peptideshaker: searchgui.xml annotate

annotate searchgui.xml @ 54:f5236b38562c draft default tip

"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit fc2810c412d9954fa584ae74497562b986c52764"

author	galaxyp
date	Thu, 12 Aug 2021 14:06:16 +0000
parents	166173739c8d
children

rev	line source
50 f2f4695ad996 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 44a20633e04b2396fad4b568904a257769b2bbc1" galaxyp parents: 49 diff changeset	1 <tool id="search_gui"
f2f4695ad996 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 44a20633e04b2396fad4b568904a257769b2bbc1" galaxyp parents: 49 diff changeset	2 name="Search GUI"
f2f4695ad996 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 44a20633e04b2396fad4b568904a257769b2bbc1" galaxyp parents: 49 diff changeset	3 version="@SEARCHGUI_VERSION@+galaxy@SEARCHGUI_VERSION_SUFFIX@"
f2f4695ad996 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 44a20633e04b2396fad4b568904a257769b2bbc1" galaxyp parents: 49 diff changeset	4 profile="20.01"
f2f4695ad996 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 44a20633e04b2396fad4b568904a257769b2bbc1" galaxyp parents: 49 diff changeset	5 >
0 a9e90cdcb97a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty galaxyp parents: diff changeset	6 <description>
a9e90cdcb97a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty galaxyp parents: diff changeset	7 Perform protein identification using various search engines and prepare results for input to Peptide Shaker
a9e90cdcb97a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty galaxyp parents: diff changeset	8 </description>
3 8d6c1807c5a5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit d369c3451aaf7bfc8cc4f6f1dc52f6ea604e66bc-dirty iracooke parents: 2 diff changeset	9 <macros>
48 b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 45 diff changeset	10 <import>macros_basic.xml</import>
3 8d6c1807c5a5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit d369c3451aaf7bfc8cc4f6f1dc52f6ea604e66bc-dirty iracooke parents: 2 diff changeset	11 </macros>
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>
40 fec15a483a5c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 69b2ae0ff05482e85ee086005462e7859b383064 galaxyp parents: 39 diff changeset	13 <requirement type="package" version="@SEARCHGUI_VERSION@">searchgui</requirement>
fec15a483a5c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 69b2ae0ff05482e85ee086005462e7859b383064 galaxyp parents: 39 diff changeset	14 <requirement type="package" version="3.0">zip</requirement>
0 a9e90cdcb97a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty galaxyp parents: diff changeset	15 </requirements>
a9e90cdcb97a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty galaxyp parents: diff changeset	16 <expand macro="stdio" />
40 fec15a483a5c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 69b2ae0ff05482e85ee086005462e7859b383064 galaxyp parents: 39 diff changeset	17 <command use_shared_home="false">
50 f2f4695ad996 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 44a20633e04b2396fad4b568904a257769b2bbc1" galaxyp parents: 49 diff changeset	18
0 a9e90cdcb97a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty galaxyp parents: diff changeset	19 <![CDATA[
a9e90cdcb97a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty galaxyp parents: diff changeset	20 #from datetime import datetime
48 b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 45 diff changeset	21 #import json
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 45 diff changeset	22 #import os
0 a9e90cdcb97a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty galaxyp parents: diff changeset	23 #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	24 #set $samp_str = "Sample_%s" % datetime.now().strftime("%Y%m%d%H%M%s")
18 ffed32e397cb Uploaded galaxyp parents: 17 diff changeset	25 #set $bin_dir = "bin"
0 a9e90cdcb97a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty galaxyp parents: diff changeset	26
a9e90cdcb97a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty galaxyp parents: diff changeset	27 mkdir output;
a9e90cdcb97a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty galaxyp parents: diff changeset	28 mkdir output_reports;
49 560a08e0de13 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f2f9adb0e2389a95599d651b4eecab6b10244c75" galaxyp parents: 48 diff changeset	29 mkdir temp_folder;
560a08e0de13 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f2f9adb0e2389a95599d651b4eecab6b10244c75" galaxyp parents: 48 diff changeset	30 mkdir log_folder;
50 f2f4695ad996 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 44a20633e04b2396fad4b568904a257769b2bbc1" galaxyp parents: 49 diff changeset	31 trap ">&2 cat log_folder/*.log" EXIT;
f2f4695ad996 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 44a20633e04b2396fad4b568904a257769b2bbc1" galaxyp parents: 49 diff changeset	32
0 a9e90cdcb97a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty galaxyp parents: diff changeset	33 cwd=`pwd`;
12 d298e0b6fd72 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 464dc333f2e8d359265e1574b01386c4e7e9d840 iracooke parents: 11 diff changeset	34 export HOME=\$cwd;
d298e0b6fd72 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 464dc333f2e8d359265e1574b01386c4e7e9d840 iracooke parents: 11 diff changeset	35
40 fec15a483a5c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 69b2ae0ff05482e85ee086005462e7859b383064 galaxyp parents: 39 diff changeset	36 ## echo the search engines to run (single quotes important because X!Tandem)
fec15a483a5c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 69b2ae0ff05482e85ee086005462e7859b383064 galaxyp parents: 39 diff changeset	37 echo '$search_engines_options.engines';
48 b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 45 diff changeset	38 echo 'DB: ${input_fasta_file.element_identifier} sequences: ${input_fasta_file.metadata.sequences}';
18 ffed32e397cb Uploaded galaxyp parents: 17 diff changeset	39
15 3fa49ed11f3d Uploaded galaxyp parents: 14 diff changeset	40 ##Create a searchgui.properties file for the version, which will be added to the searchgui_results if not already present
40 fec15a483a5c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 69b2ae0ff05482e85ee086005462e7859b383064 galaxyp parents: 39 diff changeset	41 echo 'searchgui.version=@SEARCHGUI_VERSION@' >> searchgui.properties;
13 3ccfbb673089 Update to PS 1.1 and SG 2.1.1 iracooke parents: 12 diff changeset	42
48 b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 45 diff changeset	43 #for $peak_list_file in $peak_lists_files:
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 45 diff changeset	44 #set $input_name = ""
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 45 diff changeset	45 #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: 45 diff changeset	46 #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: 45 diff changeset	47 #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: 45 diff changeset	48 #set $input_name = $peak_list_file.element_identifier.split('/')[-1].replace(".mzml", "") + ".mzml"
19 ef4ac2d49ff0 Uploaded galaxyp parents: 18 diff changeset	49 #end if
48 b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 45 diff changeset	50 ln -s -f '${peak_list_file}' '${input_name}';
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 45 diff changeset	51 #set $encoded_id = $__app__.security.encode_id($peak_list_file.id)
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 45 diff changeset	52 echo 'Spectrums:${peak_list_file.element_identifier}(API:${encoded_id})';
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 45 diff changeset	53 #end for
36 24bcbed3da6a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6afe42e2f4b9d780c4cee76a4dcd9cac1e1ea0ad galaxyp parents: 35 diff changeset	54
48 b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 45 diff changeset	55 ## copy the input .par file to the working folder
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 45 diff changeset	56 cp '${input_parameters_file}' './SEARCHGUI_IdentificationParameters.par';
37 7b72e889dafd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 981be1bde91d6d565693cd691553f77465e653bb galaxyp parents: 36 diff changeset	57
48 b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 45 diff changeset	58 ## copy the input .fasta file to the working folder
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 45 diff changeset	59 cp '${input_fasta_file}' './input_fasta_file.fasta';
6 53bdfaed924d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 5943ced37a55ac06f722af5d4ccd568c300c0ea3 iracooke parents: 4 diff changeset	60
0 a9e90cdcb97a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty galaxyp parents: diff changeset	61
a9e90cdcb97a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty galaxyp parents: diff changeset	62 ################
a9e90cdcb97a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty galaxyp parents: diff changeset	63 ## Search CLI ##
a9e90cdcb97a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty galaxyp parents: diff changeset	64 ################
40 fec15a483a5c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 69b2ae0ff05482e85ee086005462e7859b383064 galaxyp parents: 39 diff changeset	65 echo 'running search gui' &&
50 f2f4695ad996 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 44a20633e04b2396fad4b568904a257769b2bbc1" galaxyp parents: 49 diff changeset	66 searchgui -Djava.awt.headless=true eu.isas.searchgui.cmd.SearchCLI
18 ffed32e397cb Uploaded galaxyp parents: 17 diff changeset	67 --exec_dir="\$cwd/${bin_dir}"
52 c506a7ccb856 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 1cb321cbce2a6528764abc9c9431687f56c57588" galaxyp parents: 51 diff changeset	68 -use_log_folder 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 -spectrum_files \$cwd
48 b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 45 diff changeset	70 -fasta_file "\$cwd/input_fasta_file.fasta"
0 a9e90cdcb97a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty galaxyp parents: diff changeset	71 -output_folder \$cwd/output
48 b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 45 diff changeset	72 -id_params ./SEARCHGUI_IdentificationParameters.par
49 560a08e0de13 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f2f9adb0e2389a95599d651b4eecab6b10244c75" galaxyp parents: 48 diff changeset	73 -temp_folder \$cwd/temp_folder
560a08e0de13 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f2f9adb0e2389a95599d651b4eecab6b10244c75" galaxyp parents: 48 diff changeset	74 -log \$cwd/log_folder
0 a9e90cdcb97a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty galaxyp parents: diff changeset	75 -threads "\${GALAXY_SLOTS:-12}"
1 cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626 iracooke parents: 0 diff changeset	76
48 b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 45 diff changeset	77 #if $searchgui_advanced.searchgui_advanced_selector == 'advanced'
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 45 diff changeset	78 -correct_titles "${searchgui_advanced.correct_titles}"
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 45 diff changeset	79 $searchgui_advanced.missing_titles
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 45 diff changeset	80 -mgf_splitting "${searchgui_advanced.mgf_splitting}"
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 45 diff changeset	81 -mgf_spectrum_count "${searchgui_advanced.mgf_spectrum_count}"
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 45 diff changeset	82 -output_gzip "${searchgui_advanced.output_gzip}"
6 53bdfaed924d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 5943ced37a55ac06f722af5d4ccd568c300c0ea3 iracooke parents: 4 diff changeset	83 #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	84
23 aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312 galaxyp parents: 22 diff changeset	85 #set $engines_list = str($search_engines_options.engines).split(',')
6 53bdfaed924d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 5943ced37a55ac06f722af5d4ccd568c300c0ea3 iracooke parents: 4 diff changeset	86 #if 'X!Tandem' in $engines_list:
1 cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626 iracooke parents: 0 diff changeset	87 -xtandem 1
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626 iracooke parents: 0 diff changeset	88 #else
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626 iracooke parents: 0 diff changeset	89 -xtandem 0
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626 iracooke parents: 0 diff changeset	90 #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	91
6 53bdfaed924d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 5943ced37a55ac06f722af5d4ccd568c300c0ea3 iracooke parents: 4 diff changeset	92 #if 'MyriMatch' in $engines_list:
1 cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626 iracooke parents: 0 diff changeset	93 -myrimatch 1
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626 iracooke parents: 0 diff changeset	94 #else
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626 iracooke parents: 0 diff changeset	95 -myrimatch 0
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626 iracooke parents: 0 diff changeset	96 #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	97
6 53bdfaed924d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 5943ced37a55ac06f722af5d4ccd568c300c0ea3 iracooke parents: 4 diff changeset	98 #if 'MSGF' in $engines_list:
1 cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626 iracooke parents: 0 diff changeset	99 -msgf 1
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626 iracooke parents: 0 diff changeset	100 #else
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626 iracooke parents: 0 diff changeset	101 -msgf 0
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626 iracooke parents: 0 diff changeset	102 #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	103
6 53bdfaed924d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 5943ced37a55ac06f722af5d4ccd568c300c0ea3 iracooke parents: 4 diff changeset	104 #if 'OMSSA' in $engines_list:
1 cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626 iracooke parents: 0 diff changeset	105 -omssa 1
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626 iracooke parents: 0 diff changeset	106 #else
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626 iracooke parents: 0 diff changeset	107 -omssa 0
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626 iracooke parents: 0 diff changeset	108 #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	109
6 53bdfaed924d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 5943ced37a55ac06f722af5d4ccd568c300c0ea3 iracooke parents: 4 diff changeset	110 #if 'Comet' in $engines_list:
1 cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626 iracooke parents: 0 diff changeset	111 -comet 1
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626 iracooke parents: 0 diff changeset	112 #else
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626 iracooke parents: 0 diff changeset	113 -comet 0
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626 iracooke parents: 0 diff changeset	114 #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	115
6 53bdfaed924d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 5943ced37a55ac06f722af5d4ccd568c300c0ea3 iracooke parents: 4 diff changeset	116 #if 'Tide' in $engines_list:
1 cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626 iracooke parents: 0 diff changeset	117 -tide 1
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626 iracooke parents: 0 diff changeset	118 #else
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626 iracooke parents: 0 diff changeset	119 -tide 0
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626 iracooke parents: 0 diff changeset	120 #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	121
1 cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626 iracooke parents: 0 diff changeset	122 #if 'MS_Amanda' in $engines_list:
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626 iracooke parents: 0 diff changeset	123 -ms_amanda 1
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626 iracooke parents: 0 diff changeset	124 #else
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626 iracooke parents: 0 diff changeset	125 -ms_amanda 0
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626 iracooke parents: 0 diff changeset	126 #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	127
15 3fa49ed11f3d Uploaded galaxyp parents: 14 diff changeset	128 #if 'Andromeda' in $engines_list:
3fa49ed11f3d Uploaded galaxyp parents: 14 diff changeset	129 -andromeda 1
3fa49ed11f3d Uploaded galaxyp parents: 14 diff changeset	130 #else
3fa49ed11f3d Uploaded galaxyp parents: 14 diff changeset	131 -andromeda 0
3fa49ed11f3d Uploaded galaxyp parents: 14 diff changeset	132 #end if
3fa49ed11f3d Uploaded galaxyp parents: 14 diff changeset	133
48 b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 45 diff changeset	134 #if 'MetaMorpheus' in $engines_list:
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 45 diff changeset	135 -meta_morpheus 1
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 45 diff changeset	136 #else
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 45 diff changeset	137 -meta_morpheus 0
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 45 diff changeset	138 #end if
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 45 diff changeset	139
18 ffed32e397cb Uploaded galaxyp parents: 17 diff changeset	140 #if 'Novor' in $engines_list:
ffed32e397cb Uploaded galaxyp parents: 17 diff changeset	141 -novor 1
ffed32e397cb Uploaded galaxyp parents: 17 diff changeset	142 #else
ffed32e397cb Uploaded galaxyp parents: 17 diff changeset	143 -novor 0
ffed32e397cb Uploaded galaxyp parents: 17 diff changeset	144 #end if
ffed32e397cb Uploaded galaxyp parents: 17 diff changeset	145
ffed32e397cb Uploaded galaxyp parents: 17 diff changeset	146 #if 'DirecTag' in $engines_list:
ffed32e397cb Uploaded galaxyp parents: 17 diff changeset	147 -directag 1
ffed32e397cb Uploaded galaxyp parents: 17 diff changeset	148 #else
ffed32e397cb Uploaded galaxyp parents: 17 diff changeset	149 -directag 0
ffed32e397cb Uploaded galaxyp parents: 17 diff changeset	150 #end if
ffed32e397cb Uploaded galaxyp parents: 17 diff changeset	151
0 a9e90cdcb97a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty galaxyp parents: diff changeset	152 ## single zip file
a9e90cdcb97a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty galaxyp parents: diff changeset	153 -output_option 0
a9e90cdcb97a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty galaxyp parents: diff changeset	154
a9e90cdcb97a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty galaxyp parents: diff changeset	155 ## mgf and database in output
a9e90cdcb97a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty galaxyp parents: diff changeset	156 -output_data 1
a9e90cdcb97a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty galaxyp parents: diff changeset	157
50 f2f4695ad996 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 44a20633e04b2396fad4b568904a257769b2bbc1" galaxyp parents: 49 diff changeset	158 &&
f2f4695ad996 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 44a20633e04b2396fad4b568904a257769b2bbc1" galaxyp parents: 49 diff changeset	159
f2f4695ad996 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 44a20633e04b2396fad4b568904a257769b2bbc1" galaxyp parents: 49 diff changeset	160 echo '>log_folder:' &&
f2f4695ad996 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 44a20633e04b2396fad4b568904a257769b2bbc1" galaxyp parents: 49 diff changeset	161
f2f4695ad996 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 44a20633e04b2396fad4b568904a257769b2bbc1" galaxyp parents: 49 diff changeset	162 ls -l \$cwd/log_folder &&
f2f4695ad996 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 44a20633e04b2396fad4b568904a257769b2bbc1" galaxyp parents: 49 diff changeset	163
f2f4695ad996 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 44a20633e04b2396fad4b568904a257769b2bbc1" galaxyp parents: 49 diff changeset	164 mv output/searchgui_out.zip searchgui_out.zip
0 a9e90cdcb97a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty galaxyp parents: diff changeset	165
a9e90cdcb97a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty galaxyp parents: diff changeset	166 &&
a9e90cdcb97a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty galaxyp parents: diff changeset	167
50 f2f4695ad996 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 44a20633e04b2396fad4b568904a257769b2bbc1" galaxyp parents: 49 diff changeset	168 zip -u searchgui_out.zip searchgui.properties
0 a9e90cdcb97a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty galaxyp parents: diff changeset	169 ]]>
a9e90cdcb97a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty galaxyp parents: diff changeset	170 </command>
a9e90cdcb97a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty galaxyp parents: diff changeset	171 <inputs>
48 b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 45 diff changeset	172 <param format="json" name="input_parameters_file" type="data" label="Identification Parameters file"/>
1 cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626 iracooke parents: 0 diff changeset	173
51 c807a13df45f "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0f6ab8b5647a33b2b051d7aa808ef42546436b23" galaxyp parents: 50 diff changeset	174 <param format="fasta" name="input_fasta_file" type="data" label="Fasta file" help="For postprocessing with PeptideShaker the sequences must have UniProt style headers and contain decoy sequences (see help)."/>
48 b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 45 diff changeset	175
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 45 diff changeset	176 <param name="peak_lists_files" format="mgf,mzml" type="data" multiple="true" label="Input Peak Lists"
52 c506a7ccb856 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 1cb321cbce2a6528764abc9c9431687f56c57588" galaxyp parents: 51 diff changeset	177 help="Select appropriate MGF/MZML dataset(s) from history.
c506a7ccb856 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 1cb321cbce2a6528764abc9c9431687f56c57588" galaxyp parents: 51 diff changeset	178 Remember to choose only .mzML files when using MetaMorpheus." />
0 a9e90cdcb97a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty galaxyp parents: diff changeset	179
6 53bdfaed924d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 5943ced37a55ac06f722af5d4ccd568c300c0ea3 iracooke parents: 4 diff changeset	180 <!-- Search Engine Selection -->
37 7b72e889dafd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 981be1bde91d6d565693cd691553f77465e653bb galaxyp parents: 36 diff changeset	181 <section name="search_engines_options" expanded="true" title="Search Engine Options">
23 aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312 galaxyp parents: 22 diff changeset	182 <param name="engines" type="select" display="checkboxes" multiple="True" label="DB-Search Engines">
54 f5236b38562c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit fc2810c412d9954fa584ae74497562b986c52764" galaxyp parents: 53 diff changeset	183 <help>Comet and Tide shouldn't both be selected since they use a similar algoritm. OMSSA might not work into isolated environments like containers. Ms Amanda may not work either when executed into isolated environments based on MacOS X (use SG 4.0.22 to solve any problem running MsAmanda).
52 c506a7ccb856 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 1cb321cbce2a6528764abc9c9431687f56c57588" galaxyp parents: 51 diff changeset	184 MetaMorpheus only produce results when using mzML format.</help>
23 aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312 galaxyp parents: 22 diff changeset	185 <option value="X!Tandem" selected="True">X!Tandem</option>
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312 galaxyp parents: 22 diff changeset	186 <option value="MSGF" selected="True">MS-GF+</option>
48 b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 45 diff changeset	187 <option value="OMSSA">OMSSA</option>
23 aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312 galaxyp parents: 22 diff changeset	188 <option value="Comet">Comet</option>
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312 galaxyp parents: 22 diff changeset	189 <option value="Tide">Tide</option>
36 24bcbed3da6a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6afe42e2f4b9d780c4cee76a4dcd9cac1e1ea0ad galaxyp parents: 35 diff changeset	190 <option value="MyriMatch">MyriMatch</option>
23 aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312 galaxyp parents: 22 diff changeset	191 <option value="MS_Amanda">MS_Amanda</option>
52 c506a7ccb856 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 1cb321cbce2a6528764abc9c9431687f56c57588" galaxyp parents: 51 diff changeset	192 <option value="MetaMorpheus">MetaMorpheus</option>
23 aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312 galaxyp parents: 22 diff changeset	193 <!-- Windows only
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312 galaxyp parents: 22 diff changeset	194 <option value="Andromeda">Andromeda</option>
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312 galaxyp parents: 22 diff changeset	195 -->
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312 galaxyp parents: 22 diff changeset	196 <!-- New with version 3.0
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312 galaxyp parents: 22 diff changeset	197 -->
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312 galaxyp parents: 22 diff changeset	198 <!--working in tests
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312 galaxyp parents: 22 diff changeset	199 -->
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312 galaxyp parents: 22 diff changeset	200 <option value="DirecTag">DirecTag</option>
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312 galaxyp parents: 22 diff changeset	201 <option value="Novor">Novor (Select for non-commercial use only)</option>
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312 galaxyp parents: 22 diff changeset	202 <validator type="no_options" message="Please select at least one output file" />
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312 galaxyp parents: 22 diff changeset	203 </param>
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312 galaxyp parents: 22 diff changeset	204 </section>
0 a9e90cdcb97a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty galaxyp parents: diff changeset	205
48 b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 45 diff changeset	206 <conditional name="searchgui_advanced">
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 45 diff changeset	207 <param name="searchgui_advanced_selector" type="select" label="SearchGUI Options">
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 45 diff changeset	208 <option value="basic" selected="True">Default</option>
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 45 diff changeset	209 <option value="advanced">Advanced</option>
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 45 diff changeset	210 </param>
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 45 diff changeset	211 <when value="basic" />
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 45 diff changeset	212 <when value="advanced">
23 aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312 galaxyp parents: 22 diff changeset	213 <param name="correct_titles" type="select" label="How should PeptideShaker deal with duplicate spectra?"
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312 galaxyp parents: 22 diff changeset	214 help="Unless you suspect some input files to be genuine duplicates then rename spectra is the safest option">
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312 galaxyp parents: 22 diff changeset	215 <option value="0">no correction</option>
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312 galaxyp parents: 22 diff changeset	216 <option value="1" selected="True">rename spectra</option>
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312 galaxyp parents: 22 diff changeset	217 <option value="2">delete spectra</option>
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312 galaxyp parents: 22 diff changeset	218 </param>
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312 galaxyp parents: 22 diff changeset	219 <param name="missing_titles" type="boolean" checked="false" truevalue="-missing_titles 1" falsevalue="-missing_titles 0"
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312 galaxyp parents: 22 diff changeset	220 label="Add missing spectrum titles" help="(-missing_titles)"/>
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312 galaxyp parents: 22 diff changeset	221 <param name="mgf_splitting" type="integer" value="1000" label="The maximum mgf file size in MB before splitting the mgf"
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312 galaxyp parents: 22 diff changeset	222 help="Choose a smaller value if you are running on a machine with limited memory"/>
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312 galaxyp parents: 22 diff changeset	223 <param name="mgf_spectrum_count" type="integer" value="25000" label="The maximum number of spectra per mgf file when splitting"
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312 galaxyp parents: 22 diff changeset	224 help="Choose a smaller value if you are running on a machine with limited memory"/>
48 b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 45 diff changeset	225 <param name="output_gzip" type="boolean" checked="true" truevalue="1" falsevalue="0"
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 45 diff changeset	226 label="Gzip result files"/>
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 45 diff changeset	227 </when>
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 45 diff changeset	228 </conditional>
36 24bcbed3da6a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6afe42e2f4b9d780c4cee76a4dcd9cac1e1ea0ad galaxyp parents: 35 diff changeset	229
0 a9e90cdcb97a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty galaxyp parents: diff changeset	230 </inputs>
a9e90cdcb97a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty galaxyp parents: diff changeset	231 <outputs>
6 53bdfaed924d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 5943ced37a55ac06f722af5d4ccd568c300c0ea3 iracooke parents: 4 diff changeset	232 <data name="searchgui_results" format="searchgui_archive" from_work_dir="searchgui_out.zip" label="${tool.name} on ${on_string}" />
0 a9e90cdcb97a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty galaxyp parents: diff changeset	233 </outputs>
a9e90cdcb97a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty galaxyp parents: diff changeset	234 <tests>
9 21e5a77a7b57 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ac193f61dd02d3adbe8bc504f0b94edb1335f79d iracooke parents: 7 diff changeset	235
48 b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 45 diff changeset	236 <!-- Test that specifying non-default search engines with default parameters works -->
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 45 diff changeset	237 <test>
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 45 diff changeset	238 <param name="peak_lists_files" value="searchgui_tinyspectra1.mgf"/>
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 45 diff changeset	239 <param name="input_parameters_file" value="Identification_Parameters_default.par"/>
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 45 diff changeset	240 <param name="input_fasta_file" value="fastacli_searchgui_tinydb1_concatenated_target_decoy.fasta" ftype="fasta" />
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 45 diff changeset	241 <param name="engines" value="X!Tandem,MSGF,MyriMatch,Comet"/>
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 45 diff changeset	242 <output name="searchgui_results" file="searchgui_tiny_result_default_4engines.zip" ftype="searchgui_archive" compare="sim_size" delta="30000" />
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 45 diff changeset	243 </test>
53 166173739c8d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 62d0c9c13383dc58cc75cd273e0395e53a42b003" galaxyp parents: 52 diff changeset	244
166173739c8d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 62d0c9c13383dc58cc75cd273e0395e53a42b003" galaxyp parents: 52 diff changeset	245
52 c506a7ccb856 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 1cb321cbce2a6528764abc9c9431687f56c57588" galaxyp parents: 51 diff changeset	246 <!-- Test that search works with MetaMorpheus with default parameters works-->
c506a7ccb856 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 1cb321cbce2a6528764abc9c9431687f56c57588" galaxyp parents: 51 diff changeset	247 <!-- Test data has been taken from metamorpheus galaxy tool -->
c506a7ccb856 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 1cb321cbce2a6528764abc9c9431687f56c57588" galaxyp parents: 51 diff changeset	248 <test>
c506a7ccb856 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 1cb321cbce2a6528764abc9c9431687f56c57588" galaxyp parents: 51 diff changeset	249 <param name="peak_lists_files" value="searchgui_smallCalibratible_Yeast.mzML"/>
c506a7ccb856 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 1cb321cbce2a6528764abc9c9431687f56c57588" galaxyp parents: 51 diff changeset	250 <param name="input_parameters_file" value="Identification_Parameters_default.par"/>
c506a7ccb856 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 1cb321cbce2a6528764abc9c9431687f56c57588" galaxyp parents: 51 diff changeset	251 <param name="input_fasta_file" value="searchgui_smallYeast.fasta" ftype="fasta" />
c506a7ccb856 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 1cb321cbce2a6528764abc9c9431687f56c57588" galaxyp parents: 51 diff changeset	252 <param name="engines" value="MetaMorpheus"/>
c506a7ccb856 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 1cb321cbce2a6528764abc9c9431687f56c57588" galaxyp parents: 51 diff changeset	253 <output name="searchgui_results" ftype="searchgui_archive">
c506a7ccb856 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 1cb321cbce2a6528764abc9c9431687f56c57588" galaxyp parents: 51 diff changeset	254 <assert_contents>
c506a7ccb856 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 1cb321cbce2a6528764abc9c9431687f56c57588" galaxyp parents: 51 diff changeset	255 <has_size value="798597" delta="10000"/>
c506a7ccb856 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 1cb321cbce2a6528764abc9c9431687f56c57588" galaxyp parents: 51 diff changeset	256 </assert_contents>
c506a7ccb856 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 1cb321cbce2a6528764abc9c9431687f56c57588" galaxyp parents: 51 diff changeset	257 </output>
c506a7ccb856 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 1cb321cbce2a6528764abc9c9431687f56c57588" galaxyp parents: 51 diff changeset	258 </test>
48 b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 45 diff changeset	259
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 45 diff changeset	260 <!-- Test that search works with MSAmanda with default parameters works-->
0 a9e90cdcb97a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty galaxyp parents: diff changeset	261 <test>
48 b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 45 diff changeset	262 <param name="peak_lists_files" value="searchgui_smallspectra.mgf"/>
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 45 diff changeset	263 <param name="input_parameters_file" value="Identification_Parameters_default.par"/>
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 45 diff changeset	264 <param name="input_fasta_file" value="fastacli_searchgui_tinydb1_concatenated_target_decoy.fasta" ftype="fasta" />
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 45 diff changeset	265 <param name="engines" value="MS_Amanda"/>
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 45 diff changeset	266 <output name="searchgui_results" ftype="searchgui_archive">
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 45 diff changeset	267 <assert_contents>
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 45 diff changeset	268 <has_size value="635138" delta="5000"/>
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 45 diff changeset	269 </assert_contents>
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 45 diff changeset	270 </output>
0 a9e90cdcb97a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty galaxyp parents: diff changeset	271 </test>
48 b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 45 diff changeset	272
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 45 diff changeset	273 <!-- Test that specifying non-default search engines with non-default parameters works -->
11 76d14dc397ed planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 327a3944f2f56668d607c3d6cb08ae7d588e208c iracooke parents: 10 diff changeset	274 <test>
48 b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 45 diff changeset	275 <param name="peak_lists_files" value="searchgui_tinyspectra1.mgf"/>
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 45 diff changeset	276 <param name="input_parameters_file" value="Identification_Parameters_specific.par"/>
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 45 diff changeset	277 <param name="input_fasta_file" value="fastacli_searchgui_tinydb1_concatenated_target_decoy.fasta" ftype="fasta" />
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 45 diff changeset	278 <param name="engines" value="X!Tandem,MSGF,MyriMatch,Comet"/>
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 45 diff changeset	279 <output name="searchgui_results" ftype="searchgui_archive">
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 45 diff changeset	280 <assert_contents>
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 45 diff changeset	281 <has_size value="159330" delta="20000"/>
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 45 diff changeset	282 </assert_contents>
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 45 diff changeset	283 </output>
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 45 diff changeset	284 </test>
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 45 diff changeset	285
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 45 diff changeset	286 <!--
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 45 diff changeset	287 NOTE: Identification_Parameters_specific.par is equivalent to the default .par plus these parameters:
11 76d14dc397ed planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 327a3944f2f56668d607c3d6cb08ae7d588e208c iracooke parents: 10 diff changeset	288 <param name="precursor_ion_tol" value="100"/>
39 f63401dd6cbb planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 57426db0c017009ac7ab0498f8580efc453398c8 galaxyp parents: 38 diff changeset	289 <param name="min_charge" value="1"/>
f63401dd6cbb planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 57426db0c017009ac7ab0498f8580efc453398c8 galaxyp parents: 38 diff changeset	290 <param name="max_charge" value="3"/>
48 b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 45 diff changeset	291 <param name="xtandem\|xtandem_advanced" value="yes"/>
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 45 diff changeset	292 <param name="xtandem\|xtandem_advanced\|xtandem_refine_selector" value="yes"/>
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 45 diff changeset	293 -->
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 45 diff changeset	294
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 45 diff changeset	295 <!-- Test that specifying MsAmanda as search engine with non-default parameters works -->
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 45 diff changeset	296 <test>
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 45 diff changeset	297 <param name="peak_lists_files" value="searchgui_smallspectra.mgf"/>
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 45 diff changeset	298 <param name="input_parameters_file" value="Identification_Parameters_specific.par"/>
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 45 diff changeset	299 <param name="input_fasta_file" value="fastacli_searchgui_tinydb1_concatenated_target_decoy.fasta" ftype="fasta" />
39 f63401dd6cbb planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 57426db0c017009ac7ab0498f8580efc453398c8 galaxyp parents: 38 diff changeset	300 <param name="engines" value="MS_Amanda"/>
48 b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 45 diff changeset	301 <output name="searchgui_results" ftype="searchgui_archive">
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 45 diff changeset	302 <assert_contents>
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 45 diff changeset	303 <has_size value="635158" delta="5000"/>
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 45 diff changeset	304 </assert_contents>
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 45 diff changeset	305 </output>
39 f63401dd6cbb planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 57426db0c017009ac7ab0498f8580efc453398c8 galaxyp parents: 38 diff changeset	306 </test>
f63401dd6cbb planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 57426db0c017009ac7ab0498f8580efc453398c8 galaxyp parents: 38 diff changeset	307
48 b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 45 diff changeset	308 <!-- Test that specifying non-default search engines with default parameters works using modifications -->
39 f63401dd6cbb planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 57426db0c017009ac7ab0498f8580efc453398c8 galaxyp parents: 38 diff changeset	309 <test>
48 b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 45 diff changeset	310 <param name="peak_lists_files" value="searchgui_tinyspectra1.mgf"/>
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 45 diff changeset	311 <param name="input_parameters_file" value="Identification_Parameters_default_modifications.par"/>
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 45 diff changeset	312 <param name="input_fasta_file" value="fastacli_searchgui_tinydb1_concatenated_target_decoy.fasta" ftype="fasta" />
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 45 diff changeset	313 <param name="engines" value="X!Tandem,MSGF,MyriMatch,Comet"/>
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 45 diff changeset	314 <output name="searchgui_results" file="searchgui_tiny_result_default_4engines_modifications.zip" ftype="searchgui_archive" compare="sim_size" delta="30000" />
39 f63401dd6cbb planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 57426db0c017009ac7ab0498f8580efc453398c8 galaxyp parents: 38 diff changeset	315 </test>
48 b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 45 diff changeset	316
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 45 diff changeset	317 <!--
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 45 diff changeset	318 NOTE: Identification_Parameters_default_modifications.par adds:
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 45 diff changeset	319 - "Carbamidomethylation of C" as fixed modification
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 45 diff changeset	320 - "Oxidation of M" as variable modification
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 45 diff changeset	321 -->
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 45 diff changeset	322
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 45 diff changeset	323 <!-- Test that search works with MSAmanda with default default parameters - with modifications -->
39 f63401dd6cbb planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 57426db0c017009ac7ab0498f8580efc453398c8 galaxyp parents: 38 diff changeset	324 <test>
48 b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 45 diff changeset	325 <param name="peak_lists_files" value="searchgui_tinyspectra1.mgf"/>
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 45 diff changeset	326 <param name="input_parameters_file" value="Identification_Parameters_default_modifications.par"/>
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 45 diff changeset	327 <param name="input_fasta_file" value="fastacli_searchgui_tinydb1_concatenated_target_decoy.fasta" ftype="fasta" />
11 76d14dc397ed planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 327a3944f2f56668d607c3d6cb08ae7d588e208c iracooke parents: 10 diff changeset	328 <param name="engines" value="MS_Amanda"/>
48 b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 45 diff changeset	329 <output name="searchgui_results" ftype="searchgui_archive">
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 45 diff changeset	330 <assert_contents>
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 45 diff changeset	331 <has_size value="118136" delta="30000"/>
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 45 diff changeset	332 </assert_contents>
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 45 diff changeset	333 </output>
11 76d14dc397ed planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 327a3944f2f56668d607c3d6cb08ae7d588e208c iracooke parents: 10 diff changeset	334 </test>
48 b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 45 diff changeset	335
0 a9e90cdcb97a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty galaxyp parents: diff changeset	336 </tests>
a9e90cdcb97a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty galaxyp parents: diff changeset	337 <help>
a9e90cdcb97a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty galaxyp parents: diff changeset	338 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	339
48 b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 45 diff changeset	340 Runs multiple search engines on any number of MGF peak lists using SearchGUI.
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 45 diff changeset	341
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 45 diff changeset	342 Default: X! Tandem and MS-GF+ are executed.
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 45 diff changeset	343
52 c506a7ccb856 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 1cb321cbce2a6528764abc9c9431687f56c57588" galaxyp parents: 51 diff changeset	344 Optional: MyriMatch, MS-Amanda, MetaMorpheus, OMSSA (it may not work into isolated environments like containers), Comet, Tide, DirecTag and Novor can be executed.
0 a9e90cdcb97a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty galaxyp parents: diff changeset	345
51 c807a13df45f "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0f6ab8b5647a33b2b051d7aa808ef42546436b23" galaxyp parents: 50 diff changeset	346 Input FASTA
c807a13df45f "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0f6ab8b5647a33b2b051d7aa808ef42546436b23" galaxyp parents: 50 diff changeset	347
c807a13df45f "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0f6ab8b5647a33b2b051d7aa808ef42546436b23" galaxyp parents: 50 diff changeset	348 In order to allow for postprocessing with PeptideShaker the sequences must contain decoy sequences (see _here: https://github.com/compomics/searchgui/wiki/DatabaseHelp#decoy-sequences)
c807a13df45f "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0f6ab8b5647a33b2b051d7aa808ef42546436b23" galaxyp parents: 50 diff changeset	349 and the FASTA header must either contain no "\|" characters (then the whole header will be used as ID) or have the following format:
c807a13df45f "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0f6ab8b5647a33b2b051d7aa808ef42546436b23" galaxyp parents: 50 diff changeset	350
c807a13df45f "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0f6ab8b5647a33b2b051d7aa808ef42546436b23" galaxyp parents: 50 diff changeset	351 >generic[your tag]\|[protein accession]\|[protein description]
c807a13df45f "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0f6ab8b5647a33b2b051d7aa808ef42546436b23" galaxyp parents: 50 diff changeset	352
53 166173739c8d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 62d0c9c13383dc58cc75cd273e0395e53a42b003" galaxyp parents: 52 diff changeset	353 or
51 c807a13df45f "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0f6ab8b5647a33b2b051d7aa808ef42546436b23" galaxyp parents: 50 diff changeset	354
c807a13df45f "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0f6ab8b5647a33b2b051d7aa808ef42546436b23" galaxyp parents: 50 diff changeset	355 >generic[your tag]\|[protein accession]
c807a13df45f "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0f6ab8b5647a33b2b051d7aa808ef42546436b23" galaxyp parents: 50 diff changeset	356
c807a13df45f "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0f6ab8b5647a33b2b051d7aa808ef42546436b23" galaxyp parents: 50 diff changeset	357 See _here: https://github.com/compomics/searchgui/wiki/DatabaseHelp#non-standard-fasta.
c807a13df45f "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0f6ab8b5647a33b2b051d7aa808ef42546436b23" galaxyp parents: 50 diff changeset	358
c807a13df45f "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0f6ab8b5647a33b2b051d7aa808ef42546436b23" galaxyp parents: 50 diff changeset	359
c807a13df45f "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0f6ab8b5647a33b2b051d7aa808ef42546436b23" galaxyp parents: 50 diff changeset	360
0 a9e90cdcb97a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty galaxyp parents: diff changeset	361 </help>
a9e90cdcb97a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty galaxyp parents: diff changeset	362 <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	363 </tool>

Mercurial > repos > galaxyp > peptideshaker

annotate searchgui.xml @ 54:f5236b38562c draft default tip