Mercurial > repos > jjohnson > peptideshaker

annotate peptide_shaker.xml @ 3:8cf04d7a6683 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 01cd2c9b3fb3157202628579311943601218eb0b-dirty
author jjohnson
date Thu, 12 Jul 2018 09:01:01 -0400
parents eea7e945f479
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
2
eea7e945f479 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit b9d1c94d4c92009d99c5d4264e1085e7210208be-dirty
jjohnson
parents: 1
diff changeset
1 <tool id="peptide_shaker" name="Peptide Shaker" version="1.16.26">
0
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
2 <description>
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
3 Perform protein identification using various search engines based on results from SearchGUI
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
4 </description>
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
5 <macros>
2
eea7e945f479 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit b9d1c94d4c92009d99c5d4264e1085e7210208be-dirty
jjohnson
parents: 1
diff changeset
6 <import>macros.xml</import>
0
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
7 </macros>
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
8 <requirements>
2
eea7e945f479 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit b9d1c94d4c92009d99c5d4264e1085e7210208be-dirty
jjohnson
parents: 1
diff changeset
9 <requirement type="package" version="1.16.26">peptide-shaker</requirement>
0
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
10 </requirements>
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
11 <expand macro="stdio" />
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
12 <command>
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
13 <![CDATA[
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
14 #from datetime import datetime
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
15 #set $exp_str = "Galaxy_Experiment_%s" % datetime.now().strftime("%Y%m%d%H%M%s")
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
16 #set $samp_str = "Sample_%s" % datetime.now().strftime("%Y%m%d%H%M%s")
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
17 #set $temp_stderr = "peptideshaker_stderr"
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
18 #set $bin_dir = "bin"
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
19
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
20
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
21 mkdir output_reports;
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
22 cwd=`pwd`;
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
23
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
24 ln -s '$searchgui_input' searchgui_input.zip &&
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
25 jar xvf searchgui_input.zip SEARCHGUI_IdentificationParameters.par &&
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
26 ######################
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
27 ## PeptideShakerCLI ##
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
28 ######################
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
29 (peptide-shaker eu.isas.peptideshaker.cmd.PeptideShakerCLI
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
30 --exec_dir="\$cwd/${bin_dir}"
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
31 -temp_folder \$cwd/PeptideShakerCLI
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
32 -experiment '$exp_str'
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
33 -sample '$samp_str'
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
34 -replicate 1
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
35 -identification_files \$cwd/searchgui_input.zip
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
36 -id_params \$cwd/SEARCHGUI_IdentificationParameters.par
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
37 -out \$cwd/peptideshaker_output.cpsx
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
38 -zip \$cwd/peptideshaker_output.zip
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
39 #set $cleaned_list = str($outputs).split(',')
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
40 #if 'cps' in $cleaned_list:
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
41 #silent $cleaned_list.remove('cps')
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
42 #end if
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
43 #if 'mzidentML' in $cleaned_list:
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
44 #silent $cleaned_list.remove('mzidentML')
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
45 #end if
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
46 #if 'zip' in $cleaned_list:
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
47 #silent $cleaned_list.remove('zip')
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
48 #end if
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
49 #if len($cleaned_list) > 0
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
50 ## Only numbers are left over. These corresponds to different reports.
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
51 -reports #echo ','.join($cleaned_list)#
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
52 #end if
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
53
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
54 -threads "\${GALAXY_SLOTS:-12}"
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
55
2
eea7e945f479 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit b9d1c94d4c92009d99c5d4264e1085e7210208be-dirty
jjohnson
parents: 1
diff changeset
56 ##Optional processing parameters:
eea7e945f479 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit b9d1c94d4c92009d99c5d4264e1085e7210208be-dirty
jjohnson
parents: 1
diff changeset
57 #if $processing_options.processing_options_selector == "yes"
eea7e945f479 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit b9d1c94d4c92009d99c5d4264e1085e7210208be-dirty
jjohnson
parents: 1
diff changeset
58 -protein_fdr "${processing_options.protein_fdr}"
eea7e945f479 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit b9d1c94d4c92009d99c5d4264e1085e7210208be-dirty
jjohnson
parents: 1
diff changeset
59 -peptide_fdr "${processing_options.peptide_fdr}"
eea7e945f479 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit b9d1c94d4c92009d99c5d4264e1085e7210208be-dirty
jjohnson
parents: 1
diff changeset
60 -psm_fdr "${processing_options.psm_fdr}"
eea7e945f479 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit b9d1c94d4c92009d99c5d4264e1085e7210208be-dirty
jjohnson
parents: 1
diff changeset
61 -ptm_score "${processing_options.ptm_score.ptm_score_selector}"
eea7e945f479 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit b9d1c94d4c92009d99c5d4264e1085e7210208be-dirty
jjohnson
parents: 1
diff changeset
62 #if $processing_options.ptm_score.ptm_score_selector == 1
eea7e945f479 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit b9d1c94d4c92009d99c5d4264e1085e7210208be-dirty
jjohnson
parents: 1
diff changeset
63 -score_neutral_losses "${processing_options.ptm_score.neutral_losses}"
eea7e945f479 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit b9d1c94d4c92009d99c5d4264e1085e7210208be-dirty
jjohnson
parents: 1
diff changeset
64 #if str($processing_options.ptm_score.ptm_threshold) != ''
eea7e945f479 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit b9d1c94d4c92009d99c5d4264e1085e7210208be-dirty
jjohnson
parents: 1
diff changeset
65 -ptm_threshold "${processing_options.ptm_score.ptm_threshold}"
eea7e945f479 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit b9d1c94d4c92009d99c5d4264e1085e7210208be-dirty
jjohnson
parents: 1
diff changeset
66 #end if
eea7e945f479 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit b9d1c94d4c92009d99c5d4264e1085e7210208be-dirty
jjohnson
parents: 1
diff changeset
67 #end if
eea7e945f479 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit b9d1c94d4c92009d99c5d4264e1085e7210208be-dirty
jjohnson
parents: 1
diff changeset
68 -ptm_alignment "${processing_options.ptm_alignment}"
eea7e945f479 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit b9d1c94d4c92009d99c5d4264e1085e7210208be-dirty
jjohnson
parents: 1
diff changeset
69 -ptm_sequence_matching_type "${processing_options.ptm_sequence_matching_type}"
eea7e945f479 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit b9d1c94d4c92009d99c5d4264e1085e7210208be-dirty
jjohnson
parents: 1
diff changeset
70 -protein_fraction_mw_confidence "${processing_options.protein_fraction_mw_confidence}"
eea7e945f479 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit b9d1c94d4c92009d99c5d4264e1085e7210208be-dirty
jjohnson
parents: 1
diff changeset
71 #end if
0
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
72
2
eea7e945f479 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit b9d1c94d4c92009d99c5d4264e1085e7210208be-dirty
jjohnson
parents: 1
diff changeset
73 ##Optional filtering parameters:
eea7e945f479 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit b9d1c94d4c92009d99c5d4264e1085e7210208be-dirty
jjohnson
parents: 1
diff changeset
74 #if $filtering_options.filtering_options_selector == "yes":
eea7e945f479 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit b9d1c94d4c92009d99c5d4264e1085e7210208be-dirty
jjohnson
parents: 1
diff changeset
75 -import_peptide_length_min "${filtering_options.min_peptide_length}"
eea7e945f479 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit b9d1c94d4c92009d99c5d4264e1085e7210208be-dirty
jjohnson
parents: 1
diff changeset
76 -import_peptide_length_max "${filtering_options.max_peptide_length}"
eea7e945f479 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit b9d1c94d4c92009d99c5d4264e1085e7210208be-dirty
jjohnson
parents: 1
diff changeset
77 -import_precurosor_mz "${filtering_options.max_precursor_error}"
eea7e945f479 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit b9d1c94d4c92009d99c5d4264e1085e7210208be-dirty
jjohnson
parents: 1
diff changeset
78 -import_precurosor_mz_ppm "${filtering_options.max_precursor_error_type}"
eea7e945f479 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit b9d1c94d4c92009d99c5d4264e1085e7210208be-dirty
jjohnson
parents: 1
diff changeset
79 ##-max_xtandem_e "${filtering_options.max_xtandem_e}"
eea7e945f479 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit b9d1c94d4c92009d99c5d4264e1085e7210208be-dirty
jjohnson
parents: 1
diff changeset
80 ##-max_omssa_e "${filtering_options.max_omssa_e}"
eea7e945f479 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit b9d1c94d4c92009d99c5d4264e1085e7210208be-dirty
jjohnson
parents: 1
diff changeset
81 ##-max_mascot_e "${filtering_options.max_mascot_e}"
eea7e945f479 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit b9d1c94d4c92009d99c5d4264e1085e7210208be-dirty
jjohnson
parents: 1
diff changeset
82 -exclude_unknown_ptms "${filtering_options.exclude_unknown_ptms}"
eea7e945f479 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit b9d1c94d4c92009d99c5d4264e1085e7210208be-dirty
jjohnson
parents: 1
diff changeset
83 #end if
0
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
84
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
85 2>> $temp_stderr)
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
86
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
87 &&
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
88
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
89 echo "Running Reports";
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
90
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
91 ##################################
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
92 ## PeptideShaker Report options ##
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
93 ##################################
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
94
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
95 #if 'mzidentML' in str($outputs).split(','):
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
96 echo "Generating mzIdentML";
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
97 (peptide-shaker eu.isas.peptideshaker.cmd.MzidCLI
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
98 --exec_dir="\$cwd/${bin_dir}"
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
99 -in \$cwd/peptideshaker_output.zip
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
100 -output_file \$cwd/output.mzid
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
101 #if $contact_options.contact_options_selector == "yes":
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
102 -contact_first_name "$contact_options.contact_first_name"
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
103 -contact_last_name "$contact_options.contact_last_name"
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
104 -contact_email "$contact_options.contact_email"
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
105 -contact_address "$contact_options.contact_address"
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
106 #if str($contact_options.contact_url).strip() != '':
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
107 -contact_url = "$contact_options.contact_url"
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
108 #end if
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
109 -organization_name "$contact_options.organization_name"
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
110 -organization_email "$contact_options.organization_email"
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
111 -organization_address "$contact_options.organization_address"
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
112 #if str($contact_options.organization_url).strip() != '':
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
113 -organization_url = "$contact_options.organization_url"
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
114 #end if
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
115 #else:
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
116 -contact_first_name "Proteomics"
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
117 -contact_last_name "Galaxy"
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
118 -contact_email "galaxyp@umn.edu"
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
119 -contact_address "galaxyp@umn.edu"
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
120 -organization_name "University of Minnesota"
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
121 -organization_email "galaxyp@umn.edu"
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
122 -organization_address "Minneapolis, MN 55455, Vereinigte Staaten"
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
123 #end if
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
124 2>> $temp_stderr)
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
125 &&
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
126 #end if
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
127
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
128 ## Generate Reports if the user has selected one of the 8 additional reports
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
129 ## 'cps', 'mzidentML' and 'zip' are not valid options for PeptideShaker
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
130 ## and will not be passed to the command line
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
131 #if set(["0","1","2","3","4","5","6","7"]).intersection( set( str( $outputs ).split(',') ) ):
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
132
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
133 (peptide-shaker eu.isas.peptideshaker.cmd.ReportCLI
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
134 --exec_dir="\$cwd/${bin_dir}"
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
135 -temp_folder \$cwd/ReportCLI
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
136 -in \$cwd/peptideshaker_output.zip
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
137 -out_reports \$cwd/output_reports
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
138 #set $cleaned_list = str($outputs).split(',')
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
139 #if 'cps' in $cleaned_list:
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
140 #silent $cleaned_list.remove('cps')
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
141 #end if
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
142 #if 'mzidentML' in $cleaned_list:
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
143 #silent $cleaned_list.remove('mzidentML')
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
144 #end if
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
145 #if 'zip' in $cleaned_list:
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
146 #silent $cleaned_list.remove('zip')
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
147 #end if
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
148 ## Only numbers are left over. These corresponds to different reports.
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
149 -reports #echo ','.join($cleaned_list)#
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
150
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
151 2>> $temp_stderr)
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
152 &&
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
153 #end if
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
154
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
155 ## # ls -l \$cwd/output_reports/* ;
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
156
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
157 #if '0' in str($outputs).split(','):
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
158 find \$cwd/output_reports -name '*Certificate_of_Analysis*' -exec bash -c 'mv "$0" "certificate.txt"' {} \;
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
159 ;
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
160 #end if
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
161 #if '1' in str($outputs).split(','):
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
162 find \$cwd/output_reports -name '*Hierarchical*' -exec bash -c 'mv "$0" "hierarchical.txt"' {} \;
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
163 ;
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
164 #end if
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
165 #if '2' in str($outputs).split(','):
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
166 find \$cwd/output_reports -name '*PSM_Phosphorylation_Report*' -exec bash -c 'mv "$0" "psm_phospho.txt"' {} \;
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
167 ;
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
168 #end if
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
169 #if '8' in str($outputs).split(','):
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
170 find \$cwd/output_reports -name '*Extended_PSM_Report*' -exec bash -c 'mv "$0" "psmx.txt"' {} \;
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
171 ;
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
172 #end if
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
173 #if '3' in str($outputs).split(','):
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
174 find \$cwd/output_reports -name '*PSM_Report*' -exec bash -c 'mv "$0" "psm.txt"' {} \;
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
175 ;
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
176 #end if
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
177 #if '4' in str($outputs).split(','):
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
178 find \$cwd/output_reports -name '*Peptide_Phosphorylation_Report*' -exec bash -c 'mv "$0" "peptides_phospho.txt"' {} \;
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
179 ;
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
180 #end if
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
181 #if '5' in str($outputs).split(','):
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
182 find \$cwd/output_reports -name '*Peptide_Report*' -exec bash -c 'mv "$0" "peptides.txt"' {} \;
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
183 ;
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
184 #end if
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
185 #if '6' in str($outputs).split(','):
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
186 find \$cwd/output_reports -name '*Protein_Phosphorylation_Report*' -exec bash -c 'mv "$0" "proteins_phospho.txt"' {} \;
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
187 ;
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
188 #end if
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
189 #if '7' in str($outputs).split(','):
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
190 find \$cwd/output_reports -name '*Protein_Report*' -exec bash -c 'mv "$0" "proteins.txt"' {} \;
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
191 ;
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
192 #end if
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
193
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
194 exit_code_for_galaxy=\$?;
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
195 cat $temp_stderr 2>&1;
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
196 (exit \$exit_code_for_galaxy)
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
197
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
198 ]]>
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
199 </command>
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
200 <inputs>
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
201 <param name="searchgui_input" format="searchgui_archive" type="data" label="Compressed SearchGUI results"
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
202 help="SearchGUI Results from History">
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
203 <options options_filter_attribute="metadata.searchgui_major_version" >
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
204 <filter type="add_value" value="@SEARCHGUI_MAJOR_VERSION@" />
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
205 </options>
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
206 </param>
2
eea7e945f479 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit b9d1c94d4c92009d99c5d4264e1085e7210208be-dirty
jjohnson
parents: 1
diff changeset
207 <conditional name="processing_options">
eea7e945f479 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit b9d1c94d4c92009d99c5d4264e1085e7210208be-dirty
jjohnson
parents: 1
diff changeset
208 <param name="processing_options_selector" type="select" label="Specify Advanced PeptideShaker Processing Options">
eea7e945f479 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit b9d1c94d4c92009d99c5d4264e1085e7210208be-dirty
jjohnson
parents: 1
diff changeset
209 <option value="no" selected="True">Default Processing Options</option>
eea7e945f479 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit b9d1c94d4c92009d99c5d4264e1085e7210208be-dirty
jjohnson
parents: 1
diff changeset
210 <option value="yes">Advanced Processing Options</option>
eea7e945f479 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit b9d1c94d4c92009d99c5d4264e1085e7210208be-dirty
jjohnson
parents: 1
diff changeset
211 </param>
eea7e945f479 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit b9d1c94d4c92009d99c5d4264e1085e7210208be-dirty
jjohnson
parents: 1
diff changeset
212 <when value="no" />
eea7e945f479 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit b9d1c94d4c92009d99c5d4264e1085e7210208be-dirty
jjohnson
parents: 1
diff changeset
213 <when value="yes">
eea7e945f479 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit b9d1c94d4c92009d99c5d4264e1085e7210208be-dirty
jjohnson
parents: 1
diff changeset
214 <param name="protein_fdr" label="FDR at the protein level" help="In percent (default 1% FDR: '1')" value="1" type="float" />
eea7e945f479 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit b9d1c94d4c92009d99c5d4264e1085e7210208be-dirty
jjohnson
parents: 1
diff changeset
215 <param name="peptide_fdr" label="FDR at the peptide level" help="In percent (default 1% FDR: '1')" value="1" type="float" />
eea7e945f479 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit b9d1c94d4c92009d99c5d4264e1085e7210208be-dirty
jjohnson
parents: 1
diff changeset
216 <param name="psm_fdr" label="FDR at the PSM level" help="In percent (default 1% FDR: '1')" value="1" type="float" />
eea7e945f479 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit b9d1c94d4c92009d99c5d4264e1085e7210208be-dirty
jjohnson
parents: 1
diff changeset
217 <param name="protein_fraction_mw_confidence" value="95.0" type="float" label="Minimum confidence required for a protein in the fraction MW plot"
eea7e945f479 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit b9d1c94d4c92009d99c5d4264e1085e7210208be-dirty
jjohnson
parents: 1
diff changeset
218 help="default 95%: '95.0'" />
eea7e945f479 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit b9d1c94d4c92009d99c5d4264e1085e7210208be-dirty
jjohnson
parents: 1
diff changeset
219 <conditional name="ptm_score">
eea7e945f479 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit b9d1c94d4c92009d99c5d4264e1085e7210208be-dirty
jjohnson
parents: 1
diff changeset
220 <param name="ptm_score_selector" type="select" label="The PTM probabilistic score to use for PTM localization">
eea7e945f479 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit b9d1c94d4c92009d99c5d4264e1085e7210208be-dirty
jjohnson
parents: 1
diff changeset
221 <option value="0" selected="True">A-score</option>
eea7e945f479 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit b9d1c94d4c92009d99c5d4264e1085e7210208be-dirty
jjohnson
parents: 1
diff changeset
222 <option value="1">PhosphoRS</option>
eea7e945f479 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit b9d1c94d4c92009d99c5d4264e1085e7210208be-dirty
jjohnson
parents: 1
diff changeset
223 <option value="2">None</option>
eea7e945f479 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit b9d1c94d4c92009d99c5d4264e1085e7210208be-dirty
jjohnson
parents: 1
diff changeset
224 </param>
eea7e945f479 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit b9d1c94d4c92009d99c5d4264e1085e7210208be-dirty
jjohnson
parents: 1
diff changeset
225 <when value="0" />
eea7e945f479 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit b9d1c94d4c92009d99c5d4264e1085e7210208be-dirty
jjohnson
parents: 1
diff changeset
226 <when value="1">
eea7e945f479 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit b9d1c94d4c92009d99c5d4264e1085e7210208be-dirty
jjohnson
parents: 1
diff changeset
227 <param name="score_neutral_losses" label="Include Neutral Losses in A Score" type="boolean" truevalue="1" falsevalue="0" />
eea7e945f479 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit b9d1c94d4c92009d99c5d4264e1085e7210208be-dirty
jjohnson
parents: 1
diff changeset
228 <param name="ptm_threshold" label="The threshold to use for the PTM scores" optional="true" value="" type="float"
eea7e945f479 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit b9d1c94d4c92009d99c5d4264e1085e7210208be-dirty
jjohnson
parents: 1
diff changeset
229 help="Automatic mode will be used if not set" />
eea7e945f479 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit b9d1c94d4c92009d99c5d4264e1085e7210208be-dirty
jjohnson
parents: 1
diff changeset
230 </when>
eea7e945f479 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit b9d1c94d4c92009d99c5d4264e1085e7210208be-dirty
jjohnson
parents: 1
diff changeset
231 <when value="2" />
eea7e945f479 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit b9d1c94d4c92009d99c5d4264e1085e7210208be-dirty
jjohnson
parents: 1
diff changeset
232 </conditional>
eea7e945f479 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit b9d1c94d4c92009d99c5d4264e1085e7210208be-dirty
jjohnson
parents: 1
diff changeset
233 <param name="ptm_sequence_matching_type" type="select" label="The PTM to peptide sequence matching type">
eea7e945f479 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit b9d1c94d4c92009d99c5d4264e1085e7210208be-dirty
jjohnson
parents: 1
diff changeset
234 <option value="0">Character Sequence</option>
eea7e945f479 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit b9d1c94d4c92009d99c5d4264e1085e7210208be-dirty
jjohnson
parents: 1
diff changeset
235 <option value="1" selected="true">Amino Acids</option>
eea7e945f479 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit b9d1c94d4c92009d99c5d4264e1085e7210208be-dirty
jjohnson
parents: 1
diff changeset
236 <option value="2">Indistinguishable Amino Acids</option>
eea7e945f479 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit b9d1c94d4c92009d99c5d4264e1085e7210208be-dirty
jjohnson
parents: 1
diff changeset
237 </param>
eea7e945f479 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit b9d1c94d4c92009d99c5d4264e1085e7210208be-dirty
jjohnson
parents: 1
diff changeset
238 <param name="ptm_alignment" label="Align peptide ambiguously localized PTMs on confident sites" type="boolean" truevalue="1" falsevalue="0" checked="true"/>
eea7e945f479 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit b9d1c94d4c92009d99c5d4264e1085e7210208be-dirty
jjohnson
parents: 1
diff changeset
239 <!-- SKIPPING -protein_fraction_mw_confidence ${processing_options.protein_fraction_mw_confidence} -->
eea7e945f479 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit b9d1c94d4c92009d99c5d4264e1085e7210208be-dirty
jjohnson
parents: 1
diff changeset
240 </when>
eea7e945f479 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit b9d1c94d4c92009d99c5d4264e1085e7210208be-dirty
jjohnson
parents: 1
diff changeset
241 </conditional>
eea7e945f479 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit b9d1c94d4c92009d99c5d4264e1085e7210208be-dirty
jjohnson
parents: 1
diff changeset
242 <conditional name="filtering_options">
eea7e945f479 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit b9d1c94d4c92009d99c5d4264e1085e7210208be-dirty
jjohnson
parents: 1
diff changeset
243 <param name="filtering_options_selector" type="select" label="Specify Advanced Filtering Options"
eea7e945f479 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit b9d1c94d4c92009d99c5d4264e1085e7210208be-dirty
jjohnson
parents: 1
diff changeset
244 help="Filter based on peptide lengths, precursor mass error, E value errors from X! Tandem and OMSSA, and include/exclude unknown PTM’s">
eea7e945f479 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit b9d1c94d4c92009d99c5d4264e1085e7210208be-dirty
jjohnson
parents: 1
diff changeset
245 <option value="no" selected="True">Default Filtering Options</option>
eea7e945f479 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit b9d1c94d4c92009d99c5d4264e1085e7210208be-dirty
jjohnson
parents: 1
diff changeset
246 <option value="yes">Advanced Filtering Options</option>
eea7e945f479 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit b9d1c94d4c92009d99c5d4264e1085e7210208be-dirty
jjohnson
parents: 1
diff changeset
247 </param>
eea7e945f479 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit b9d1c94d4c92009d99c5d4264e1085e7210208be-dirty
jjohnson
parents: 1
diff changeset
248 <when value="no" />
eea7e945f479 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit b9d1c94d4c92009d99c5d4264e1085e7210208be-dirty
jjohnson
parents: 1
diff changeset
249 <when value="yes">
eea7e945f479 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit b9d1c94d4c92009d99c5d4264e1085e7210208be-dirty
jjohnson
parents: 1
diff changeset
250 <param name="min_peptide_length" type="integer" label="Minimum Peptide Length" value="6" />
eea7e945f479 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit b9d1c94d4c92009d99c5d4264e1085e7210208be-dirty
jjohnson
parents: 1
diff changeset
251 <param name="max_peptide_length" type="integer" label="Maximum Peptide Length" value="30" />
eea7e945f479 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit b9d1c94d4c92009d99c5d4264e1085e7210208be-dirty
jjohnson
parents: 1
diff changeset
252 <param name="max_precursor_error" type="float" label="Maximum Precursor Error" value="10"
eea7e945f479 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit b9d1c94d4c92009d99c5d4264e1085e7210208be-dirty
jjohnson
parents: 1
diff changeset
253 help="Next option specifies units (Da or ppm)" />
eea7e945f479 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit b9d1c94d4c92009d99c5d4264e1085e7210208be-dirty
jjohnson
parents: 1
diff changeset
254 <param name="max_precursor_error_type" label="Maximum Precursor Error Type" type="select">
eea7e945f479 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit b9d1c94d4c92009d99c5d4264e1085e7210208be-dirty
jjohnson
parents: 1
diff changeset
255 <option value="1">ppm</option>
eea7e945f479 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit b9d1c94d4c92009d99c5d4264e1085e7210208be-dirty
jjohnson
parents: 1
diff changeset
256 <option value="0">Daltons</option>
eea7e945f479 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit b9d1c94d4c92009d99c5d4264e1085e7210208be-dirty
jjohnson
parents: 1
diff changeset
257 </param>
eea7e945f479 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit b9d1c94d4c92009d99c5d4264e1085e7210208be-dirty
jjohnson
parents: 1
diff changeset
258 <!--param name="max_xtandem_e" label="Maximum X! Tandem e-value" value="100" type="float" help="" /-->
eea7e945f479 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit b9d1c94d4c92009d99c5d4264e1085e7210208be-dirty
jjohnson
parents: 1
diff changeset
259 <!--param name="max_omssa_e" label="Maximum OMSSA e-value" value="100" type="float" help="" /-->
eea7e945f479 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit b9d1c94d4c92009d99c5d4264e1085e7210208be-dirty
jjohnson
parents: 1
diff changeset
260 <!--param name="max_mascot_e" label="Maximum Mascot e-value filter" value="100" type="float" help="" /-->
eea7e945f479 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit b9d1c94d4c92009d99c5d4264e1085e7210208be-dirty
jjohnson
parents: 1
diff changeset
261 <param name="exclude_unknown_ptms" label="Exclude Unknown PTMs" type="boolean" truevalue="1" falsevalue="0" checked="true" />
eea7e945f479 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit b9d1c94d4c92009d99c5d4264e1085e7210208be-dirty
jjohnson
parents: 1
diff changeset
262 </when>
eea7e945f479 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit b9d1c94d4c92009d99c5d4264e1085e7210208be-dirty
jjohnson
parents: 1
diff changeset
263 </conditional>
0
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
264 <conditional name="contact_options">
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
265 <param name="contact_options_selector" type="select" label="Specify Contact Information for mzIdendML"
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
266 help="Create a Galaxy workflow to save these values">
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
267 <option value="no" selected="True">GalaxyP Project contact (Not suitable for PRIDE submission)</option>
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
268 <option value="yes">Specify Contact Information</option>
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
269 </param>
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
270 <when value="no" />
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
271 <when value="yes">
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
272 <param name="contact_first_name" type="text" value="" label="Contact first name.">
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
273 <validator type="regex" message="">\S+.*</validator>
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
274 </param>
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
275 <param name="contact_last_name" type="text" value="" label="Contact last name.">
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
276 <validator type="regex" message="">\S+.*</validator>
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
277 </param>
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
278 <param name="contact_email" type="text" value="" label="Contact e-mail.">
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
279 <validator type="regex" message="">\S+@\S+</validator>
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
280 </param>
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
281 <param name="contact_address" type="text" value="" label="Contact address.">
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
282 <validator type="regex" message="">\S+.*</validator>
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
283 </param>
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
284 <param name="contact_url" type="text" value="" optional="true" label="Contact URL.">
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
285 </param>
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
286 <param name="organization_name" type="text" value="" label="Organization name.">
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
287 <validator type="regex" message="">\S+.*</validator>
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
288 </param>
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
289 <param name="organization_email" type="text" value="" label="Organization e-mail.">
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
290 <validator type="regex" message="">\S+@\S+</validator>
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
291 </param>
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
292 <param name="organization_address" type="text" value="" label="Organization address.">
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
293 <validator type="regex" message="">\S+.*</validator>
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
294 </param>
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
295 <param name="organization_url" type="text" value="" optional="true" label="Organization URL.">
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
296 </param>
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
297 </when>
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
298 </conditional>
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
299
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
300 <param name="include_sequences" type="boolean" truevalue="1" falsevalue="0" checked="false" label="Include the protein sequences in mzIdentML" />
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
301 <param name="outputs" type="select" display="checkboxes" multiple="True" label="Output options">
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
302 <option value="zip">Zip File for import to Desktop App</option>
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
303 <option value="mzidentML" selected="True">mzidentML File</option>
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
304 <option value="3">PSM Report</option>
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
305 <option value="8">Extended PSM Report</option>
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
306 <option value="2">PSM Phosphorylation Report</option>
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
307 <option value="5">Peptide Report</option>
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
308 <option value="4">Peptide Phosphorylation Report</option>
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
309 <option value="7">Protein Report</option>
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
310 <option value="6">Protein Phosphorylation Report</option>
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
311 <option value="0">Certificate of Analysis</option>
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
312 <option value="1">Hierarchical Report</option>
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
313 <option value="cps">CPS file</option>
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
314 <validator type="no_options" message="Please select at least one output file" />
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
315 </param>
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
316
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
317 </inputs>
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
318 <outputs>
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
319 <data format="mzid" name="mzidentML" from_work_dir="output.mzid" label="${tool.name} on ${on_string}: mzidentML file">
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
320 <filter>'mzidentML' in outputs</filter>
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
321 </data>
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
322 <data format="peptideshaker_archive" name="output_cps" from_work_dir="peptideshaker_output.cpsx" label="${tool.name} on ${on_string}: CPS file">
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
323 <filter>'cps' in outputs</filter>
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
324 </data>
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
325 <data format="zip" name="output_zip" from_work_dir="peptideshaker_output.zip" label="${tool.name} on ${on_string}: Archive">
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
326 <filter>'zip' in outputs</filter>
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
327 </data>
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
328 <data format="txt" name="output_certificate" from_work_dir="certificate.txt" label="${tool.name} on ${on_string}: Parameters">
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
329 <filter>'0' in outputs</filter>
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
330 </data>
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
331 <data format="tabular" name="output_hierarchical" from_work_dir="hierarchical.txt" label="${tool.name} on ${on_string}: Hierarchical Report">
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
332 <filter>'1' in outputs</filter>
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
333 </data>
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
334 <data format="tabular" name="output_psm_phosphorylation" from_work_dir="psm_phospho.txt" label="${tool.name} on ${on_string}: PSM Phosphorylation Report">
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
335 <filter>'2' in outputs</filter>
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
336 </data>
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
337 <data format="tabular" name="output_psm" from_work_dir="psm.txt" label="${tool.name} on ${on_string}: PSM Report">
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
338 <filter>'3' in outputs</filter>
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
339 </data>
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
340 <data format="tabular" name="output_extended_psm" from_work_dir="psmx.txt" label="${tool.name} on ${on_string}: Extended PSM Report">
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
341 <filter>'8' in outputs</filter>
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
342 </data>
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
343 <data format="tabular" name="output_peptides_phosphorylation" from_work_dir="peptides_phospho.txt" label="${tool.name} on ${on_string}: Peptide Phosphorylation Report">
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
344 <filter>'4' in outputs</filter>
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
345 </data>
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
346 <data format="tabular" name="output_peptides" from_work_dir="peptides.txt" label="${tool.name} on ${on_string}: Peptide Report">
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
347 <filter>'5' in outputs</filter>
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
348 </data>
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
349 <data format="tabular" name="output_proteins_phosphorylation" from_work_dir="proteins_phospho.txt" label="${tool.name} on ${on_string}: Protein Phosphorylation Report">
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
350 <filter>'6' in outputs</filter>
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
351 </data>
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
352 <data format="tabular" name="output_proteins" from_work_dir="proteins.txt" label="${tool.name} on ${on_string}: Protein Report">
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
353 <filter>'7' in outputs</filter>
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
354 </data>
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
355 </outputs>
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
356 <tests>
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
357 <test>
2
eea7e945f479 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit b9d1c94d4c92009d99c5d4264e1085e7210208be-dirty
jjohnson
parents: 1
diff changeset
358 <param name="searchgui_input" value="tiny_searchgui_modifications_result1.zip" ftype="searchgui_archive"/>
0
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
359 <param name="processing_options_selector" value="no"/>
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
360 <param name="filtering_options_selector" value="no"/>
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
361 <param name="outputs" value="zip,3"/>
2
eea7e945f479 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit b9d1c94d4c92009d99c5d4264e1085e7210208be-dirty
jjohnson
parents: 1
diff changeset
362 <output name="output_zip" file="peptide_shaker_modifications_result1.zip" ftype="zip" compare="sim_size" delta="3000" />
0
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
363 <output name="output_psm">
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
364 <assert_contents>
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
365 <has_text text="cds.comp41779_c0_seq1" />
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
366 </assert_contents>
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
367 </output>
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
368 </test>
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
369 <test>
2
eea7e945f479 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit b9d1c94d4c92009d99c5d4264e1085e7210208be-dirty
jjohnson
parents: 1
diff changeset
370 <param name="searchgui_input" value="tiny_searchgui_modifications_result1.zip" ftype="searchgui_archive"/>
0
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
371 <param name="processing_options_selector" value="no"/>
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
372 <param name="filtering_options_selector" value="yes"/>
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
373 <param name="min_peptide_length" value="1"/>
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
374 <param name="outputs" value="0,1,2,3,4,5,6,7"/>
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
375 <output name="output_certificate">
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
376 <assert_contents>
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
377 <has_text text="Tolerance: 100" />
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
378 <has_text text="Carbamidomethylation of C" />
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
379 </assert_contents>
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
380 </output>
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
381 <output name="output_hierarchical">
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
382 <assert_contents>
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
383 <has_text_matching expression="1.1\tcds.comp" />
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
384 </assert_contents>
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
385 </output>
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
386 <output name="output_psm">
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
387 <assert_contents>
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
388 <not_has_text text="Phosphosite" />
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
389 <has_text text="cds.comp41779_c0_seq1" />
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
390 </assert_contents>
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
391 </output>
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
392 <output name="output_psm_phosphorylation">
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
393 <assert_contents>
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
394 <has_text text="Phosphosite" />
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
395 <has_text text="cds.comp41779_c0_seq1" />
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
396 </assert_contents>
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
397 </output>
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
398 <output name="output_peptides">
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
399 <assert_contents>
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
400 <has_text text="Modification" />
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
401 <has_text text="cds.comp41779_c0_seq1" />
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
402 </assert_contents>
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
403 </output>
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
404 <output name="output_peptides_phosphorylation">
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
405 <assert_contents>
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
406 <has_text text="Phosphosite" />
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
407 <has_text text="cds.comp41779_c0_seq1" />
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
408 </assert_contents>
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
409 </output>
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
410 <output name="output_proteins">
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
411 <assert_contents>
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
412 <has_text text="Modification" />
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
413 <has_text text="cds.comp41779_c0_seq1" />
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
414 </assert_contents>
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
415 </output>
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
416 <output name="output_proteins_phosphorylation">
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
417 <assert_contents>
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
418 <has_text text="Phosphosite" />
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
419 <has_text text="cds.comp41779_c0_seq1" />
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
420 </assert_contents>
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
421 </output>
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
422 </test>
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
423 <test>
2
eea7e945f479 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit b9d1c94d4c92009d99c5d4264e1085e7210208be-dirty
jjohnson
parents: 1
diff changeset
424 <param name="searchgui_input" value="tiny_searchgui_modifications_result1.zip" ftype="searchgui_archive"/>
0
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
425 <param name="processing_options_selector" value="no"/>
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
426 <param name="filtering_options_selector" value="no"/>
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
427 <param name="outputs" value="3,cps"/>
2
eea7e945f479 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit b9d1c94d4c92009d99c5d4264e1085e7210208be-dirty
jjohnson
parents: 1
diff changeset
428 <output name="output_cps" file="peptide_shaker_modifications_result1.cpsx" ftype="peptideshaker_archive" compare="sim_size" delta="3000"/>
0
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
429 <output name="output_psm">
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
430 <assert_contents>
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
431 <has_text text="cds.comp41779_c0_seq1" />
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
432 </assert_contents>
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
433 </output>
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
434 </test>
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
435 </tests>
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
436 <help>
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
437 **What it does**
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
438
2
eea7e945f479 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit b9d1c94d4c92009d99c5d4264e1085e7210208be-dirty
jjohnson
parents: 1
diff changeset
439 Runs multiple search engines (X! Tandem, OMSSA and MS-GF+) on any number of MGF peak lists using the SearchGUI application and combines the results.
0
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
440
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
441 http://compomics.github.io/projects/peptide-shaker.html
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
442 http://compomics.github.io/projects/searchgui.html
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
443
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
444 ----
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
445
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
446 Reports
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
447 =======
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
448
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
449
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
450 PSM Report
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
451 ----------
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
452
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
453 * Protein(s): Protein(s) to which the peptide can be attached
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
454 * Sequence: Sequence of the peptide
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
455 * Variable Modifications: The variable modifications
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
456 * D-score: D-score for variable PTM localization
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
457 * probabilistic PTM score: The probabilistic score (e.g. A-score or PhosphoRS) used for variable PTM localization.
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
458 * Localization Confidence: The confidence in variable PTM localization.
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
459 * Fixed Modifications: The fixed modifications.
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
460 * Spectrum File: The spectrum file.
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
461 * Spectrum Title: The title of the spectrum.
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
462 * Spectrum Scan Number: The spectrum scan number.
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
463 * RT: Retention time
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
464 * m/z: Measured m/z
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
465 * Measured Charge: The charge as given in the spectrum file.
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
466 * Identification Charge: The charge as inferred by the search engine.
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
467 * Theoretical Mass: The theoretical mass of the peptide.
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
468 * Isotope Number: The isotope number targetted by the instrument.
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
469 * Precursor m/z Error: The precursor m/z matching error.
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
470 * Score: Score of the retained peptide as a combination of the algorithm scores (used to rank PSMs).
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
471 * Confidence: Confidence in percent associated to the retained PSM.
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
472 * Decoy: Indicates whether the peptide is a decoy (1: yes, 0: no).
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
473 * Validation: Indicates the validation level of the protein group.
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
474
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
475
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
476 Protein Report
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
477 --------------
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
478
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
479 * Main Accession: Main accession of the protein group.
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
480 * Description: Description of the protein designed by the main accession.
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
481 * Gene Name: The gene names of the Ensembl gene ID associated to the main accession.
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
482 * Chromosome: The chromosome of the Ensembl gene ID associated to the main accession.
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
483 * PI: Protein Inference status of the protein group.
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
484 * Secondary Accessions: Other accessions in the protein group (alphabetical order).
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
485 * Protein Group: The complete protein group (alphabetical order).
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
486 * #Peptides: Total number of peptides.
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
487 * #Validated Peptides: Number of validated peptides.
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
488 * #Unique: Total number of peptides unique to this protein group.
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
489 * #PSMs: Number of PSMs
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
490 * #Validated PSMs: Number of validated PSMs
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
491 * Coverage (%): Sequence coverage in percent of the protein designed by the main accession.
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
492 * Possible Coverage (%): Possible sequence coverage in percent of the protein designed by the main accession according to the search settings.
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
493 * MW (kDa): Molecular Weight.
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
494 * Spectrum Counting NSAF: Normalized Spectrum Abundance Factor (NSAF)
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
495 * Spectrum Counting emPAI: exponentially modified Protein Abundance Index (emPAI)
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
496 * Confident Modification Sites: Number of Confident Modification Sites List of the sites where a variable modification was confidently localized.
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
497 * Other Modification Sites: Number of other Modification Sites List of the non*confident sites where a variable modification was localized.
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
498 * Score: Score of the protein group.
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
499 * Confidence: Confidence in percent associated to the protein group.
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
500 * Decoy: Indicates whether the protein group is a decoy (1: yes, 0: no).
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
501 * Validation: Indicates the validation level of the protein group.
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
502
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
503
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
504 Peptide Report
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
505 --------------
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
506
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
507
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
508 * Protein(s): Protein(s) to which this peptide can be attached.
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
509 * AAs Before: The amino-acids before the sequence.
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
510 * Sequence: Sequence of the peptide.
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
511 * AAs After: The amino-acids after the sequence.
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
512 * Modified Sequence: The peptide sequence annotated with variable modifications.
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
513 * Variable Modifications: The variable modifications.
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
514 * Localization Confidence: The confidence in PTMs localization.
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
515 * Fixed Modifications: The fixed modifications.
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
516 * #Validated PSMs: Number of validated PSMs.
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
517 * #PSMs: Number of PSMs.
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
518 * Score: Score of the peptide.
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
519 * Confidence: Confidence in percent associated to the peptide.
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
520 * Decoy: Indicates whether the peptide is a decoy (1: yes, 0: no).
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
521 * Validation: Indicates the validation level of the protein group.
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
522
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
523
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
524 Hierachical Report
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
525 ------------------
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
526
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
527 * Main Accession: Main accession of the protein group.
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
528 * Description: Description of the protein designed by the main accession.
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
529 * PI: Protein Inference status of the protein group.
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
530 * Secondary Accessions: Other accessions in the protein group (alphabetical order).
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
531 * Protein Group: The complete protein group (alphabetical order).
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
532 * #Peptides: Total number of peptides.
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
533 * #Validated Peptides: Number of validated peptides.
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
534 * #Unique: Total number of peptides unique to this protein group.
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
535 * #PSMs: Number of PSMs
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
536 * #Validated PSMs: Number of validated PSMs
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
537 * Coverage (%): Sequence coverage in percent of the protein designed by the main accession.
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
538 * Possible Coverage (%): Possible sequence coverage in percent of the protein designed by the main accession according to the search settings.
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
539 * MW (kDa): Molecular Weight.
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
540 * Spectrum Counting NSAF: Normalized Spectrum Abundance Factor (NSAF)
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
541 * Spectrum Counting emPAI: exponentially modified Protein Abundance Index (emPAI)
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
542 * Confident Modification Sites: # Confident Modification Sites List of the sites where a variable modification was confidently localized.
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
543 * Other Modification Sites: # Other Modification Sites List of the non-confident sites where a variable modification was localized.
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
544 * Score: Score of the protein group.
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
545 * Confidence: Confidence in percent associated to the protein group.
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
546 * Decoy: Indicates whether the protein group is a decoy (1: yes, 0: no).
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
547 * Validation: Indicates the validation level of the protein group.
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
548 * Protein(s): Protein(s) to which this peptide can be attached.
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
549 * AAs Before: The amino-acids before the sequence.
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
550 * Sequence: Sequence of the peptide.
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
551 * AAs After: The amino-acids after the sequence.
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
552 * Variable Modifications: The variable modifications.
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
553 * Localization Confidence: The confidence in PTMs localization.
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
554 * Fixed Modifications: The fixed modifications.
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
555 * #Validated PSMs: Number of validated PSMs.
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
556 * #PSMs: Number of PSMs.
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
557 * Score: Score of the peptide.
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
558 * Confidence: Confidence in percent associated to the peptide.
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
559 * Decoy: Indicates whether the peptide is a decoy (1: yes, 0: no).
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
560 * Validation: Indicates the validation level of the protein group.
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
561 * Protein(s): Protein(s) to which the peptide can be attached.
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
562 * Sequence: Sequence of the peptide.
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
563 * Modified Sequence: The peptide sequence annotated with variable modifications.
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
564 * Variable Modifications: The variable modifications.
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
565 * D-score: D-score for variable PTM localization.
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
566 * probabilistic PTM score: The probabilistic score (e.g. A-score or PhosphoRS) used for variable PTM localization.
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
567 * Localization Confidence: The confidence in variable PTM localization.
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
568 * Fixed Modifications: The fixed modifications.
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
569 * Spectrum File: The spectrum file.
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
570 * Spectrum Title: The title of the spectrum.
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
571 * Spectrum Scan Number: The spectrum scan number.
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
572 * RT: Retention time
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
573 * m/z: Measured m/z
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
574 * Measured Charge: The charge as given in the spectrum file.
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
575 * Identification Charge: The charge as inferred by the search engine.
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
576 * Theoretical Mass: The theoretical mass of the peptide.
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
577 * Isotope Number: The isotope number targetted by the instrument.
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
578 * Precursor m/z Error: The precursor m/z matching error.
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
579 * Score: Score of the retained peptide as a combination of the algorithm scores (used to rank PSMs).
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
580 * Confidence: Confidence in percent associated to the retained PSM.
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
581 * Decoy: Indicates whether the peptide is a decoy (1: yes, 0: no).
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
582 * Validation: Indicates the validation level of the protein group.
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
583
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
584
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
585 ------
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
586
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
587 **Citation**
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
588
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
589 To cite the underlying tools (PeptideShaker and SearchGUI) please refer to the list of papers at http://compomics.github.io
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
590
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
591 If you use this tool in Galaxy, please cite Chilton J, Ira Cooke, Bjoern Gruening et al.
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
592 </help>
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
593 <expand macro="citations" />
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
594 </tool>