyp parents: diff changeset	30 ln -s '$searchgui_input' searchgui_input.zip &&
42 80ed6522192c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6e846f7195a9e939047ac975c6523e8cf99da6b4 galaxyp parents: 39 diff changeset	31
48 b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	32 ## OPTIONAL MAIN PARAMETERS
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	33 ## If we have a specific Identification Parameters file to use, we will use it instead of the one provided in the search_gui file
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	34 #if $optional_main_parameters.input_optional_identification_parameters:
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	35 cp '${optional_main_parameters.input_optional_identification_parameters}' SEARCHGUI_IdentificationParameters.par &&
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	36 #else:
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	37 jar xvf searchgui_input.zip SEARCHGUI_IdentificationParameters.par &&
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	38 #end if
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	39 ## Optional Fasta file
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	40 #if $optional_main_parameters.input_fasta_file:
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	41 ## copy the input .fasta file to the working folder
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	42 cp '${optional_main_parameters.input_fasta_file}' './input_fasta_file.fasta' &&
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	43 #end if
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	44 ## Optional Spectrum files: if the user specified input spectra files, we use them
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	45 ## NOTE: != None DOES NOT SEEM TO WORK ANYMORE ON MODERN GALAXIES
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	46 #if str($optional_main_parameters.input_optional_spectrum_files) != 'None' and str($optional_main_parameters.input_optional_spectrum_files) != '':
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	47 mkdir peaklist_input_files &&
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	48 #for $peak_list_file in $optional_main_parameters.input_optional_spectrum_files:
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	49 #if $peak_list_file.is_of_type("mgf"):
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	50 #set $input_name = $peak_list_file.element_identifier.split('/')[-1].replace(".mgf", "") + ".mgf"
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	51 #else if $peak_list_file.is_of_type("mzml"):
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	52 #set $input_name = $peak_list_file.element_identifier.split('/')[-1].replace(".mzml", "") + ".mzml"
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	53 #end if
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	54 ln -s -f '${peak_list_file}' 'peaklist_input_files/${input_name}' &&
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	55 #end for
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	56 #end if
42 80ed6522192c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6e846f7195a9e939047ac975c6523e8cf99da6b4 galaxyp parents: 39 diff changeset	57
48 b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	58 #if str($exporting_options.output_reports) != "None" and str($exporting_options.output_reports) != ""
42 80ed6522192c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6e846f7195a9e939047ac975c6523e8cf99da6b4 galaxyp parents: 39 diff changeset	59 #set $output_reports_list = set(str($exporting_options.output_reports).split(','))
80ed6522192c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6e846f7195a9e939047ac975c6523e8cf99da6b4 galaxyp parents: 39 diff changeset	60 #else
80ed6522192c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6e846f7195a9e939047ac975c6523e8cf99da6b4 galaxyp parents: 39 diff changeset	61 #set $output_reports_list = set()
48 b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	62 #end if
42 80ed6522192c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6e846f7195a9e939047ac975c6523e8cf99da6b4 galaxyp parents: 39 diff changeset	63
0 a9e90cdcb97a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty galaxyp parents: diff changeset	64 ######################
a9e90cdcb97a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty galaxyp parents: diff changeset	65 ## PeptideShakerCLI ##
a9e90cdcb97a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty galaxyp parents: diff changeset	66 ######################
42 80ed6522192c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6e846f7195a9e939047ac975c6523e8cf99da6b4 galaxyp parents: 39 diff changeset	67 (peptide-shaker -Djava.awt.headless=true eu.isas.peptideshaker.cmd.PeptideShakerCLI
80ed6522192c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6e846f7195a9e939047ac975c6523e8cf99da6b4 galaxyp parents: 39 diff changeset	68 -gui 0
0 a9e90cdcb97a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty galaxyp parents: diff changeset	69 -temp_folder \$cwd/PeptideShakerCLI
48 b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	70 -log \$cwd/resources
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	71 -reference '$exp_str'
0 a9e90cdcb97a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty galaxyp parents: diff changeset	72 -identification_files \$cwd/searchgui_input.zip
18 ffed32e397cb Uploaded galaxyp parents: 17 diff changeset	73 -id_params \$cwd/SEARCHGUI_IdentificationParameters.par
48 b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	74 #if $optional_main_parameters.input_fasta_file:
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	75 -fasta_file './input_fasta_file.fasta'
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	76 #end if
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	77 #if str($optional_main_parameters.input_optional_spectrum_files) != 'None' and str($optional_main_parameters.input_optional_spectrum_files) != '':
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	78 -spectrum_files \$cwd/peaklist_input_files
42 80ed6522192c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6e846f7195a9e939047ac975c6523e8cf99da6b4 galaxyp parents: 39 diff changeset	79 #end if
80ed6522192c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6e846f7195a9e939047ac975c6523e8cf99da6b4 galaxyp parents: 39 diff changeset	80
48 b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	81 #if $exporting_options.zip_conditional.zip_output_boolean == 'zip':
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	82 -zip \$cwd/peptideshaker_output.zip
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	83 -out \$cwd/peptideshaker_output.psdb
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	84 #if $exporting_options.zip_conditional.export_mgf_when_zip:
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	85 -output_mgf 1
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	86 #end if
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	87 #else:
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	88 #if $exporting_options.zip_conditional.export_psdb:
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	89 -out \$cwd/peptideshaker_output.psdb
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	90 #end if
42 80ed6522192c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6e846f7195a9e939047ac975c6523e8cf99da6b4 galaxyp parents: 39 diff changeset	91 #end if
0 a9e90cdcb97a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty galaxyp parents: diff changeset	92
48 b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	93 -threads "\${GALAXY_SLOTS:-12}"
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	94
42 80ed6522192c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6e846f7195a9e939047ac975c6523e8cf99da6b4 galaxyp parents: 39 diff changeset	95 ##################################
80ed6522192c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6e846f7195a9e939047ac975c6523e8cf99da6b4 galaxyp parents: 39 diff changeset	96 ## mzidCLI options ##
80ed6522192c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6e846f7195a9e939047ac975c6523e8cf99da6b4 galaxyp parents: 39 diff changeset	97 ##################################
80ed6522192c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6e846f7195a9e939047ac975c6523e8cf99da6b4 galaxyp parents: 39 diff changeset	98
80ed6522192c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6e846f7195a9e939047ac975c6523e8cf99da6b4 galaxyp parents: 39 diff changeset	99 #if $exporting_options.mzidentml_conditional.mzidentml_creation == 1:
80ed6522192c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6e846f7195a9e939047ac975c6523e8cf99da6b4 galaxyp parents: 39 diff changeset	100 -output_file \$cwd/output.mzid
80ed6522192c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6e846f7195a9e939047ac975c6523e8cf99da6b4 galaxyp parents: 39 diff changeset	101 -include_sequences ${exporting_options.mzidentml_conditional.include_sequences}
48 b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	102 #if $exporting_options.mzidentml_conditional.contact_options.contact_options_selector == "yes":
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	103 -contact_first_name "$exporting_options.mzidentml_conditional.contact_options.contact_first_name"
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	104 -contact_last_name "$exporting_options.mzidentml_conditional.contact_options.contact_last_name"
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	105 -contact_email "$exporting_options.mzidentml_conditional.contact_options.contact_email"
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	106 -contact_address "$exporting_options.mzidentml_conditional.contact_options.contact_address"
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	107 #if str($exporting_options.mzidentml_conditional.contact_options.contact_url).strip() != '':
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	108 -contact_url = "$exporting_options.mzidentml_conditional.contact_options.contact_url"
42 80ed6522192c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6e846f7195a9e939047ac975c6523e8cf99da6b4 galaxyp parents: 39 diff changeset	109 #end if
48 b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	110 -organization_name "$exporting_options.mzidentml_conditional.contact_options.organization_name"
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	111 -organization_email "$exporting_options.mzidentml_conditional.contact_options.organization_email"
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	112 -organization_address "$exporting_options.mzidentml_conditional.contact_options.organization_address"
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	113 #if str($exporting_options.mzidentml_conditional.contact_options.organization_url).strip() != '':
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	114 -organization_url = "$exporting_options.mzidentml_conditional.contact_options.organization_url"
42 80ed6522192c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6e846f7195a9e939047ac975c6523e8cf99da6b4 galaxyp parents: 39 diff changeset	115 #end if
80ed6522192c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6e846f7195a9e939047ac975c6523e8cf99da6b4 galaxyp parents: 39 diff changeset	116 #else:
80ed6522192c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6e846f7195a9e939047ac975c6523e8cf99da6b4 galaxyp parents: 39 diff changeset	117 -contact_first_name "Proteomics"
80ed6522192c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6e846f7195a9e939047ac975c6523e8cf99da6b4 galaxyp parents: 39 diff changeset	118 -contact_last_name "Galaxy"
80ed6522192c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6e846f7195a9e939047ac975c6523e8cf99da6b4 galaxyp parents: 39 diff changeset	119 -contact_email "galaxyp@umn.edu"
80ed6522192c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6e846f7195a9e939047ac975c6523e8cf99da6b4 galaxyp parents: 39 diff changeset	120 -contact_address "galaxyp@umn.edu"
80ed6522192c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6e846f7195a9e939047ac975c6523e8cf99da6b4 galaxyp parents: 39 diff changeset	121 -organization_name "University of Minnesota"
80ed6522192c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6e846f7195a9e939047ac975c6523e8cf99da6b4 galaxyp parents: 39 diff changeset	122 -organization_email "galaxyp@umn.edu"
80ed6522192c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6e846f7195a9e939047ac975c6523e8cf99da6b4 galaxyp parents: 39 diff changeset	123 -organization_address "Minneapolis, MN 55455, Vereinigte Staaten"
0 a9e90cdcb97a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty galaxyp parents: diff changeset	124 #end if
42 80ed6522192c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6e846f7195a9e939047ac975c6523e8cf99da6b4 galaxyp parents: 39 diff changeset	125 #end if
0 a9e90cdcb97a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty galaxyp parents: diff changeset	126
48 b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	127 ####################################################################
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	128 ## PeptideShaker Identification Features Reports options ##
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	129 ####################################################################
42 80ed6522192c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6e846f7195a9e939047ac975c6523e8cf99da6b4 galaxyp parents: 39 diff changeset	130 ## Generate Reports if the user has selected one of the 11 additional reports
80ed6522192c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6e846f7195a9e939047ac975c6523e8cf99da6b4 galaxyp parents: 39 diff changeset	131 #if len($output_reports_list) > 0
80ed6522192c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6e846f7195a9e939047ac975c6523e8cf99da6b4 galaxyp parents: 39 diff changeset	132 -out_reports \$cwd/output_reports
80ed6522192c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6e846f7195a9e939047ac975c6523e8cf99da6b4 galaxyp parents: 39 diff changeset	133 -reports #echo ','.join($output_reports_list)#
0 a9e90cdcb97a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty galaxyp parents: diff changeset	134 #end if
a9e90cdcb97a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty galaxyp parents: diff changeset	135
48 b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	136 ####################################################
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	137 ## PeptideShaker Follow-Up Analysis options ##
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	138 ####################################################
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	139 ## TODO: When done in the app, export graph databases, TPP export, recalibrate espectra
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	140
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	141 #if $exporting_options.followup_conditional.followup_conditional_selector == "yes"
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	142 #if $exporting_options.followup_conditional.followup_export_spectra != "off"
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	143 #set $exporting_followup_boolean = True
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	144 -spectrum_folder \$cwd/output_reports -psm_type $exporting_options.followup_conditional.followup_export_spectra
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	145 #end if
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	146 #if $exporting_options.followup_conditional.followup_export_accession_numbers != "off"
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	147 #set $exporting_followup_boolean = True
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	148 -accessions_file \$cwd/output_reports/proteins_accession_numbers.txt -accessions_type $exporting_options.followup_conditional.followup_export_accession_numbers
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	149 #end if
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	150 #if $exporting_options.followup_conditional.followup_export_sequences != "off"
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	151 #set $exporting_followup_boolean = True
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	152 -sequences_file \$cwd/output_reports/proteins_sequences.fasta -sequences_type $exporting_options.followup_conditional.followup_export_sequences
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	153 #end if
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	154 #if $exporting_options.followup_conditional.followup_export_proteoforms != "off"
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	155 #set $exporting_followup_boolean = True
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	156 -proteoforms_file \$cwd/output_reports/proteins_proteoforms.txt
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	157 #end if
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	158 #if $exporting_options.followup_conditional.followup_export_progenesis_conditional.followup_export_progenesis_selector != "off"
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	159 #set $exporting_followup_boolean = True
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	160 -progenesis_file \$cwd/output_reports/progenesis.txt -progenesis_type $exporting_options.followup_conditional.followup_export_progenesis_conditional.followup_export_progenesis_selector
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	161 #if $exporting_options.followup_conditional.followup_export_progenesis_conditional.followup_export_progenesis_selector == "3"
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	162 #set $progenesis_ptms = $exporting_options.followup_conditional.followup_export_progenesis_conditional.followup_export_progenesis_ptms or ''
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	163 #if $progenesis_ptms
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	164 -progenesis_ptms "$progenesis_ptms"
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	165 #end if
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	166 #end if
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	167 #end if
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	168 #if $exporting_options.followup_conditional.followup_export_inclusion_list_conditional.followup_export_inclusion_list_selector != "off"
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	169 #set $exporting_followup_boolean = True
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	170 -inclusion_list_file \$cwd/output_reports/inclusion_list.txt -inclusion_list_format $exporting_options.followup_conditional.followup_export_inclusion_list_conditional.followup_export_inclusion_list_selector
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	171 #set $peptide_filters = $exporting_options.followup_conditional.followup_export_inclusion_list_conditional.followup_export_inclusion_list_peptide_filters or ''
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	172 #if $peptide_filters
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	173 -inclusion_list_peptide_filters "$peptide_filters"
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	174 #end if
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	175 #set $protein_filters = $exporting_options.followup_conditional.followup_export_inclusion_list_conditional.followup_export_inclusion_list_protein_filters or ''
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	176 #if $protein_filters
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	177 -inclusion_list_protein_filters "$protein_filters"
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	178 #end if
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	179 #if $exporting_options.followup_conditional.followup_export_inclusion_list_conditional.followup_export_inclusion_list_rt_window
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	180 -inclusion_list_rt_window $exporting_options.followup_conditional.followup_export_inclusion_list_conditional.followup_export_inclusion_list_rt_window
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	181 #end if
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	182 #end if
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	183 #end if
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	184
42 80ed6522192c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6e846f7195a9e939047ac975c6523e8cf99da6b4 galaxyp parents: 39 diff changeset	185 2>> $temp_stderr)
0 a9e90cdcb97a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty galaxyp parents: diff changeset	186
46 bfda5aacff85 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 1327a0e10d66e5ed6a8b63b211672a724fcac424 galaxyp parents: 45 diff changeset	187 ## If the user chose to zip the results but also export reports out of the zip, we have to unzip them
48 b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	188 #if $exporting_options.zip_conditional.zip_output_boolean == 'zip' and $exporting_options.zip_conditional.export_reports_when_zip and (len(output_reports_list)>0 or $exporting_followup_boolean):
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	189 ## This unzipping command creates a reports folder into the current folder!
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	190 && unzip \$cwd/peptideshaker_output.zip "reports/*" -d \$cwd
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	191 && mv reports/* output_reports
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	192 && rm -r reports
46 bfda5aacff85 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 1327a0e10d66e5ed6a8b63b211672a724fcac424 galaxyp parents: 45 diff changeset	193 #end if
bfda5aacff85 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 1327a0e10d66e5ed6a8b63b211672a724fcac424 galaxyp parents: 45 diff changeset	194
48 b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	195 ## If the user chose to export mgf file/s out of the zip file
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	196 #if $exporting_options.zip_conditional.zip_output_boolean == 'zip' and $exporting_options.zip_conditional.export_mgf_when_zip:
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	197 && mkdir output_mgf
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	198 && mkdir output_cui
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	199 && mv \$cwd/*.mgf output_mgf
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	200 && mv \$cwd/*.cui output_cui
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	201 #end if
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	202
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	203 ## Renaming identification features reports to findable names and moving them to the root folder
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	204 #if len(output_reports_list)>0:
42 80ed6522192c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6e846f7195a9e939047ac975c6523e8cf99da6b4 galaxyp parents: 39 diff changeset	205 #if '0' in $output_reports_list:
80ed6522192c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6e846f7195a9e939047ac975c6523e8cf99da6b4 galaxyp parents: 39 diff changeset	206 && find \$cwd/output_reports -name '*Certificate_of_Analysis.txt' -exec bash -c 'mv "$0" "certificate.txt"' {} \;
80ed6522192c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6e846f7195a9e939047ac975c6523e8cf99da6b4 galaxyp parents: 39 diff changeset	207 #end if
80ed6522192c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6e846f7195a9e939047ac975c6523e8cf99da6b4 galaxyp parents: 39 diff changeset	208 #if '1' in $output_reports_list:
80ed6522192c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6e846f7195a9e939047ac975c6523e8cf99da6b4 galaxyp parents: 39 diff changeset	209 && find \$cwd/output_reports -name '*Default_Hierarchical_Report.txt' -exec bash -c 'mv "$0" "hierarchical.txt"' {} \;
80ed6522192c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6e846f7195a9e939047ac975c6523e8cf99da6b4 galaxyp parents: 39 diff changeset	210 #end if
80ed6522192c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6e846f7195a9e939047ac975c6523e8cf99da6b4 galaxyp parents: 39 diff changeset	211 #if '2' in $output_reports_list:
80ed6522192c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6e846f7195a9e939047ac975c6523e8cf99da6b4 galaxyp parents: 39 diff changeset	212 && find \$cwd/output_reports -name '*Default_PSM_Phosphorylation_Report.txt' -exec bash -c 'mv "$0" "psm_phospho.txt"' {} \;
47 5da80a2c0ef9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit e17bb5a0e4a22c7376b2e7a70cf690262a44a0c6" galaxyp parents: 46 diff changeset	213 #end if
42 80ed6522192c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6e846f7195a9e939047ac975c6523e8cf99da6b4 galaxyp parents: 39 diff changeset	214 #if '3' in $output_reports_list:
80ed6522192c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6e846f7195a9e939047ac975c6523e8cf99da6b4 galaxyp parents: 39 diff changeset	215 && find \$cwd/output_reports -name '*Default_PSM_Report.txt' -exec bash -c 'mv "$0" "psm.txt"' {} \;
80ed6522192c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6e846f7195a9e939047ac975c6523e8cf99da6b4 galaxyp parents: 39 diff changeset	216 #end if
80ed6522192c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6e846f7195a9e939047ac975c6523e8cf99da6b4 galaxyp parents: 39 diff changeset	217 #if '4' in $output_reports_list:
80ed6522192c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6e846f7195a9e939047ac975c6523e8cf99da6b4 galaxyp parents: 39 diff changeset	218 && find \$cwd/output_reports -name '*Default_PSM_Report_with_non-validated_matches.txt' -exec bash -c 'mv "$0" "psm_nonvalidated.txt"' {} \;
80ed6522192c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6e846f7195a9e939047ac975c6523e8cf99da6b4 galaxyp parents: 39 diff changeset	219 #end if
80ed6522192c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6e846f7195a9e939047ac975c6523e8cf99da6b4 galaxyp parents: 39 diff changeset	220 #if '5' in $output_reports_list:
80ed6522192c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6e846f7195a9e939047ac975c6523e8cf99da6b4 galaxyp parents: 39 diff changeset	221 && find \$cwd/output_reports -name '*Default_Peptide_Phosphorylation_Report.txt' -exec bash -c 'mv "$0" "peptides_phospho.txt"' {} \;
80ed6522192c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6e846f7195a9e939047ac975c6523e8cf99da6b4 galaxyp parents: 39 diff changeset	222 #end if
80ed6522192c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6e846f7195a9e939047ac975c6523e8cf99da6b4 galaxyp parents: 39 diff changeset	223 #if '6' in $output_reports_list:
80ed6522192c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6e846f7195a9e939047ac975c6523e8cf99da6b4 galaxyp parents: 39 diff changeset	224 && find \$cwd/output_reports -name '*Default_Peptide_Report.txt' -exec bash -c 'mv "$0" "peptides.txt"' {} \;
80ed6522192c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6e846f7195a9e939047ac975c6523e8cf99da6b4 galaxyp parents: 39 diff changeset	225 #end if
80ed6522192c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6e846f7195a9e939047ac975c6523e8cf99da6b4 galaxyp parents: 39 diff changeset	226 #if '7' in $output_reports_list:
80ed6522192c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6e846f7195a9e939047ac975c6523e8cf99da6b4 galaxyp parents: 39 diff changeset	227 && find \$cwd/output_reports -name '*Default_Peptide_Report_with_non-validated_matches.txt' -exec bash -c 'mv "$0" "peptides_nonvalidated.txt"' {} \;
80ed6522192c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6e846f7195a9e939047ac975c6523e8cf99da6b4 galaxyp parents: 39 diff changeset	228 #end if
80ed6522192c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6e846f7195a9e939047ac975c6523e8cf99da6b4 galaxyp parents: 39 diff changeset	229 #if '8' in $output_reports_list:
80ed6522192c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6e846f7195a9e939047ac975c6523e8cf99da6b4 galaxyp parents: 39 diff changeset	230 && find \$cwd/output_reports -name '*Default_Protein_Phosphorylation_Report.txt' -exec bash -c 'mv "$0" "proteins_phospho.txt"' {} \;
80ed6522192c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6e846f7195a9e939047ac975c6523e8cf99da6b4 galaxyp parents: 39 diff changeset	231 #end if
80ed6522192c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6e846f7195a9e939047ac975c6523e8cf99da6b4 galaxyp parents: 39 diff changeset	232 #if '9' in $output_reports_list:
80ed6522192c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6e846f7195a9e939047ac975c6523e8cf99da6b4 galaxyp parents: 39 diff changeset	233 && find \$cwd/output_reports -name '*Default_Protein_Report.txt' -exec bash -c 'mv "$0" "proteins.txt"' {} \;
80ed6522192c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6e846f7195a9e939047ac975c6523e8cf99da6b4 galaxyp parents: 39 diff changeset	234 #end if
80ed6522192c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6e846f7195a9e939047ac975c6523e8cf99da6b4 galaxyp parents: 39 diff changeset	235 #if '10' in $output_reports_list:
80ed6522192c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6e846f7195a9e939047ac975c6523e8cf99da6b4 galaxyp parents: 39 diff changeset	236 && find \$cwd/output_reports -name '*Default_Protein_Report_with_non-validated_matches.txt' -exec bash -c 'mv "$0" "proteins_nonvalidated.txt"' {} \;
80ed6522192c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6e846f7195a9e939047ac975c6523e8cf99da6b4 galaxyp parents: 39 diff changeset	237 #end if
80ed6522192c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6e846f7195a9e939047ac975c6523e8cf99da6b4 galaxyp parents: 39 diff changeset	238 #if '11' in $output_reports_list:
80ed6522192c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6e846f7195a9e939047ac975c6523e8cf99da6b4 galaxyp parents: 39 diff changeset	239 && find \$cwd/output_reports -name '*Extended_PSM_Report.txt' -exec bash -c 'mv "$0" "psmx.txt"' {} \;
80ed6522192c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6e846f7195a9e939047ac975c6523e8cf99da6b4 galaxyp parents: 39 diff changeset	240 #end if
0 a9e90cdcb97a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty galaxyp parents: diff changeset	241 #end if
a9e90cdcb97a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty galaxyp parents: diff changeset	242
48 b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	243 ## Moving followup analysis to the root folder (it is necessary if zip option was not chosen, or it was chosen but also exporting out of the zip)
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	244 #if $exporting_options.followup_conditional.followup_conditional_selector == "yes" and ($exporting_options.zip_conditional.zip_output_boolean != 'zip' or ($exporting_options.zip_conditional.zip_output_boolean == 'zip' and $exporting_options.zip_conditional.export_reports_when_zip)):
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	245 ## Spectrum analysis are already expected to be into the output_reports folder itself
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	246 #if $exporting_options.followup_conditional.followup_export_accession_numbers != "off"
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	247 && mv \$cwd/output_reports/proteins_accession_numbers.txt \$cwd/proteins_accession_numbers.txt
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	248 #end if
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	249 #if $exporting_options.followup_conditional.followup_export_sequences != "off"
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	250 && mv \$cwd/output_reports/proteins_sequences.fasta \$cwd/proteins_sequences.fasta
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	251 #end if
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	252 #if $exporting_options.followup_conditional.followup_export_proteoforms != "off"
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	253 && mv \$cwd/output_reports/proteins_proteoforms.txt \$cwd/proteins_proteoforms.txt
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	254 #end if
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	255 #if $exporting_options.followup_conditional.followup_export_progenesis_conditional.followup_export_progenesis_selector != "off"
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	256 && mv \$cwd/output_reports/progenesis.txt \$cwd/progenesis.txt
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	257 #end if
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	258 #if $exporting_options.followup_conditional.followup_export_inclusion_list_conditional.followup_export_inclusion_list_selector != "off"
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	259 && mv \$cwd/output_reports/inclusion_list.txt \$cwd/inclusion_list.txt
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	260 #end if
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	261 #end if
42 80ed6522192c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6e846f7195a9e939047ac975c6523e8cf99da6b4 galaxyp parents: 39 diff changeset	262 && cat $temp_stderr 2>&1;
0 a9e90cdcb97a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty galaxyp parents: diff changeset	263 ]]>
a9e90cdcb97a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty galaxyp parents: diff changeset	264 </command>
a9e90cdcb97a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty galaxyp parents: diff changeset	265 <inputs>
6 53bdfaed924d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 5943ced37a55ac06f722af5d4ccd568c300c0ea3 iracooke parents: 3 diff changeset	266 <param name="searchgui_input" format="searchgui_archive" type="data" label="Compressed SearchGUI results"
13 3ccfbb673089 Update to PS 1.1 and SG 2.1.1 iracooke parents: 12 diff changeset	267 help="SearchGUI Results from History">
3ccfbb673089 Update to PS 1.1 and SG 2.1.1 iracooke parents: 12 diff changeset	268 <options options_filter_attribute="metadata.searchgui_major_version" >
3ccfbb673089 Update to PS 1.1 and SG 2.1.1 iracooke parents: 12 diff changeset	269 <filter type="add_value" value="@SEARCHGUI_MAJOR_VERSION@" />
3ccfbb673089 Update to PS 1.1 and SG 2.1.1 iracooke parents: 12 diff changeset	270 </options>
3ccfbb673089 Update to PS 1.1 and SG 2.1.1 iracooke parents: 12 diff changeset	271 </param>
48 b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	272
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	273 <section name="optional_main_parameters" expanded="false" title="Optional main parameters">
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	274 <param format="json" name="input_optional_identification_parameters" type="data" label="Identification parameters" optional="true" help="This optional parameter file will be used instead of the default one"/>
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	275 <param format="fasta" name="input_fasta_file" type="data" label="Fasta file" optional="true" help="This optional fasta file will be used instead of the one included in the SearchGUI file (if it exists). If the SearchGUI file does not include the fasta file, this parameter is must be considered as mandatory."/>
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	276 <param format="mgf,mzml" name="input_optional_spectrum_files" type="data" label="Spectrum files" optional="true" multiple="true" help="Optional spectrum files will be used together with spectra included in the SearchGUI output"/>
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	277 </section>
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	278
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	279 <section name="exporting_options" expanded="true" title="Exporting options" help="All different outputs PeptideShaker may produce">
18 ffed32e397cb Uploaded galaxyp parents: 17 diff changeset	280
48 b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	281 <conditional name="zip_conditional">
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	282 <param name="zip_output_boolean" type="boolean" truevalue="zip" falsevalue="separate" checked="false" label="Compress results into a single zip file" />
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	283 <when value="separate">
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	284 <param name="export_psdb" type="boolean" truevalue="1" falsevalue="0" checked="false" label="Exports PeptideShakers‘ .psdb file" />
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	285 </when>
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	286 <when value="zip">
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	287 <param name="export_reports_when_zip" type="boolean" truevalue="1" falsevalue="0" checked="false" label="Also export reports out of the zip" />
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	288 <param name="export_mgf_when_zip" type="boolean" truevalue="1" falsevalue="0" checked="false" label="Also export mgf file/s out of the zip" help=".cui index files are exported as a different collection too" />
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	289 </when>
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	290 </conditional>
42 80ed6522192c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6e846f7195a9e939047ac975c6523e8cf99da6b4 galaxyp parents: 39 diff changeset	291
80ed6522192c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6e846f7195a9e939047ac975c6523e8cf99da6b4 galaxyp parents: 39 diff changeset	292 <conditional name="mzidentml_conditional">
80ed6522192c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6e846f7195a9e939047ac975c6523e8cf99da6b4 galaxyp parents: 39 diff changeset	293 <param name="mzidentml_creation" type="boolean" truevalue="1" falsevalue="0" checked="true" label="Creates a mzIdentML file" />
80ed6522192c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6e846f7195a9e939047ac975c6523e8cf99da6b4 galaxyp parents: 39 diff changeset	294 <when value="1">
80ed6522192c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6e846f7195a9e939047ac975c6523e8cf99da6b4 galaxyp parents: 39 diff changeset	295 <param name="include_sequences" type="boolean" truevalue="1" falsevalue="0" checked="false" label="Include the protein sequences in the mzIdentML file" />
48 b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	296
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	297 <conditional name="contact_options">
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	298 <param name="contact_options_selector" type="select" label="Contact Information"
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	299 help="Create a Galaxy workflow to save these values">
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	300 <option value="no" selected="True">GalaxyP Project contact (Not suitable for PRIDE submission)</option>
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	301 <option value="yes">Specify Contact Information</option>
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	302 </param>
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	303 <when value="no" />
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	304 <when value="yes">
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	305 <param name="contact_first_name" type="text" value="" label="Contact first name.">
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	306 <validator type="regex" message="">\S+.*</validator>
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	307 </param>
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	308 <param name="contact_last_name" type="text" value="" label="Contact last name.">
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	309 <validator type="regex" message="">\S+.*</validator>
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	310 </param>
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	311 <param name="contact_email" type="text" value="" label="Contact e-mail.">
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	312 <validator type="regex" message="">\S+@\S+</validator>
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	313 </param>
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	314 <param name="contact_address" type="text" value="" label="Contact address.">
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	315 <validator type="regex" message="">\S+.*</validator>
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	316 </param>
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	317 <param name="contact_url" type="text" value="" optional="true" label="Contact URL.">
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	318 </param>
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	319 <param name="organization_name" type="text" value="" label="Organization name.">
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	320 <validator type="regex" message="">\S+.*</validator>
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	321 </param>
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	322 <param name="organization_email" type="text" value="" label="Organization e-mail.">
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	323 <validator type="regex" message="">\S+@\S+</validator>
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	324 </param>
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	325 <param name="organization_address" type="text" value="" label="Organization address.">
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	326 <validator type="regex" message="">\S+.*</validator>
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	327 </param>
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	328 <param name="organization_url" type="text" value="" optional="true" label="Organization URL.">
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	329 </param>
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	330 </when>
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	331 </conditional>
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	332
42 80ed6522192c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6e846f7195a9e939047ac975c6523e8cf99da6b4 galaxyp parents: 39 diff changeset	333 </when>
80ed6522192c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6e846f7195a9e939047ac975c6523e8cf99da6b4 galaxyp parents: 39 diff changeset	334 <when value="0" />
80ed6522192c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6e846f7195a9e939047ac975c6523e8cf99da6b4 galaxyp parents: 39 diff changeset	335 </conditional>
80ed6522192c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6e846f7195a9e939047ac975c6523e8cf99da6b4 galaxyp parents: 39 diff changeset	336
48 b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	337 <!-- FOLLOW-UP REPORTS -->
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	338 <conditional name="followup_conditional">
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	339 <param name="followup_conditional_selector" type="select" label="Follow-up analysis export options">
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	340 <option value="yes">Export follow-up analysis</option>
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	341 <option value="no" selected="True">Do not export</option>
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	342 </param>
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	343 <when value="no" />
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	344 <when value="yes">
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	345 <param name="followup_export_spectra" label="Spectra: Export spectrum files as MGF" type="select" help="Commonly: spectra of Non-Validated PSMs">
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	346 <option value="0" >Spectra of Non-Validated PSMs</option>
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	347 <option value="1" >Spectra of Non-Validated Peptides</option>
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	348 <option value="2" >Spectra of Non-Validated Proteins</option>
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	349 <option value="3" >Spectra of Validated PSMs</option>
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	350 <option value="4" >Spectra of Validated PSMs of Validated Peptides</option>
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	351 <option value="5" >Spectra of validated PSMs of Validated Peptides of Validated Proteins</option>
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	352 <option value="off" selected="True">Do not export</option>
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	353 </param>
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	354 <param name="followup_export_accession_numbers" label="Proteins: Export accession numbers as TXT" type="select" help="Commonly: Main Accession of Validated Protein Groups">
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	355 <option value="0" >Main Accession of Validated Protein Groups</option>
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	356 <option value="1" >All Accessions of Validated Protein Groups</option>
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	357 <option value="2" >Non-Validated Accessions</option>
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	358 <option value="off" selected="True">Do not export</option>
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	359 </param>
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	360 <param name="followup_export_sequences" label="Proteins: Export protein details/sequences in fasta format" type="select" help="Commonly: Main Accession of Validated Protein Groups">
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	361 <option value="0" >Main Accession of Validated Protein Groups</option>
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	362 <option value="1" >All Accessions of Validated Protein Groups</option>
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	363 <option value="2" >Non-Validated Accessions</option>
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	364 <option value="off" selected="True">Do not export</option>
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	365 </param>
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	366 <param name="followup_export_proteoforms" label="Proteins: Export proteoforms as TXT" type="select">
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	367 <option value="on">Export</option>
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	368 <option value="off" selected="True">Do not export</option>
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	369 </param>
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	370 <conditional name="followup_export_progenesis_conditional">
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	371 <param name="followup_export_progenesis_selector" label="Label free quantification: Exports identification results in Progenesis LC-MS compatible format as TXT" type="select" help="Commonly: Validated PSMs of Validated Peptides of Validated Proteins">
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	372 <option value="0">Validated PSMs of Validated Peptides of Validated Proteins</option>
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	373 <option value="1">Validated PSMs of Validated Peptides</option>
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	374 <option value="2">Validated PSMs</option>
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	375 <option value="3">Confidently localized PTMs of Validated PSMs of Validated Peptides of Validated Proteins</option>
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	376 <option value="off" selected="True">Do not export</option>
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	377 </param>
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	378 <when value="0"/>
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	379 <when value="1"/>
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	380 <when value="2"/>
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	381 <when value="3">
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	382 <param name="followup_export_progenesis_ptms" type="select" label="Targeted PTMs" multiple="true"
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	383 help="">
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	384 <expand macro="modifications"/>
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	385 </param>
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	386 </when>
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	387 <when value="off"/>
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	388 </conditional>
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	389 <conditional name="followup_export_inclusion_list_conditional">
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	390 <param name="followup_export_inclusion_list_selector" label="Inclusion/Exclusion list: Exports a file for an inclusion list of validated hits" type="select" help="Commonly: Thermo">
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	391 <option value="0" >Thermo</option>
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	392 <option value="1" >ABI</option>
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	393 <option value="2" >Bruker</option>
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	394 <option value="3" >MassLynx</option>
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	395 <option value="off" selected="True">Do not export</option>
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	396 </param>
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	397 <when value="0">
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	398 <param name="followup_export_inclusion_list_peptide_filters" type="select" label="Peptide Filters" multiple="true" optional="true" display="checkboxes"
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	399 help="">
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	400 <option value="0">Miscleaved Peptides</option>
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	401 <option value="1">Reactive Peptides</option>
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	402 <option value="2">Degenerated Peptides</option>
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	403 </param>
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	404 <param name="followup_export_inclusion_list_protein_filters" type="select" label="Protein Filters" multiple="true" optional="true" display="checkboxes"
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	405 help="">
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	406 <option value="1">Related Proteins</option>
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	407 <option value="2">Related and Unrelated Proteins</option>
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	408 <option value="3">Unrelated Proteins</option>
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	409 </param>
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	410 <param name="followup_export_inclusion_list_rt_window" type="integer" value="20" label="Retention time window for the inclusion list export (in seconds)"
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	411 help=""/>
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	412 </when>
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	413 <when value="1">
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	414 <param name="followup_export_inclusion_list_peptide_filters" type="select" label="Peptide Filters" multiple="true" optional="true" display="checkboxes"
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	415 help="">
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	416 <option value="0">Miscleaved Peptides</option>
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	417 <option value="1">Reactive Peptides</option>
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	418 <option value="2">Degenerated Peptides</option>
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	419 </param>
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	420 <param name="followup_export_inclusion_list_protein_filters" type="select" label="Protein Filters" multiple="true" optional="true" display="checkboxes"
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	421 help="">
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	422 <option value="1">Related Proteins</option>
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	423 <option value="2">Related and Unrelated Proteins</option>
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	424 <option value="3">Unrelated Proteins</option>
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	425 </param>
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	426 <param name="followup_export_inclusion_list_rt_window" type="integer" value="20" label="Retention time window for the inclusion list export (in seconds)"
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	427 help=""/>
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	428 </when>
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	429 <when value="2">
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	430 <param name="followup_export_inclusion_list_peptide_filters" type="select" label="Peptide Filters" multiple="true" optional="true" display="checkboxes"
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	431 help="">
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	432 <option value="0">Miscleaved Peptides</option>
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	433 <option value="1">Reactive Peptides</option>
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	434 <option value="2">Degenerated Peptides</option>
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	435 </param>
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	436 <param name="followup_export_inclusion_list_protein_filters" type="select" label="Protein Filters" multiple="true" optional="true" display="checkboxes"
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	437 help="">
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	438 <option value="1">Related Proteins</option>
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	439 <option value="2">Related and Unrelated Proteins</option>
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	440 <option value="3">Unrelated Proteins</option>
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	441 </param>
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	442 <param name="followup_export_inclusion_list_rt_window" type="integer" value="20" label="Retention time window for the inclusion list export (in seconds)"
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	443 help=""/>
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	444 </when>
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	445 <when value="3">
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	446 <param name="followup_export_inclusion_list_peptide_filters" type="select" label="Peptide Filters" multiple="true" optional="true" display="checkboxes"
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	447 help="">
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	448 <option value="0">Miscleaved Peptides</option>
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	449 <option value="1">Reactive Peptides</option>
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	450 <option value="2">Degenerated Peptides</option>
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	451 </param>
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	452 <param name="followup_export_inclusion_list_protein_filters" type="select" label="Protein Filters" multiple="true" optional="true" display="checkboxes"
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	453 help="">
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	454 <option value="1">Related Proteins</option>
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	455 <option value="2">Related and Unrelated Proteins</option>
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	456 <option value="3">Unrelated Proteins</option>
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	457 </param>
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	458 <param name="followup_export_inclusion_list_rt_window" type="integer" value="20" label="Retention time window for the inclusion list export (in seconds)"
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	459 help=""/>
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	460 </when>
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	461 <when value="off"/>
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	462 </conditional>
46 bfda5aacff85 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 1327a0e10d66e5ed6a8b63b211672a724fcac424 galaxyp parents: 45 diff changeset	463 </when>
42 80ed6522192c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6e846f7195a9e939047ac975c6523e8cf99da6b4 galaxyp parents: 39 diff changeset	464 </conditional>
80ed6522192c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6e846f7195a9e939047ac975c6523e8cf99da6b4 galaxyp parents: 39 diff changeset	465
48 b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	466 <!-- IDENTIFICATION FEATURES REPORTS -->
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	467 <param name="output_reports" type="select" display="checkboxes" multiple="True" optional="true" label="Identification features reports to be generated">
42 80ed6522192c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6e846f7195a9e939047ac975c6523e8cf99da6b4 galaxyp parents: 39 diff changeset	468 <option value="3">PSM Report</option>
80ed6522192c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6e846f7195a9e939047ac975c6523e8cf99da6b4 galaxyp parents: 39 diff changeset	469 <option value="4">PSM Report with non-validated matches</option>
80ed6522192c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6e846f7195a9e939047ac975c6523e8cf99da6b4 galaxyp parents: 39 diff changeset	470 <option value="2">PSM Phosphorylation Report</option>
80ed6522192c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6e846f7195a9e939047ac975c6523e8cf99da6b4 galaxyp parents: 39 diff changeset	471 <option value="11">Extended PSM Report</option>
80ed6522192c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6e846f7195a9e939047ac975c6523e8cf99da6b4 galaxyp parents: 39 diff changeset	472 <option value="6">Peptide Report</option>
80ed6522192c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6e846f7195a9e939047ac975c6523e8cf99da6b4 galaxyp parents: 39 diff changeset	473 <option value="7">Peptide Report with non-validated matches</option>
80ed6522192c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6e846f7195a9e939047ac975c6523e8cf99da6b4 galaxyp parents: 39 diff changeset	474 <option value="5">Peptide Phosphorylation Report</option>
80ed6522192c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6e846f7195a9e939047ac975c6523e8cf99da6b4 galaxyp parents: 39 diff changeset	475 <option value="9">Protein Report</option>
80ed6522192c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6e846f7195a9e939047ac975c6523e8cf99da6b4 galaxyp parents: 39 diff changeset	476 <option value="10">Protein Report with non-validated matches</option>
80ed6522192c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6e846f7195a9e939047ac975c6523e8cf99da6b4 galaxyp parents: 39 diff changeset	477 <option value="8">Protein Phosphorylation Report</option>
80ed6522192c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6e846f7195a9e939047ac975c6523e8cf99da6b4 galaxyp parents: 39 diff changeset	478 <option value="0">Certificate of Analysis</option>
80ed6522192c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6e846f7195a9e939047ac975c6523e8cf99da6b4 galaxyp parents: 39 diff changeset	479 <option value="1">Hierarchical Report</option>
80ed6522192c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6e846f7195a9e939047ac975c6523e8cf99da6b4 galaxyp parents: 39 diff changeset	480 </param>
80ed6522192c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6e846f7195a9e939047ac975c6523e8cf99da6b4 galaxyp parents: 39 diff changeset	481
80ed6522192c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6e846f7195a9e939047ac975c6523e8cf99da6b4 galaxyp parents: 39 diff changeset	482 </section>
0 a9e90cdcb97a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty galaxyp parents: diff changeset	483
a9e90cdcb97a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty galaxyp parents: diff changeset	484 </inputs>
a9e90cdcb97a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty galaxyp parents: diff changeset	485 <outputs>
a9e90cdcb97a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty galaxyp parents: diff changeset	486 <data format="zip" name="output_zip" from_work_dir="peptideshaker_output.zip" label="${tool.name} on ${on_string}: Archive">
42 80ed6522192c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6e846f7195a9e939047ac975c6523e8cf99da6b4 galaxyp parents: 39 diff changeset	487 <filter>exporting_options['zip_conditional']['zip_output_boolean'] is True</filter>
0 a9e90cdcb97a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty galaxyp parents: diff changeset	488 </data>
48 b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	489 <data format="mzid" name="mzidentML" from_work_dir="output.mzid" label="${tool.name} on ${on_string}: mzidentML file">
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	490 <filter>exporting_options['zip_conditional']['zip_output_boolean'] is False and exporting_options['mzidentml_conditional']['mzidentml_creation'] is True</filter>
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	491 </data>
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	492 <data format="peptideshaker_archive" name="output_psdb" from_work_dir="peptideshaker_output.psdb" label="${tool.name} on ${on_string}: PSDB file">
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	493 <filter>exporting_options['zip_conditional']['zip_output_boolean'] is False and exporting_options['zip_conditional']['export_psdb'] is True</filter>
42 80ed6522192c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6e846f7195a9e939047ac975c6523e8cf99da6b4 galaxyp parents: 39 diff changeset	494 </data>
48 b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	495 <collection name="output_mgf" type="list" label="${tool.name} on ${on_string}: Mgf" >
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	496 <filter>exporting_options['zip_conditional']['zip_output_boolean'] is True and exporting_options['zip_conditional']['export_mgf_when_zip'] is True</filter>
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	497 <discover_datasets pattern="__name_and_ext__" directory="output_mgf" ext="mgf"/>
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	498 </collection>
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	499 <collection name="output_cui" type="list" label="${tool.name} on ${on_string}: Cui" >
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	500 <filter>exporting_options['zip_conditional']['zip_output_boolean'] is True and exporting_options['zip_conditional']['export_mgf_when_zip'] is True</filter>
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	501 <discover_datasets pattern="__name_and_ext__" directory="output_cui" ext="cui"/>
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	502 </collection>
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	503
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	504 <!-- Follow-up analysis -->
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	505 <collection name="output_spectra" type="list" label="${tool.name} on ${on_string}: Spectra" >
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	506 <filter>(exporting_options['zip_conditional']['zip_output_boolean'] is False or exporting_options['zip_conditional']['export_reports_when_zip'] is True) and exporting_options['followup_conditional']['followup_conditional_selector'] == 'yes' and exporting_options['followup_conditional']['followup_export_spectra'] != 'off' </filter>
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	507 <discover_datasets pattern="__name_and_ext__" directory="output_reports" ext="mgf"/>
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	508 </collection>
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	509 <data format="txt" name="output_proteins_accessions" from_work_dir="proteins_accession_numbers.txt" label="${tool.name} on ${on_string}: Proteins Accession Numbers">
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	510 <filter>(exporting_options['zip_conditional']['zip_output_boolean'] is False or exporting_options['zip_conditional']['export_reports_when_zip'] is True) and exporting_options['followup_conditional']['followup_conditional_selector'] == 'yes' and exporting_options['followup_conditional']['followup_export_accession_numbers'] != 'off' </filter>
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	511 </data>
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	512 <data format="fasta" name="output_proteins_sequences" from_work_dir="proteins_sequences.fasta" label="${tool.name} on ${on_string}: Proteins Sequences">
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	513 <filter>(exporting_options['zip_conditional']['zip_output_boolean'] is False or exporting_options['zip_conditional']['export_reports_when_zip'] is True) and exporting_options['followup_conditional']['followup_conditional_selector'] == 'yes' and exporting_options['followup_conditional']['followup_export_sequences'] != 'off' </filter>
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	514 </data>
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	515 <data format="txt" name="output_proteoforms" from_work_dir="proteins_proteoforms.txt" label="${tool.name} on ${on_string}: Proteins Proteoforms">
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	516 <filter>(exporting_options['zip_conditional']['zip_output_boolean'] is False or exporting_options['zip_conditional']['export_reports_when_zip'] is True) and exporting_options['followup_conditional']['followup_conditional_selector'] == 'yes' and exporting_options['followup_conditional']['followup_export_proteoforms'] != 'off' </filter>
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	517 </data>
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	518 <data format="txt" name="output_progenesis" from_work_dir="progenesis.txt" label="${tool.name} on ${on_string}: Progenesis">
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	519 <filter>(exporting_options['zip_conditional']['zip_output_boolean'] is False or exporting_options['zip_conditional']['export_reports_when_zip'] is True) and exporting_options['followup_conditional']['followup_conditional_selector'] == 'yes' and exporting_options['followup_conditional']['followup_export_progenesis_conditional']['followup_export_progenesis_selector'] != 'off' </filter>
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	520 </data>
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	521 <data format="txt" name="output_inclusion_list" from_work_dir="inclusion_list.txt" label="${tool.name} on ${on_string}: Inclusion/Exclusion List">
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	522 <filter>(exporting_options['zip_conditional']['zip_output_boolean'] is False or exporting_options['zip_conditional']['export_reports_when_zip'] is True) and exporting_options['followup_conditional']['followup_conditional_selector'] == 'yes' and exporting_options['followup_conditional']['followup_export_inclusion_list_conditional']['followup_export_inclusion_list_selector'] != 'off' </filter>
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	523 </data>
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	524
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	525 <!-- Identification Features outputs -->
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	526 <data format="txt" name="output_certificate" from_work_dir="certificate.txt" label="${tool.name} on ${on_string}: Certificate of Analysis">
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	527 <filter>(exporting_options['zip_conditional']['zip_output_boolean'] is False or exporting_options['zip_conditional']['export_reports_when_zip'] is True) and str(exporting_options['output_reports']) != 'None' and str(exporting_options['output_reports']) != '' and '0' in exporting_options['output_reports']</filter>
0 a9e90cdcb97a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty galaxyp parents: diff changeset	528 </data>
a9e90cdcb97a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty galaxyp parents: diff changeset	529 <data format="tabular" name="output_hierarchical" from_work_dir="hierarchical.txt" label="${tool.name} on ${on_string}: Hierarchical Report">
48 b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	530 <filter>(exporting_options['zip_conditional']['zip_output_boolean'] is False or exporting_options['zip_conditional']['export_reports_when_zip'] is True) and str(exporting_options['output_reports']) != 'None' and str(exporting_options['output_reports']) != '' and '1' in exporting_options['output_reports']</filter>
0 a9e90cdcb97a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty galaxyp parents: diff changeset	531 </data>
a9e90cdcb97a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty galaxyp parents: diff changeset	532 <data format="tabular" name="output_psm_phosphorylation" from_work_dir="psm_phospho.txt" label="${tool.name} on ${on_string}: PSM Phosphorylation Report">
48 b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	533 <filter>(exporting_options['zip_conditional']['zip_output_boolean'] is False or exporting_options['zip_conditional']['export_reports_when_zip'] is True) and str(exporting_options['output_reports']) != 'None' and str(exporting_options['output_reports']) != '' and '2' in exporting_options['output_reports']</filter>
0 a9e90cdcb97a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty galaxyp parents: diff changeset	534 </data>
a9e90cdcb97a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty galaxyp parents: diff changeset	535 <data format="tabular" name="output_psm" from_work_dir="psm.txt" label="${tool.name} on ${on_string}: PSM Report">
48 b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	536 <filter>(exporting_options['zip_conditional']['zip_output_boolean'] is False or exporting_options['zip_conditional']['export_reports_when_zip'] is True) and str(exporting_options['output_reports']) != 'None' and str(exporting_options['output_reports']) != '' and '3' in exporting_options['output_reports']</filter>
42 80ed6522192c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6e846f7195a9e939047ac975c6523e8cf99da6b4 galaxyp parents: 39 diff changeset	537 </data>
80ed6522192c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6e846f7195a9e939047ac975c6523e8cf99da6b4 galaxyp parents: 39 diff changeset	538 <data format="tabular" name="output_psm_nonvalidated" from_work_dir="psm_nonvalidated.txt" label="${tool.name} on ${on_string}: PSM Report with non-validated matches">
48 b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	539 <filter>(exporting_options['zip_conditional']['zip_output_boolean'] is False or exporting_options['zip_conditional']['export_reports_when_zip'] is True) and str(exporting_options['output_reports']) != 'None' and str(exporting_options['output_reports']) != '' and '4' in exporting_options['output_reports']</filter>
0 a9e90cdcb97a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty galaxyp parents: diff changeset	540 </data>
18 ffed32e397cb Uploaded galaxyp parents: 17 diff changeset	541 <data format="tabular" name="output_extended_psm" from_work_dir="psmx.txt" label="${tool.name} on ${on_string}: Extended PSM Report">
48 b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	542 <filter>(exporting_options['zip_conditional']['zip_output_boolean'] is False or exporting_options['zip_conditional']['export_reports_when_zip'] is True) and str(exporting_options['output_reports']) != 'None' and str(exporting_options['output_reports']) != '' and '11' in exporting_options['output_reports']</filter>
18 ffed32e397cb Uploaded galaxyp parents: 17 diff changeset	543 </data>
0 a9e90cdcb97a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty galaxyp parents: diff changeset	544 <data format="tabular" name="output_peptides_phosphorylation" from_work_dir="peptides_phospho.txt" label="${tool.name} on ${on_string}: Peptide Phosphorylation Report">
48 b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	545 <filter>(exporting_options['zip_conditional']['zip_output_boolean'] is False or exporting_options['zip_conditional']['export_reports_when_zip'] is True) and str(exporting_options['output_reports']) != 'None' and str(exporting_options['output_reports']) != '' and '5' in exporting_options['output_reports']</filter>
0 a9e90cdcb97a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty galaxyp parents: diff changeset	546 </data>
a9e90cdcb97a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty galaxyp parents: diff changeset	547 <data format="tabular" name="output_peptides" from_work_dir="peptides.txt" label="${tool.name} on ${on_string}: Peptide Report">
48 b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	548 <filter>(exporting_options['zip_conditional']['zip_output_boolean'] is False or exporting_options['zip_conditional']['export_reports_when_zip'] is True) and str(exporting_options['output_reports']) != 'None' and str(exporting_options['output_reports']) != '' and '6' in exporting_options['output_reports']</filter>
42 80ed6522192c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6e846f7195a9e939047ac975c6523e8cf99da6b4 galaxyp parents: 39 diff changeset	549 </data>
80ed6522192c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6e846f7195a9e939047ac975c6523e8cf99da6b4 galaxyp parents: 39 diff changeset	550 <data format="tabular" name="output_peptides_nonvalidated" from_work_dir="peptides_nonvalidated.txt" label="${tool.name} on ${on_string}: Peptide Report with non-validated matches">
48 b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	551 <filter>(exporting_options['zip_conditional']['zip_output_boolean'] is False or exporting_options['zip_conditional']['export_reports_when_zip'] is True) and str(exporting_options['output_reports']) != 'None' and str(exporting_options['output_reports']) != '' and '7' in exporting_options['output_reports']</filter>
0 a9e90cdcb97a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty galaxyp parents: diff changeset	552 </data>
a9e90cdcb97a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty galaxyp parents: diff changeset	553 <data format="tabular" name="output_proteins_phosphorylation" from_work_dir="proteins_phospho.txt" label="${tool.name} on ${on_string}: Protein Phosphorylation Report">
48 b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	554 <filter>(exporting_options['zip_conditional']['zip_output_boolean'] is False or exporting_options['zip_conditional']['export_reports_when_zip'] is True) and str(exporting_options['output_reports']) != 'None' and str(exporting_options['output_reports']) != '' and '8' in exporting_options['output_reports']</filter>
0 a9e90cdcb97a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty galaxyp parents: diff changeset	555 </data>
a9e90cdcb97a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty galaxyp parents: diff changeset	556 <data format="tabular" name="output_proteins" from_work_dir="proteins.txt" label="${tool.name} on ${on_string}: Protein Report">
48 b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	557 <filter>(exporting_options['zip_conditional']['zip_output_boolean'] is False or exporting_options['zip_conditional']['export_reports_when_zip'] is True) and str(exporting_options['output_reports']) != 'None' and str(exporting_options['output_reports']) != '' and '9' in exporting_options['output_reports']</filter>
42 80ed6522192c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6e846f7195a9e939047ac975c6523e8cf99da6b4 galaxyp parents: 39 diff changeset	558 </data>
48 b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	559 <data format="tabular" name="output_proteins_nonvalidated" from_work_dir="proteins_nonvalidated.txt" label="${tool.name} on ${on_string}: Protein Report with non-validated matches">
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	560 <filter>(exporting_options['zip_conditional']['zip_output_boolean'] is False or exporting_options['zip_conditional']['export_reports_when_zip'] is True) and str(exporting_options['output_reports']) != 'None' and str(exporting_options['output_reports']) != '' and '10' in exporting_options['output_reports']</filter>
0 a9e90cdcb97a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty galaxyp parents: diff changeset	561 </data>
a9e90cdcb97a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty galaxyp parents: diff changeset	562 </outputs>
48 b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	563
0 a9e90cdcb97a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty galaxyp parents: diff changeset	564 <tests>
48 b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	565 <!-- Basic test: default identification parameters, searchgui_tinydb1.fasta, 4 search engines xx-->
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	566 <test expect_num_outputs="1">
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	567 <param name="searchgui_input" value="searchgui_tiny_result_default_4engines.zip" ftype="searchgui_archive"/>
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	568 <param name="mzidentml_creation" value="0"/>
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	569 <param name="export_psdb" value="1"/>
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	570 <output name="output_psdb" ftype="peptideshaker_archive">
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	571 <assert_contents>
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	572 <has_size value="122880" delta="3000"/>
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	573 </assert_contents>
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	574 </output>
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	575 </test>
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	576
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	577 <!-- Modifications test: default identification parameters with modifications, searchgui_tinydb1.fasta, 4 search engines -->
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	578 <test expect_num_outputs="1">
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	579 <param name="searchgui_input" value="searchgui_tiny_result_default_4engines_modifications.zip" ftype="searchgui_archive"/>
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	580 <param name="mzidentml_creation" value="0"/>
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	581 <param name="export_psdb" value="1"/>
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	582 <output name="output_zip" ftype="peptideshaker_archive">
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	583 <assert_contents>
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	584 <has_size value="126976" delta="3000"/>
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	585 </assert_contents>
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	586 </output>
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	587 </test>
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	588
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	589 <!-- Reports tests: default identification parameters, small spectra, some search engines (XTandem,MSGF+, OMSSA), all identification reports -->
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	590 <test expect_num_outputs="12">
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	591 <param name="searchgui_input" value="searchgui_smallsearch_default_somesearchengines_modifications.zip" ftype="searchgui_archive"/>
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	592 <param name="mzidentml_creation" value="0"/>
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	593 <param name="zip_output_boolean" value="separate"/>
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	594 <param name="export_psdb" value="0"/>
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	595 <param name="output_reports" value="0,1,2,3,4,5,6,7,8,9,10,11"/>
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	596 <output name="output_certificate" file="peptideshaker_reports_output_certificate.txt" ftype="txt" lines_diff="8"/>
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	597 <output name="output_hierarchical" file="peptideshaker_reports_output_hierarchical.tabular" ftype="tabular"/>
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	598 <output name="output_extended_psm" file="peptideshaker_reports_output_extendedpsm.tabular" ftype="tabular"/>
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	599 <output name="output_psm" file="peptideshaker_reports_output_psm.tabular" ftype="tabular"/>
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	600 <output name="output_psm_phosphorylation" file="peptideshaker_reports_output_psmphosphorylation.tabular" ftype="tabular"/>
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	601 <output name="output_psm_nonvalidated" file="peptideshaker_reports_output_psmnonvalidated.tabular" ftype="tabular"/>
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	602 <output name="output_peptides" file="peptideshaker_reports_output_peptides.tabular" ftype="tabular"/>
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	603 <output name="output_peptides_phosphorylation" file="peptideshaker_reports_output_peptidesphosphorylation.tabular" ftype="tabular"/>
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	604 <output name="output_peptides_nonvalidated" file="peptideshaker_reports_output_peptidesnonvalidated.tabular" ftype="tabular"/>
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	605 <output name="output_proteins" file="peptideshaker_reports_output_proteins.tabular" ftype="tabular"/>
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	606 <output name="output_proteins_phosphorylation" file="peptideshaker_reports_output_proteinsphosphorylation.tabular" ftype="tabular"/>
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	607 <output name="output_proteins_nonvalidated" file="peptideshaker_reports_output_proteinsnonvalidated.tabular" ftype="tabular"/>
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	608 </test>
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	609
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	610 <!-- followup analysis tests: default identification parameters, small spectra, some search engines (XTandem,MSGF+, OMSSA), all followup analysis -->
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	611 <test expect_num_outputs="5">
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	612 <param name="searchgui_input" value="searchgui_smallsearch_default_somesearchengines_modifications.zip" ftype="searchgui_archive"/>
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	613 <param name="mzidentml_creation" value="0"/>
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	614 <param name="zip_output_boolean" value="separate"/>
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	615 <param name="export_psdb" value="0"/>
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	616 <param name="followup_conditional_selector" value="yes"/>
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	617 <param name="followup_export_spectra" value="0"/>
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	618 <param name="followup_export_accession_numbers" value="0"/>
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	619 <param name="followup_export_sequences" value="0"/>
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	620 <param name="followup_export_proteoforms" value="on"/>
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	621 <param name="followup_export_progenesis_selector" value="0"/>
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	622 <output_collection name="output_spectra" type="list">
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	623 <element name="searchgui_smallspectra_non_validated_PSMs" ftype="mgf">
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	624 <assert_contents>
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	625 <has_line_matching expression="236.0470428 11.674492836"/>
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	626 <has_line_matching expression="520.9862671 4666.4399414063"/>
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	627 <has_line_matching expression="267.4349976 50.7710571289"/>
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	628 <has_line_matching expression="665.7418213 3.8165459633"/>
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	629 <has_line_matching expression="672.2329102 146.2656707764"/>
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	630 <has_line_matching expression="634.7792969 2367.6374511719"/>
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	631 </assert_contents>
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	632 </element>
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	633 </output_collection>
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	634 <output name="output_proteins_accessions" ftype="txt">
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	635 <assert_contents>
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	636 <has_line_matching expression="cds.comp41779_c0_seq1"/>
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	637 <has_line_matching expression="cds.comp41890_c0_seq1"/>
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	638 <has_line_matching expression="cds.comp41890_c0_seq1_REVERSED"/>
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	639 <has_line_matching expression="cds.comp8310_c0_seq2"/>
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	640 </assert_contents>
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	641 </output>
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	642 <output name="output_proteins_sequences" ftype="fasta">
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	643 <assert_contents>
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	644 <has_line_matching expression=">generic\|cds.comp41779_c0_seq1\|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-6"/>
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	645 <has_line_matching expression="METTKERKEKSTVVTKRQSMGATAHVQPKFIQVNRRSHVVGAGLGGGSMGSMNQSMSLHGGRASLGMAAGVAGGIATKDMGTMKVKREGEKKDMQNLNDRFAGYIAKVRSLQAENEQLRLKLSKKRREFDVEPLKEAYQAEIDEAKNLLLDANKENGELKISITTYEEEIEDLHATARINEDRIDELQDKVNKLIDENSHREAECSMLHKKLDELEKQVAHWRAKYNEVNTQLQATRADLKDETQQRIFLQQKVGNLEEELEFLRSVTDAEIKEYKAMLSKEDDTGTNVSAAWNNEMSNCMKELREEYDQRLADISDEMSARYESQLSQIRQSAHAEPVAAVHTKSEKSTGMVSVQKDMRIKELESQLERMKMEIITITNQLQRSNEDLENEKDLRTTEVNKLHVEMESMIEELQMLMDAKLSLELEIAAYRKLLEGEENRISTGYITENIGGFRSEAGDNLANILEFGSGGGGGGGGGGSGSGSGSGLAGDSASTSTLTGRLTIQRSSKSVISIGEVESEGQYVTLENTSSGRSKTSVNMKGWKLDRLISATSISPEHKIDFLFKDPVVLEGEQSIKIWAKNYQKMAKKGDIIATVDEWGPVNRNSVFSLYDEKDALKANLSTKVVT"/>
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	646 <has_line_matching expression="generic\|cds.comp41890_c0_seq1_REVERSED\|m.9546 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 38.58 EValue:4.0e-20-REVERSED"/>
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	647 <has_line_matching expression="LNYTTELNYTAKEDGRTNLLVTNVKAGVGLRSKNHWVLDGSNPDGMGNAWVKAFGGPKLVLNEIEYESIDINDSNQMIKWGSLDVTHSNSTNELLIFSGDRDTESIAVPGKNNKRYTSHEQLEGKVLAPTPSQY"/>
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	648 </assert_contents>
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	649 </output>
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	650 <output name="output_proteoforms" ftype="txt">
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	651 <assert_contents>
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	652 <has_line_matching expression="cds.comp8310_c0_seq2"/>
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	653 <has_line_matching expression="cds.comp41890_c0_seq1_REVERSED"/>
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	654 <has_line_matching expression="cds.comp41779_c0_seq1"/>
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	655 <has_line_matching expression="cds.comp41779_c0_seq2"/>
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	656 <has_line_matching expression="cds.comp41779_c0_seq3"/>
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	657 </assert_contents>
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	658 </output>
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	659 <output name="output_progenesis" ftype="txt">
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	660 <assert_contents>
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	661 <has_text_matching expression="NLVAEESMNMLKNK\t:::::::::::::::\t100.0\tcds.comp8310_c0_seq2\tm.1138 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 22.01 EValue:2.0e-16\tsmall.17.17."/>
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	662 <has_text_matching expression="LDRLISATSISPEHKIDFLFK\t::::::::::::::::::::::\t100.0\tcds.comp41779_c0_seq1\tm.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67\tsmall.3.3."/>
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	663 <has_n_columns n="8" />
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	664 </assert_contents>
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	665 </output>
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	666
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	667 </test>
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	668
0 a9e90cdcb97a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty galaxyp parents: diff changeset	669 </tests>
a9e90cdcb97a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty galaxyp parents: diff changeset	670 <help>
a9e90cdcb97a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty galaxyp parents: diff changeset	671 What it does
a9e90cdcb97a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty galaxyp parents: diff changeset	672
42 80ed6522192c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6e846f7195a9e939047ac975c6523e8cf99da6b4 galaxyp parents: 39 diff changeset	673 PeptideShaker is a search engine for interpretation of proteomics identification results from multiple search engines, currently supporting X!Tandem, MS-GF+, MS Amanda, OMSSA, MyriMatch, Comet, Tide, Mascot, Andromeda and mzIdentML.
0 a9e90cdcb97a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty galaxyp parents: diff changeset	674
19 ef4ac2d49ff0 Uploaded galaxyp parents: 18 diff changeset	675 http://compomics.github.io/projects/peptide-shaker.html
0 a9e90cdcb97a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty galaxyp parents: diff changeset	676
a9e90cdcb97a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty galaxyp parents: diff changeset	677 ----
a9e90cdcb97a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty galaxyp parents: diff changeset	678
48 b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	679 Outputs
0 a9e90cdcb97a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty galaxyp parents: diff changeset	680 =======
a9e90cdcb97a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty galaxyp parents: diff changeset	681
48 b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	682 zip
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	683 ------
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	684
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	685 When choosing zip option, all other outputs are compressed and included into the zip file and, by default, no other file is shown in the Galaxy history. This last behaviour may be changed in order to have all other outputs also available in the history.
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	686
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	687 psdb
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	688 ------
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	689
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	690 psdb is the native format used by PeptideShaker. It contains all the information required by PeptideShaker to run.
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	691
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	692 mzIdentML
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	693 -----------
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	694
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	695 PeptideShaker can load results from virtually any identification algorithm in the mzIdentML format as long as the minimal peptide to spectrum match information is present in the file.
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	696
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	697 The following is required:
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	698
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	699 • Spectrum file format has to be mgf.
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	700 • Each PSM has a score or e-value as a PSM score CV term.
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	701
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	702
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	703 Follow-up analysis
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	704 --------------------
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	705
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	706 Spectra
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	707 '''''''
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	708
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	709 Exports the spectra according to the category of the PSMs:
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	710
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	711 • Spectra of Non-Validated PSMs
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	712 • Spectra of Non-Validated Peptides
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	713 • Spectra of Non-Validated Proteins
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	714 • Spectra of Validated PSMs
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	715 • Spectra of Validated PSMs of Validated Peptides
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	716 • Spectra of validated PSMs of Validated Peptides of Validated Proteins.
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	717
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	718 Exported results are in mgf format.
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	719
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	720 Proteins: Accession numbers
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	721 '''''''''''''''''''''''''''
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	722
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	723 Export the protein accessions according to the category of the proteins:
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	724
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	725 • Main Accession of Validated Protein Groups
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	726 • All Accessions of Validated Protein Groups
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	727 • Non-Validated Accessions
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	728
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	729 Exported protein accessions are text format as TXT.
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	730
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	731
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	732 Proteins: Sequences
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	733 '''''''''''''''''''
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	734
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	735 Exports the protein details according to a category of proteins:
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	736
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	737 • Main Accession of Validated Protein Groups
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	738 • All Accessions of Validated Protein Groups
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	739 • Non-Validated Accessions.
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	740
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	741 Exported protein details are in fasta format.
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	742
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	743
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	744 Proteins: Proteoforms
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	745 '''''''''''''''''''''
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	746
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	747 Exports all possible proteoforms of the validated proteins.
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	748
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	749 Exported results are in text format as TXT.
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	750 Results file can be easily imported and used by PathwayMatcher_ tool.
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	751
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	752 .. _PathwayMatcher: https://toolshed.g2.bx.psu.edu/repository?repository_id=6d75f02b86acc421
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	753
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	754
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	755 Label free quantification
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	756 '''''''''''''''''''''''''
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	757
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	758 Exports the spectra from different categories of PSMs according to the export type:
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	759
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	760 • Validated PSMs of Validated Peptides of Validated Proteins
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	761 • Validated PSMs of Validated Peptides
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	762 • Validated PSMs
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	763 • Confidently localized PTMs of Validated PSMs of Validated Peptides of Validated Proteins
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	764
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	765 Exported identification results are in Progenesis LC-MS compatible format as TXT.
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	766
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	767
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	768 Inclusion/Exclusion list
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	769 ''''''''''''''''''''''''
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	770
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	771 Exports an inclusion list of validated hits.
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	772
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	773 Inclusion list may be filtered according to peptide types:
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	774
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	775 • Miscleaved Peptides
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	776 • Reactive Peptides
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	777 • Degenerated Peptides.
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	778
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	779 and also according to protein inferences:
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	780
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	781 • Related Proteins
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	782 • Related and Unrelated Proteins
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	783 • Unrelated Proteins.
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	784
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	785 Finally, a retention time window may be established as a final filter.
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	786
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	787 Exported results can be in Thermo, ABI, Bruker or MassLynx formats.
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	788
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	789
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	790
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	791 Identification Features Reports
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	792 ---------------------------------
0 a9e90cdcb97a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty galaxyp parents: diff changeset	793
a9e90cdcb97a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty galaxyp parents: diff changeset	794 PSM Report
48 b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	795 ''''''''''
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	796 ============================= ========================================
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	797 Column Description
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	798 ============================= ========================================
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	799 Protein(s) Protein(s) to which the peptide can be attached
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	800 Sequence Sequence of the peptide
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	801 AAs Before The amino acids before the sequence
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	802 AAs After The amino acids after the sequence
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	803 Position Position of the peptide in the protein sequence(s).
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	804 Modified Sequence The amino acids sequence annotated with variable modifications.
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	805 Variable Modifications The variable modifications
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	806 Fixed Modifications The fixed modifications.
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	807 Spectrum File The spectrum file.
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	808 Spectrum Title The title of the spectrum.
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	809 Spectrum Scan Number The spectrum scan number.
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	810 RT Retention time
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	811 m/z Measured m/z
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	812 Measured Charge The charge as given in the spectrum file.
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	813 Identification Charge The charge as inferred by the search engine.
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	814 Theoretical Mass The theoretical mass of the peptide.
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	815 Isotope Number The isotope number targetted by the instrument.
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	816 Precursor m/z Error [ppm] The precursor m/z matching error.
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	817 Localization Confidence The confidence in variable PTM localization.
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	818 probabilistic PTM score The probabilistic score (e.g. A-score or PhosphoRS) used for variable PTM localization.
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	819 D-score D-score for variable PTM localization
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	820 Confidence Confidence in percent associated to the retained PSM.
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	821 Validation Indicates the validation level of the protein group.
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	822 ============================= ========================================
0 a9e90cdcb97a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty galaxyp parents: diff changeset	823
48 b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	824
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	825 PSM Report with non-validated matches
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	826 '''''''''''''''''''''''''''''''''''''
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	827
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	828 Same columns as the original PSM report but also includes non-validated matches.
0 a9e90cdcb97a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty galaxyp parents: diff changeset	829
a9e90cdcb97a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty galaxyp parents: diff changeset	830
48 b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	831 PSM Phosphorylation Report
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	832 ''''''''''''''''''''''''''
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	833 ============================= =========================================================
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	834 Column Description
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	835 ============================= =========================================================
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	836 Protein(s) Protein(s) to which the peptide can be attached
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	837 Sequence Sequence of the peptide
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	838 Variable Modifications The variable modifications
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	839 Fixed Modifications The fixed modifications.
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	840 Spectrum File The spectrum file.
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	841 Spectrum Title The title of the spectrum.
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	842 Spectrum Scan Number The spectrum scan number.
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	843 RT Retention time
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	844 m/z Measured m/z
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	845 Measured Charge The charge as given in the spectrum file.
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	846 Identification Charge The charge as inferred by the search engine.
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	847 Theoretical Mass The theoretical mass of the peptide.
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	848 Isotope Number The isotope number targetted by the instrument.
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	849 Precursor m/z Error [ppm] The precursor m/z matching error.
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	850 Localization Confidence The confidence in variable PTM localization.
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	851 probabilistic PTM score The probabilistic score (e.g. A-score or PhosphoRS) used for variable PTM localization.
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	852 D-score D-score for variable PTM localization
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	853 Confident Phosphosites List of the sites where a phosphorylation was confidently localized.
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	854 #Confident Phosphosites Number of confidently localized phosphorylations.
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	855 Ambiguous Phosphosites List of the sites where a phosphorylation was ambiguously localized.
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	856 #Ambiguous Phosphosites Number of ambiguously localized phosphorylations.
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	857 Confidence [%] Confidence in percent associated to the retained PSM.
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	858 Validation Indicates the validation level of the protein group.
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	859 ============================= =========================================================
0 a9e90cdcb97a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty galaxyp parents: diff changeset	860
48 b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	861
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	862 Extended PSM Report
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	863 '''''''''''''''''''
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	864
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	865 Same as the ordinary PSM report but adds a ``Decoy`` column and lacks the ``Confidence`` column.
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	866
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	867 ============================= =========================================================
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	868 Extra column Description
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	869 ============================= =========================================================
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	870 Decoy Indicates whether the peptide is a decoy (1: yes, 0: no).
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	871
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	872 ============================= =========================================================
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	873
0 a9e90cdcb97a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty galaxyp parents: diff changeset	874
a9e90cdcb97a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty galaxyp parents: diff changeset	875
a9e90cdcb97a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty galaxyp parents: diff changeset	876 Peptide Report
48 b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	877 ''''''''''''''
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	878
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	879 ========================================== =====================================================
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	880 Column Description
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	881 ========================================== =====================================================
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	882 Protein(s): Protein(s) to which this peptide can be attached.
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	883 Protein Group(s) List of identified protein groups this peptide can map to with associated validation level.
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	884 #Validated Protein Group(s) Indicates the number of protein groups this peptide maps to.
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	885 Unique Group Indicates whether the peptide maps to a unique protein group.
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	886 Sequence Sequence of the peptide.
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	887 Modified Sequence The peptide sequence annotated with variable modifications.
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	888 Position Position of the peptide in the protein sequence(s).
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	889 AAs Before The amino acids before the sequence.
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	890 AAs After The amino acids after the sequence.
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	891 Variable Modifications The variable modifications.
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	892 Fixed Modifications The fixed modifications.
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	893 Localization Confidence The confidence in PTMs localization.
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	894 #Validated PSMs Number of validated PSMs.
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	895 #PSMs Number of PSMs.
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	896 Confidence [%] Confidence in percent associated to the peptide.
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	897 Validation Indicates the validation level of the peptide.
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	898 ========================================== =====================================================
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	899
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	900
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	901 Peptide Report with non-validated matches
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	902 '''''''''''''''''''''''''''''''''''''''''
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	903
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	904 Same columns as the original Peptide report but also includes non-validated matches.
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	905
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	906
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	907 Peptide Phosphorylation Report
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	908 ''''''''''''''''''''''''''''''
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	909
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	910 ========================================== =====================================================
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	911 Column Description
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	912 ========================================== =====================================================
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	913 Protein(s): Protein(s) to which this peptide can be attached.
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	914 Protein Group(s) List of identified protein groups this peptide can map to with associated validation level.
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	915 #Validated Protein Group(s) Indicates the number of protein groups this peptide maps to.
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	916 Unique Group Indicates whether the peptide maps to a unique protein group.
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	917 Sequence Sequence of the peptide.
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	918 Modified Sequence The peptide sequence annotated with variable modifications.
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	919 AAs Before The amino acids before the sequence.
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	920 AAs After The amino acids after the sequence.
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	921 Variable Modifications The variable modifications.
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	922 Fixed Modifications The fixed modifications.
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	923 Localization Confidence The confidence in PTMs localization.
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	924 Confident Phosphosites List of the sites where a phosphorylation was confidently localized.
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	925 #Confident Phosphosites Number of confidently localized phosphorylations.
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	926 Ambiguous Phosphosites List of the sites where a phosphorylation was ambiguously localized.
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	927 #Ambiguous Phosphosites Number of ambiguously localized phosphorylations.
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	928 #Validated PSMs Number of validated PSMs.
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	929 #PSMs Number of PSMs.
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	930 Confidence [%] Confidence in percent associated to the peptide.
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	931 Validation Indicates the validation level of the peptide.
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	932 ========================================== =====================================================
0 a9e90cdcb97a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty galaxyp parents: diff changeset	933
a9e90cdcb97a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty galaxyp parents: diff changeset	934
48 b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	935 Protein Report
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	936 ''''''''''''''
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	937
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	938 ========================================== =====================================================
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	939 Column Description
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	940 ========================================== =====================================================
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	941 Main Accession Main accession of the protein group.
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	942 Description Description of the protein designed by the main accession.
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	943 Gene Name The gene names of the Ensembl gene ID associated to the main accession.
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	944 Chromosome The chromosome of the Ensembl gene ID associated to the main accession.
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	945 MW (kDa) Molecular Weight.
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	946 Possible Coverage (%) Possible sequence coverage in percent of the protein designed by the main accession according to the search settings.
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	947 Coverage (%) Sequence coverage in percent of the protein designed by the main accession.
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	948 Spectrum Counting The selected spectrum counting metric.
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	949 Confidently Localized Modification Sites List of the sites where a variable modification was confidently localized.
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	950 # Confidently Localized Modification Sites Number of sites where a variable modification was confidently localized.
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	951 Ambiguously Localized Modification Sites List of the sites where ambiguously localized variable modification could possibly be located.
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	952 #Ambiguously Localized Modification Sites Number of ambiguously localized modifications.
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	953 Protein Inference Protein Inference status of the protein group.
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	954 Secondary Accessions Other accessions in the protein group (alphabetical order).
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	955 Protein Group The complete protein group (alphabetical order).
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	956 #Validated Peptides Number of validated peptides.
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	957 #Peptides Total number of peptides.
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	958 #Unique Total number of peptides unique to this protein group.
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	959 #Validated Unique Total number of peptides unique to this protein group.
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	960 #Validated PSMs Number of validated PSMs.
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	961 #PSMs Number of PSMs.
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	962 Confidence [%] Confidence in percent associated to the protein group.
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	963 Validation Indicates the validation level of the protein group.
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	964 ========================================== =====================================================
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	965
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	966
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	967 Protein Report with non-validated matches
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	968 '''''''''''''''''''''''''''''''''''''''''
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	969
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	970 Same columns as the original Protein report but also includes non-validated matches.
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	971
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	972
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	973 Protein Phosphorylation Report
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	974 ''''''''''''''''''''''''''''''
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	975
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	976 ========================================== =====================================================
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	977 Column Description
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	978 ========================================== =====================================================
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	979 Main Accession Main accession of the protein group.
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	980 Description Description of the protein designed by the main accession.
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	981 Gene Name The gene names of the Ensembl gene ID associated to the main accession.
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	982 Chromosome The chromosome of the Ensembl gene ID associated to the main accession.
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	983 MW (kDa) Molecular Weight.
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	984 Possible Coverage (%) Possible sequence coverage in percent of the protein designed by the main accession according to the search settings.
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	985 Coverage (%) Sequence coverage in percent of the protein designed by the main accession.
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	986 Spectrum Counting NSAF Raw Normalized Spectrum Abundance Factor (NSAF).
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	987 Confident Phosphosites List of the sites where a phosphorylation was confidently localized.
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	988 #Confident Phosphosites Number of sites where a phosphorylation was confidently localized.
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	989 Ambiguous Phosphosites List of the sites where a phosphorylation was ambiguously localized.
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	990 #Ambiguous Phosphosites Number of sites where a phosphorylation was ambiguously localized.
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	991 Protein Inference Protein Inference status of the protein group.
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	992 Secondary Accessions Other accessions in the protein group (alphabetical order).
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	993 Protein Group The complete protein group (alphabetical order).
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	994 #Validated Peptides Number of validated peptides.
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	995 #Peptides Total number of peptides.
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	996 #Unique Total number of peptides unique to this protein group.
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	997 #Validated Unique Total number of peptides unique to this protein group.
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	998 #Validated PSMs Number of validated PSMs.
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	999 #PSMs Number of PSMs.
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	1000 Confidence [%] Confidence in percent associated to the protein group.
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	1001 Validation Indicates the validation level of the protein group.
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	1002 ========================================== =====================================================
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	1003
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	1004
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	1005 Certificate of Analysis
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	1006 '''''''''''''''''''''''
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	1007
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	1008 Presents a summary of the most important statistics of the search, grouped by:
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	1009
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	1010 * Project Details:
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	1011 ‣ PeptideShaker Version, Date, Experiment, Sample, Replicate Number, Identification Algorithms.
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	1012 * Database Search Parameters:
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	1013 ‣ Precursor Tolerance Unit, Precursor Ion m/z Tolerance, Fragment Ion Tolerance Unit, Fragment Ion m/z Tolerance, Cleavage, Enzyme, Missed Cleavages, Specificity, Database, Forward Ion, Rewind Ion, Fixed Modifications, Variable Modifications, Refinement Variable Modifications, Refinement Fixed Modifications.
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	1014 * Input Filters:
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	1015 ‣ Minimal Peptide Length, Maximal Peptide Length, Precursor m/z Tolerance, Precursor m/z Tolerance Unit, Unrecognized Modifications Discarded.
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	1016 * Validation Summary:
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	1017 • Proteins:
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	1018 ‣ #Validated, Total Possible TP, FDR Limit [%], FNR Limit [%], Confidence Limit, PEP Limit [%], Confidence Accuracy [%].
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	1019 • Peptides:
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	1020 ‣ #Validated, Total Possible TP, FDR Limit [%], FNR Limit [%], Confidence Limit [%], PEP Limit [%], Confidence Accuracy [%].
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	1021 • PSMs:
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	1022 ‣ #Validated PSM, Total Possible TP, FDR Limit [%]: PSMs, Confidence Limit [%], PEP Limit [%], Confidence Accuracy [%].
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	1023 * PTM Scoring Settings:
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	1024 ‣ Probabilistic Score, Accounting for Neutral Losses, Threshold.
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	1025 * Spectrum Counting Parameters:
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	1026 ‣ Method, Validated Matches Only
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	1027 * Annotation Settings:
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	1028 ‣ Intensity Limit, Automatic Annotation, Selected Ions, Neutral Losses, Neutral Losses Sequence Dependence, Fragment Ion m/z Tolerance.
0 a9e90cdcb97a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty galaxyp parents: diff changeset	1029
a9e90cdcb97a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty galaxyp parents: diff changeset	1030
a9e90cdcb97a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty galaxyp parents: diff changeset	1031 Hierachical Report
48 b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	1032 ''''''''''''''''''
0 a9e90cdcb97a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty galaxyp parents: diff changeset	1033
48 b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	1034 ========================================== =====================================================
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	1035 Column Description
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	1036 ========================================== =====================================================
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	1037 Main Accession Main accession of the protein group.
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	1038 Description Description of the protein designed by the main accession.
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	1039 MW (kDa) Molecular Weight.
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	1040 Possible Coverage (%) Possible sequence coverage in percent of the protein designed by the main accession according to the search settings.
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	1041 Coverage (%) Sequence coverage in percent of the protein designed by the main accession.
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	1042 Spectrum Counting NSAF Normalized Spectrum Abundance Factor (NSAF)
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	1043 Confidently Localized Modification Sites List of the sites where a variable modification was confidently localized.
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	1044 # Confidently Localized Modification Sites Number of sites where a variable modification was confidently localized.
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	1045 Ambiguously Localized Modification Sites List of the sites where ambiguously localized variable modification could possibly be located.
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	1046 #Ambiguously Localized Modification Sites Number of ambiguously localized modifications.
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	1047 Protein Inference Protein Inference status of the protein group.
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	1048 Secondary Accessions Other accessions in the protein group (alphabetical order).
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	1049 Protein Group The complete protein group (alphabetical order).
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	1050 #Validated Peptides Number of validated peptides.
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	1051 #Peptides Total number of peptides.
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	1052 #Unique Total number of peptides unique to this protein group.
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	1053 #Validated PSMs Number of validated PSMs
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	1054 #PSMs Number of PSMs
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	1055 Confidence Confidence in percent associated to the protein group.
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	1056 Decoy Indicates whether the protein group is a decoy (1: yes, 0: no).
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	1057 Validation Indicates the validation level of the protein group.
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 47 diff changeset	1058 ========================================== =====================================================
0 a9e90cdcb97a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty galaxyp parents: diff changeset	1059
a9e90cdcb97a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty galaxyp parents: diff changeset	1060 ------
a9e90cdcb97a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty galaxyp parents: diff changeset	1061
a9e90cdcb97a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty galaxyp parents: diff changeset	1062 Citation
a9e90cdcb97a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty galaxyp parents: diff changeset	1063
19 ef4ac2d49ff0 Uploaded galaxyp parents: 18 diff changeset	1064 To cite the underlying tools (PeptideShaker and SearchGUI) please refer to the list of papers at http://compomics.github.io
0 a9e90cdcb97a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty galaxyp parents: diff changeset	1065
19 ef4ac2d49ff0 Uploaded galaxyp parents: 18 diff changeset	1066 If you use this tool in Galaxy, please cite Chilton J, Ira Cooke, Bjoern Gruening et al.
0 a9e90cdcb97a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty galaxyp parents: diff changeset	1067 </help>
a9e90cdcb97a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty galaxyp parents: diff changeset	1068 <expand macro="citations" />
a9e90cdcb97a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty galaxyp parents: diff changeset	1069 </tool>

Mercurial > repos > galaxyp > peptideshaker

annotate peptide_shaker.xml @ 48:b72821cab1d7 draft