Mercurial > repos > galaxyp > peptideshaker

annotate peptide_shaker.xml @ 37:7f2aeb19650f 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 51e887df61a85708547a1513b9a6616bd014d073
author galaxyp
date Thu, 23 Mar 2017 18:47:12 -0400
parents bced7eb9e197
children 79e37eff006d
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
37
7f2aeb19650f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 51e887df61a85708547a1513b9a6616bd014d073
galaxyp
parents: 36
diff changeset
1 <tool id="peptide_shaker" name="Peptide Shaker" version="1.16.3">
18
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
2 <description>
20
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
iracooke
parents: 18
diff changeset
3 Perform protein identification using various search engines based on results from SearchGUI
18
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
4 </description>
20
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
iracooke
parents: 18
diff changeset
5 <macros>
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
iracooke
parents: 18
diff changeset
6 <import>macros.xml</import>
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
iracooke
parents: 18
diff changeset
7 </macros>
21
dfaea053e32f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 327a3944f2f56668d607c3d6cb08ae7d588e208c
iracooke
parents: 20
diff changeset
8 <requirements>
37
7f2aeb19650f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 51e887df61a85708547a1513b9a6616bd014d073
galaxyp
parents: 36
diff changeset
9 <requirement type="package" version="1.16.3">peptide-shaker</requirement>
21
dfaea053e32f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 327a3944f2f56668d607c3d6cb08ae7d588e208c
iracooke
parents: 20
diff changeset
10 </requirements>
20
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
iracooke
parents: 18
diff changeset
11 <expand macro="stdio" />
18
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
12 <command>
20
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
iracooke
parents: 18
diff changeset
13 <![CDATA[
18
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
14 #from datetime import datetime
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
15 #set $exp_str = "Galaxy_Experiment_%s" % datetime.now().strftime("%Y%m%d%H%M%s")
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
16 #set $samp_str = "Sample_%s" % datetime.now().strftime("%Y%m%d%H%M%s")
20
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
iracooke
parents: 18
diff changeset
17 #set $temp_stderr = "peptideshaker_stderr"
30
ad60446b1e93 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit bdb5ee12705a3494eee96d1963f16f68bbe41d5c
galaxyp
parents: 29
diff changeset
18 #set $bin_dir = "bin"
18
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
19
22
e3be595c0bf5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 5ca27ef280bee8b65fd3d0d2cd5ff280a2cebb3d
iracooke
parents: 21
diff changeset
20
18
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
21 mkdir output_reports;
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
22 cwd=`pwd`;
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
23
20
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
iracooke
parents: 18
diff changeset
24 ln -s '$searchgui_input' searchgui_input.zip &&
30
ad60446b1e93 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit bdb5ee12705a3494eee96d1963f16f68bbe41d5c
galaxyp
parents: 29
diff changeset
25 jar xvf searchgui_input.zip SEARCHGUI_IdentificationParameters.par &&
18
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
26 ######################
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
27 ## PeptideShakerCLI ##
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
28 ######################
30
ad60446b1e93 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit bdb5ee12705a3494eee96d1963f16f68bbe41d5c
galaxyp
parents: 29
diff changeset
29 (peptide-shaker eu.isas.peptideshaker.cmd.PeptideShakerCLI
ad60446b1e93 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit bdb5ee12705a3494eee96d1963f16f68bbe41d5c
galaxyp
parents: 29
diff changeset
30 --exec_dir="\$cwd/${bin_dir}"
20
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
iracooke
parents: 18
diff changeset
31 -temp_folder \$cwd/PeptideShakerCLI
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
iracooke
parents: 18
diff changeset
32 -experiment '$exp_str'
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
iracooke
parents: 18
diff changeset
33 -sample '$samp_str'
18
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
34 -replicate 1
20
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
iracooke
parents: 18
diff changeset
35 -identification_files \$cwd/searchgui_input.zip
30
ad60446b1e93 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit bdb5ee12705a3494eee96d1963f16f68bbe41d5c
galaxyp
parents: 29
diff changeset
36 -id_params \$cwd/SEARCHGUI_IdentificationParameters.par
24
815f93bb3e1b Uploaded
galaxyp
parents: 22
diff changeset
37 -out \$cwd/peptideshaker_output.cpsx
20
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
iracooke
parents: 18
diff changeset
38 -zip \$cwd/peptideshaker_output.zip
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
iracooke
parents: 18
diff changeset
39
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
iracooke
parents: 18
diff changeset
40 -threads "\${GALAXY_SLOTS:-12}"
18
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
41
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
42 ##Optional processing parameters:
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
43 #if $processing_options.processing_options_selector == "yes"
26
3ef5a7dd1a36 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6dcfe37e286523588aa2738599af8d3273290f28-dirty
galaxyp
parents: 25
diff changeset
44 -protein_fdr "${processing_options.protein_fdr}"
3ef5a7dd1a36 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6dcfe37e286523588aa2738599af8d3273290f28-dirty
galaxyp
parents: 25
diff changeset
45 -peptide_fdr "${processing_options.peptide_fdr}"
3ef5a7dd1a36 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6dcfe37e286523588aa2738599af8d3273290f28-dirty
galaxyp
parents: 25
diff changeset
46 -psm_fdr "${processing_options.psm_fdr}"
18
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
47 -ptm_score "${processing_options.ptm_score.ptm_score_selector}"
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
48 #if $processing_options.ptm_score.ptm_score_selector == 1
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
49 -score_neutral_losses "${processing_options.ptm_score.neutral_losses}"
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
50 #if str($processing_options.ptm_score.ptm_threshold) != ''
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
51 -ptm_threshold "${processing_options.ptm_score.ptm_threshold}"
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
52 #end if
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
53 #end if
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
54 -protein_fraction_mw_confidence "${processing_options.protein_fraction_mw_confidence}"
29
78fad25eff17 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 4256c7c6fde06722b66f433f5913c2e707bc930f-dirty
galaxyp
parents: 28
diff changeset
55 -ptm_alignment "${processing_options.ptm_alignment}"
18
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
56 #end if
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
57
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
58 ##Optional filtering parameters:
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
59 #if $filtering_options.filtering_options_selector == "yes":
26
3ef5a7dd1a36 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6dcfe37e286523588aa2738599af8d3273290f28-dirty
galaxyp
parents: 25
diff changeset
60 -import_peptide_length_min "${filtering_options.min_peptide_length}"
3ef5a7dd1a36 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6dcfe37e286523588aa2738599af8d3273290f28-dirty
galaxyp
parents: 25
diff changeset
61 -import_peptide_length_max "${filtering_options.max_peptide_length}"
3ef5a7dd1a36 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6dcfe37e286523588aa2738599af8d3273290f28-dirty
galaxyp
parents: 25
diff changeset
62 -import_precurosor_mz "${filtering_options.max_precursor_error}"
3ef5a7dd1a36 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6dcfe37e286523588aa2738599af8d3273290f28-dirty
galaxyp
parents: 25
diff changeset
63 -import_precurosor_mz_ppm "${filtering_options.max_precursor_error_type}"
20
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
iracooke
parents: 18
diff changeset
64 ##-max_xtandem_e "${filtering_options.max_xtandem_e}"
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
iracooke
parents: 18
diff changeset
65 ##-max_omssa_e "${filtering_options.max_omssa_e}"
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
iracooke
parents: 18
diff changeset
66 ##-max_mascot_e "${filtering_options.max_mascot_e}"
18
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
67 -exclude_unknown_ptms "${filtering_options.exclude_unknown_ptms}"
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
68 #end if
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
69
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
70 2>> $temp_stderr)
20
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
iracooke
parents: 18
diff changeset
71
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
iracooke
parents: 18
diff changeset
72 &&
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
iracooke
parents: 18
diff changeset
73
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
iracooke
parents: 18
diff changeset
74 echo "Running Reports";
18
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
75
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
76 ##################################
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
77 ## PeptideShaker Report options ##
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
78 ##################################
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
79
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
80 #if 'mzidentML' in str($outputs).split(','):
20
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
iracooke
parents: 18
diff changeset
81 echo "Generating mzIdentML";
30
ad60446b1e93 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit bdb5ee12705a3494eee96d1963f16f68bbe41d5c
galaxyp
parents: 29
diff changeset
82 (peptide-shaker eu.isas.peptideshaker.cmd.MzidCLI
ad60446b1e93 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit bdb5ee12705a3494eee96d1963f16f68bbe41d5c
galaxyp
parents: 29
diff changeset
83 --exec_dir="\$cwd/${bin_dir}"
20
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
iracooke
parents: 18
diff changeset
84 -in \$cwd/peptideshaker_output.zip
33
bce45e9e6d70 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 32
diff changeset
85 -output_file \$cwd/output.mzid
30
ad60446b1e93 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit bdb5ee12705a3494eee96d1963f16f68bbe41d5c
galaxyp
parents: 29
diff changeset
86 #if $contact_options.contact_options_selector == "yes":
ad60446b1e93 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit bdb5ee12705a3494eee96d1963f16f68bbe41d5c
galaxyp
parents: 29
diff changeset
87 -contact_first_name "$contact_options.contact_first_name"
ad60446b1e93 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit bdb5ee12705a3494eee96d1963f16f68bbe41d5c
galaxyp
parents: 29
diff changeset
88 -contact_last_name "$contact_options.contact_last_name"
ad60446b1e93 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit bdb5ee12705a3494eee96d1963f16f68bbe41d5c
galaxyp
parents: 29
diff changeset
89 -contact_email "$contact_options.contact_email"
ad60446b1e93 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit bdb5ee12705a3494eee96d1963f16f68bbe41d5c
galaxyp
parents: 29
diff changeset
90 -contact_address "$contact_options.contact_address"
ad60446b1e93 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit bdb5ee12705a3494eee96d1963f16f68bbe41d5c
galaxyp
parents: 29
diff changeset
91 #if str($contact_options.contact_url).strip() != '':
ad60446b1e93 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit bdb5ee12705a3494eee96d1963f16f68bbe41d5c
galaxyp
parents: 29
diff changeset
92 -contact_url = "$contact_options.contact_url"
ad60446b1e93 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit bdb5ee12705a3494eee96d1963f16f68bbe41d5c
galaxyp
parents: 29
diff changeset
93 #end if
ad60446b1e93 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit bdb5ee12705a3494eee96d1963f16f68bbe41d5c
galaxyp
parents: 29
diff changeset
94 -organization_name "$contact_options.organization_name"
ad60446b1e93 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit bdb5ee12705a3494eee96d1963f16f68bbe41d5c
galaxyp
parents: 29
diff changeset
95 -organization_email "$contact_options.organization_email"
ad60446b1e93 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit bdb5ee12705a3494eee96d1963f16f68bbe41d5c
galaxyp
parents: 29
diff changeset
96 -organization_address "$contact_options.organization_address"
ad60446b1e93 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit bdb5ee12705a3494eee96d1963f16f68bbe41d5c
galaxyp
parents: 29
diff changeset
97 #if str($contact_options.organization_url).strip() != '':
ad60446b1e93 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit bdb5ee12705a3494eee96d1963f16f68bbe41d5c
galaxyp
parents: 29
diff changeset
98 -organization_url = "$contact_options.organization_url"
ad60446b1e93 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit bdb5ee12705a3494eee96d1963f16f68bbe41d5c
galaxyp
parents: 29
diff changeset
99 #end if
ad60446b1e93 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit bdb5ee12705a3494eee96d1963f16f68bbe41d5c
galaxyp
parents: 29
diff changeset
100 #else:
ad60446b1e93 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit bdb5ee12705a3494eee96d1963f16f68bbe41d5c
galaxyp
parents: 29
diff changeset
101 -contact_first_name "Proteomics"
ad60446b1e93 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit bdb5ee12705a3494eee96d1963f16f68bbe41d5c
galaxyp
parents: 29
diff changeset
102 -contact_last_name "Galaxy"
ad60446b1e93 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit bdb5ee12705a3494eee96d1963f16f68bbe41d5c
galaxyp
parents: 29
diff changeset
103 -contact_email "galaxyp@umn.edu"
ad60446b1e93 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit bdb5ee12705a3494eee96d1963f16f68bbe41d5c
galaxyp
parents: 29
diff changeset
104 -contact_address "galaxyp@umn.edu"
ad60446b1e93 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit bdb5ee12705a3494eee96d1963f16f68bbe41d5c
galaxyp
parents: 29
diff changeset
105 -organization_name "University of Minnesota"
ad60446b1e93 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit bdb5ee12705a3494eee96d1963f16f68bbe41d5c
galaxyp
parents: 29
diff changeset
106 -organization_email "galaxyp@umn.edu"
ad60446b1e93 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit bdb5ee12705a3494eee96d1963f16f68bbe41d5c
galaxyp
parents: 29
diff changeset
107 -organization_address "Minneapolis, MN 55455, Vereinigte Staaten"
ad60446b1e93 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit bdb5ee12705a3494eee96d1963f16f68bbe41d5c
galaxyp
parents: 29
diff changeset
108 #end if
20
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
iracooke
parents: 18
diff changeset
109 2>> $temp_stderr)
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
iracooke
parents: 18
diff changeset
110 &&
18
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
111 #end if
20
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
iracooke
parents: 18
diff changeset
112
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
iracooke
parents: 18
diff changeset
113 ## Generate Reports if the user has selected one of the 8 additional reports
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
iracooke
parents: 18
diff changeset
114 ## 'cps', 'mzidentML' and 'zip' are not valid options for PeptideShaker
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
iracooke
parents: 18
diff changeset
115 ## and will not be passed to the command line
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
iracooke
parents: 18
diff changeset
116 #if set(["0","1","2","3","4","5","6","7"]).intersection( set( str( $outputs ).split(',') ) ):
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
iracooke
parents: 18
diff changeset
117
30
ad60446b1e93 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit bdb5ee12705a3494eee96d1963f16f68bbe41d5c
galaxyp
parents: 29
diff changeset
118 (peptide-shaker eu.isas.peptideshaker.cmd.ReportCLI
ad60446b1e93 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit bdb5ee12705a3494eee96d1963f16f68bbe41d5c
galaxyp
parents: 29
diff changeset
119 --exec_dir="\$cwd/${bin_dir}"
20
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
iracooke
parents: 18
diff changeset
120 -temp_folder \$cwd/ReportCLI
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
iracooke
parents: 18
diff changeset
121 -in \$cwd/peptideshaker_output.zip
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
iracooke
parents: 18
diff changeset
122 -out_reports \$cwd/output_reports
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
iracooke
parents: 18
diff changeset
123 #set $cleaned_list = str($outputs).split(',')
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
iracooke
parents: 18
diff changeset
124 #if 'cps' in $cleaned_list:
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
iracooke
parents: 18
diff changeset
125 #silent $cleaned_list.remove('cps')
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
iracooke
parents: 18
diff changeset
126 #end if
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
iracooke
parents: 18
diff changeset
127 #if 'mzidentML' in $cleaned_list:
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
iracooke
parents: 18
diff changeset
128 #silent $cleaned_list.remove('mzidentML')
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
iracooke
parents: 18
diff changeset
129 #end if
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
iracooke
parents: 18
diff changeset
130 #if 'zip' in $cleaned_list:
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
iracooke
parents: 18
diff changeset
131 #silent $cleaned_list.remove('zip')
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
iracooke
parents: 18
diff changeset
132 #end if
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
iracooke
parents: 18
diff changeset
133 ## Only numbers are left over. These corresponds to different reports.
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
iracooke
parents: 18
diff changeset
134 -reports #echo ','.join($cleaned_list)#
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
iracooke
parents: 18
diff changeset
135
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
iracooke
parents: 18
diff changeset
136 2>> $temp_stderr)
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
iracooke
parents: 18
diff changeset
137 &&
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
iracooke
parents: 18
diff changeset
138 #end if
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
iracooke
parents: 18
diff changeset
139
30
ad60446b1e93 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit bdb5ee12705a3494eee96d1963f16f68bbe41d5c
galaxyp
parents: 29
diff changeset
140 ## # ls -l \$cwd/output_reports/* ;
20
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
iracooke
parents: 18
diff changeset
141
18
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
142 #if '0' in str($outputs).split(','):
20
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
iracooke
parents: 18
diff changeset
143 find \$cwd/output_reports -name '*Certificate_of_Analysis*' -exec bash -c 'mv "$0" "certificate.txt"' {} \;
18
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
144 ;
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
145 #end if
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
146 #if '1' in str($outputs).split(','):
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
147 find \$cwd/output_reports -name '*Hierarchical*' -exec bash -c 'mv "$0" "hierarchical.txt"' {} \;
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
148 ;
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
149 #end if
20
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
iracooke
parents: 18
diff changeset
150 #if '2' in str($outputs).split(','):
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
iracooke
parents: 18
diff changeset
151 find \$cwd/output_reports -name '*PSM_Phosphorylation_Report*' -exec bash -c 'mv "$0" "psm_phospho.txt"' {} \;
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
iracooke
parents: 18
diff changeset
152 ;
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
iracooke
parents: 18
diff changeset
153 #end if
30
ad60446b1e93 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit bdb5ee12705a3494eee96d1963f16f68bbe41d5c
galaxyp
parents: 29
diff changeset
154 #if '8' in str($outputs).split(','):
ad60446b1e93 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit bdb5ee12705a3494eee96d1963f16f68bbe41d5c
galaxyp
parents: 29
diff changeset
155 find \$cwd/output_reports -name '*Extended_PSM_Report*' -exec bash -c 'mv "$0" "psmx.txt"' {} \;
ad60446b1e93 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit bdb5ee12705a3494eee96d1963f16f68bbe41d5c
galaxyp
parents: 29
diff changeset
156 ;
ad60446b1e93 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit bdb5ee12705a3494eee96d1963f16f68bbe41d5c
galaxyp
parents: 29
diff changeset
157 #end if
20
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
iracooke
parents: 18
diff changeset
158 #if '3' in str($outputs).split(','):
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
iracooke
parents: 18
diff changeset
159 find \$cwd/output_reports -name '*PSM_Report*' -exec bash -c 'mv "$0" "psm.txt"' {} \;
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
iracooke
parents: 18
diff changeset
160 ;
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
iracooke
parents: 18
diff changeset
161 #end if
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
iracooke
parents: 18
diff changeset
162 #if '4' in str($outputs).split(','):
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
iracooke
parents: 18
diff changeset
163 find \$cwd/output_reports -name '*Peptide_Phosphorylation_Report*' -exec bash -c 'mv "$0" "peptides_phospho.txt"' {} \;
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
iracooke
parents: 18
diff changeset
164 ;
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
iracooke
parents: 18
diff changeset
165 #end if
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
iracooke
parents: 18
diff changeset
166 #if '5' in str($outputs).split(','):
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
iracooke
parents: 18
diff changeset
167 find \$cwd/output_reports -name '*Peptide_Report*' -exec bash -c 'mv "$0" "peptides.txt"' {} \;
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
iracooke
parents: 18
diff changeset
168 ;
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
iracooke
parents: 18
diff changeset
169 #end if
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
iracooke
parents: 18
diff changeset
170 #if '6' in str($outputs).split(','):
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
iracooke
parents: 18
diff changeset
171 find \$cwd/output_reports -name '*Protein_Phosphorylation_Report*' -exec bash -c 'mv "$0" "proteins_phospho.txt"' {} \;
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
iracooke
parents: 18
diff changeset
172 ;
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
iracooke
parents: 18
diff changeset
173 #end if
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
iracooke
parents: 18
diff changeset
174 #if '7' in str($outputs).split(','):
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
iracooke
parents: 18
diff changeset
175 find \$cwd/output_reports -name '*Protein_Report*' -exec bash -c 'mv "$0" "proteins.txt"' {} \;
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
iracooke
parents: 18
diff changeset
176 ;
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
iracooke
parents: 18
diff changeset
177 #end if
18
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
178
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
179 exit_code_for_galaxy=\$?;
20
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
iracooke
parents: 18
diff changeset
180 cat $temp_stderr 2>&1;
18
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
181 (exit \$exit_code_for_galaxy)
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
182
20
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
iracooke
parents: 18
diff changeset
183 ]]>
18
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
184 </command>
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
185 <inputs>
21
dfaea053e32f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 327a3944f2f56668d607c3d6cb08ae7d588e208c
iracooke
parents: 20
diff changeset
186 <param name="searchgui_input" format="searchgui_archive" type="data" label="Compressed SearchGUI results"
24
815f93bb3e1b Uploaded
galaxyp
parents: 22
diff changeset
187 help="SearchGUI Results from History">
815f93bb3e1b Uploaded
galaxyp
parents: 22
diff changeset
188 <options options_filter_attribute="metadata.searchgui_major_version" >
815f93bb3e1b Uploaded
galaxyp
parents: 22
diff changeset
189 <filter type="add_value" value="@SEARCHGUI_MAJOR_VERSION@" />
815f93bb3e1b Uploaded
galaxyp
parents: 22
diff changeset
190 </options>
815f93bb3e1b Uploaded
galaxyp
parents: 22
diff changeset
191 </param>
18
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
192 <conditional name="processing_options">
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
193 <param name="processing_options_selector" type="select" label="Specify Advanced PeptideShaker Processing Options">
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
194 <option value="no" selected="True">Default Processing Options</option>
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
195 <option value="yes">Advanced Processing Options</option>
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
196 </param>
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
197 <when value="no" />
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
198 <when value="yes">
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
199 <param name="protein_fdr" label="FDR at the protein level" help="In percent (default 1% FDR: '1')" value="1" type="float" />
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
200 <param name="peptide_fdr" label="FDR at the peptide level" help="In percent (default 1% FDR: '1')" value="1" type="float" />
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
201 <param name="psm_fdr" label="FDR at the PSM level" help="In percent (default 1% FDR: '1')" value="1" type="float" />
20
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
iracooke
parents: 18
diff changeset
202 <param name="protein_fraction_mw_confidence" value="95.0" type="float" label="Minimum confidence required for a protein in the fraction MW plot"
18
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
203 help="default 95%: '95.0'" />
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
204 <conditional name="ptm_score">
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
205 <param name="ptm_score_selector" type="select" label="The PTM probabilistic score to use for PTM localization">
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
206 <option value="0" selected="True">A-score</option>
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
207 <option value="1">PhosphoRS</option>
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
208 </param>
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
209 <when value="0" />
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
210 <when value="1">
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
211 <param name="score_neutral_losses" label="Include Neutral Losses in A Score" type="boolean" truevalue="1" falsevalue="0" />
25
0986f68fb410 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit bdb474693831a3375db79755e88641ad32b3b4e6-dirty
galaxyp
parents: 24
diff changeset
212 <param name="ptm_threshold" label="The threshold to use for the PTM scores" optional="true" value="" type="float"
18
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
213 help="Automatic mode will be used if not set" />
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
214 </when>
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
215 </conditional>
29
78fad25eff17 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 4256c7c6fde06722b66f433f5913c2e707bc930f-dirty
galaxyp
parents: 28
diff changeset
216 <param name="ptm_alignment" label="Align peptide ambiguously localized PTMs on confident sites" type="boolean" truevalue="1" falsevalue="0" checked="true"/>
18
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
217 <!-- SKIPPING -protein_fraction_mw_confidence ${processing_options.protein_fraction_mw_confidence} -->
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
218 </when>
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
219 </conditional>
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
220 <conditional name="filtering_options">
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
221 <param name="filtering_options_selector" type="select" label="Specify Advanced Filtering Options"
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
222 help="Filter based on peptide lengths, precursor mass error, E value errors from X! Tandem and OMSSA, and include/exclude unknown PTM’s">
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
223 <option value="no" selected="True">Default Filtering Options</option>
20
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
iracooke
parents: 18
diff changeset
224 <option value="yes">Advanced Filtering Options</option>
18
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
225 </param>
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
226 <when value="no" />
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
227 <when value="yes">
20
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
iracooke
parents: 18
diff changeset
228 <param name="min_peptide_length" type="integer" label="Minimum Peptide Length" value="6" />
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
iracooke
parents: 18
diff changeset
229 <param name="max_peptide_length" type="integer" label="Maximum Peptide Length" value="30" />
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
iracooke
parents: 18
diff changeset
230 <param name="max_precursor_error" type="float" label="Maximum Precursor Error" value="10"
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
iracooke
parents: 18
diff changeset
231 help="Next option specifies units (Da or ppm)" />
18
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
232 <param name="max_precursor_error_type" label="Maximum Precursor Error Type" type="select">
26
3ef5a7dd1a36 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6dcfe37e286523588aa2738599af8d3273290f28-dirty
galaxyp
parents: 25
diff changeset
233 <option value="1">ppm</option>
3ef5a7dd1a36 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6dcfe37e286523588aa2738599af8d3273290f28-dirty
galaxyp
parents: 25
diff changeset
234 <option value="0">Daltons</option>
18
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
235 </param>
20
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
iracooke
parents: 18
diff changeset
236 <!--param name="max_xtandem_e" label="Maximum X! Tandem e-value" value="100" type="float" help="" /-->
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
iracooke
parents: 18
diff changeset
237 <!--param name="max_omssa_e" label="Maximum OMSSA e-value" value="100" type="float" help="" /-->
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
iracooke
parents: 18
diff changeset
238 <!--param name="max_mascot_e" label="Maximum Mascot e-value filter" value="100" type="float" help="" /-->
18
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
239 <param name="exclude_unknown_ptms" label="Exclude Unknown PTMs" type="boolean" truevalue="1" falsevalue="0" checked="true" />
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
240 </when>
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
241 </conditional>
30
ad60446b1e93 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit bdb5ee12705a3494eee96d1963f16f68bbe41d5c
galaxyp
parents: 29
diff changeset
242 <conditional name="contact_options">
ad60446b1e93 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit bdb5ee12705a3494eee96d1963f16f68bbe41d5c
galaxyp
parents: 29
diff changeset
243 <param name="contact_options_selector" type="select" label="Specify Contact Information for mzIdendML"
ad60446b1e93 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit bdb5ee12705a3494eee96d1963f16f68bbe41d5c
galaxyp
parents: 29
diff changeset
244 help="Create a Galaxy workflow to save these values">
ad60446b1e93 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit bdb5ee12705a3494eee96d1963f16f68bbe41d5c
galaxyp
parents: 29
diff changeset
245 <option value="no" selected="True">GalaxyP Project contact (Not suitable for PRIDE submission)</option>
ad60446b1e93 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit bdb5ee12705a3494eee96d1963f16f68bbe41d5c
galaxyp
parents: 29
diff changeset
246 <option value="yes">Specify Contact Information</option>
ad60446b1e93 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit bdb5ee12705a3494eee96d1963f16f68bbe41d5c
galaxyp
parents: 29
diff changeset
247 </param>
ad60446b1e93 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit bdb5ee12705a3494eee96d1963f16f68bbe41d5c
galaxyp
parents: 29
diff changeset
248 <when value="no" />
ad60446b1e93 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit bdb5ee12705a3494eee96d1963f16f68bbe41d5c
galaxyp
parents: 29
diff changeset
249 <when value="yes">
ad60446b1e93 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit bdb5ee12705a3494eee96d1963f16f68bbe41d5c
galaxyp
parents: 29
diff changeset
250 <param name="contact_first_name" type="text" value="" label="Contact first name.">
ad60446b1e93 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit bdb5ee12705a3494eee96d1963f16f68bbe41d5c
galaxyp
parents: 29
diff changeset
251 <validator type="regex" message="">\S+.*</validator>
ad60446b1e93 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit bdb5ee12705a3494eee96d1963f16f68bbe41d5c
galaxyp
parents: 29
diff changeset
252 </param>
ad60446b1e93 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit bdb5ee12705a3494eee96d1963f16f68bbe41d5c
galaxyp
parents: 29
diff changeset
253 <param name="contact_last_name" type="text" value="" label="Contact last name.">
ad60446b1e93 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit bdb5ee12705a3494eee96d1963f16f68bbe41d5c
galaxyp
parents: 29
diff changeset
254 <validator type="regex" message="">\S+.*</validator>
ad60446b1e93 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit bdb5ee12705a3494eee96d1963f16f68bbe41d5c
galaxyp
parents: 29
diff changeset
255 </param>
ad60446b1e93 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit bdb5ee12705a3494eee96d1963f16f68bbe41d5c
galaxyp
parents: 29
diff changeset
256 <param name="contact_email" type="text" value="" label="Contact e-mail.">
ad60446b1e93 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit bdb5ee12705a3494eee96d1963f16f68bbe41d5c
galaxyp
parents: 29
diff changeset
257 <validator type="regex" message="">\S+@\S+</validator>
ad60446b1e93 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit bdb5ee12705a3494eee96d1963f16f68bbe41d5c
galaxyp
parents: 29
diff changeset
258 </param>
ad60446b1e93 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit bdb5ee12705a3494eee96d1963f16f68bbe41d5c
galaxyp
parents: 29
diff changeset
259 <param name="contact_address" type="text" value="" label="Contact address.">
ad60446b1e93 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit bdb5ee12705a3494eee96d1963f16f68bbe41d5c
galaxyp
parents: 29
diff changeset
260 <validator type="regex" message="">\S+.*</validator>
ad60446b1e93 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit bdb5ee12705a3494eee96d1963f16f68bbe41d5c
galaxyp
parents: 29
diff changeset
261 </param>
ad60446b1e93 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit bdb5ee12705a3494eee96d1963f16f68bbe41d5c
galaxyp
parents: 29
diff changeset
262 <param name="contact_url" type="text" value="" optional="true" label="Contact URL.">
ad60446b1e93 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit bdb5ee12705a3494eee96d1963f16f68bbe41d5c
galaxyp
parents: 29
diff changeset
263 </param>
ad60446b1e93 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit bdb5ee12705a3494eee96d1963f16f68bbe41d5c
galaxyp
parents: 29
diff changeset
264 <param name="organization_name" type="text" value="" label="Organization name.">
ad60446b1e93 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit bdb5ee12705a3494eee96d1963f16f68bbe41d5c
galaxyp
parents: 29
diff changeset
265 <validator type="regex" message="">\S+.*</validator>
ad60446b1e93 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit bdb5ee12705a3494eee96d1963f16f68bbe41d5c
galaxyp
parents: 29
diff changeset
266 </param>
ad60446b1e93 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit bdb5ee12705a3494eee96d1963f16f68bbe41d5c
galaxyp
parents: 29
diff changeset
267 <param name="organization_email" type="text" value="" label="Organization e-mail.">
ad60446b1e93 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit bdb5ee12705a3494eee96d1963f16f68bbe41d5c
galaxyp
parents: 29
diff changeset
268 <validator type="regex" message="">\S+@\S+</validator>
ad60446b1e93 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit bdb5ee12705a3494eee96d1963f16f68bbe41d5c
galaxyp
parents: 29
diff changeset
269 </param>
ad60446b1e93 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit bdb5ee12705a3494eee96d1963f16f68bbe41d5c
galaxyp
parents: 29
diff changeset
270 <param name="organization_address" type="text" value="" label="Organization address.">
ad60446b1e93 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit bdb5ee12705a3494eee96d1963f16f68bbe41d5c
galaxyp
parents: 29
diff changeset
271 <validator type="regex" message="">\S+.*</validator>
ad60446b1e93 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit bdb5ee12705a3494eee96d1963f16f68bbe41d5c
galaxyp
parents: 29
diff changeset
272 </param>
ad60446b1e93 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit bdb5ee12705a3494eee96d1963f16f68bbe41d5c
galaxyp
parents: 29
diff changeset
273 <param name="organization_url" type="text" value="" optional="true" label="Organization URL.">
ad60446b1e93 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit bdb5ee12705a3494eee96d1963f16f68bbe41d5c
galaxyp
parents: 29
diff changeset
274 </param>
ad60446b1e93 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit bdb5ee12705a3494eee96d1963f16f68bbe41d5c
galaxyp
parents: 29
diff changeset
275 </when>
ad60446b1e93 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit bdb5ee12705a3494eee96d1963f16f68bbe41d5c
galaxyp
parents: 29
diff changeset
276 </conditional>
ad60446b1e93 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit bdb5ee12705a3494eee96d1963f16f68bbe41d5c
galaxyp
parents: 29
diff changeset
277
ad60446b1e93 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit bdb5ee12705a3494eee96d1963f16f68bbe41d5c
galaxyp
parents: 29
diff changeset
278 <param name="include_sequences" type="boolean" truevalue="1" falsevalue="0" checked="false" label="Include the protein sequences in mzIdentML" />
18
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
279 <param name="outputs" type="select" display="checkboxes" multiple="True" label="Output options">
20
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
iracooke
parents: 18
diff changeset
280 <option value="zip">Zip File for import to Desktop App</option>
18
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
281 <option value="mzidentML" selected="True">mzidentML File</option>
30
ad60446b1e93 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit bdb5ee12705a3494eee96d1963f16f68bbe41d5c
galaxyp
parents: 29
diff changeset
282 <option value="3">PSM Report</option>
ad60446b1e93 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit bdb5ee12705a3494eee96d1963f16f68bbe41d5c
galaxyp
parents: 29
diff changeset
283 <option value="8">Extended PSM Report</option>
20
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
iracooke
parents: 18
diff changeset
284 <option value="2">PSM Phosphorylation Report</option>
30
ad60446b1e93 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit bdb5ee12705a3494eee96d1963f16f68bbe41d5c
galaxyp
parents: 29
diff changeset
285 <option value="5">Peptide Report</option>
ad60446b1e93 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit bdb5ee12705a3494eee96d1963f16f68bbe41d5c
galaxyp
parents: 29
diff changeset
286 <option value="4">Peptide Phosphorylation Report</option>
ad60446b1e93 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit bdb5ee12705a3494eee96d1963f16f68bbe41d5c
galaxyp
parents: 29
diff changeset
287 <option value="7">Protein Report</option>
ad60446b1e93 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit bdb5ee12705a3494eee96d1963f16f68bbe41d5c
galaxyp
parents: 29
diff changeset
288 <option value="6">Protein Phosphorylation Report</option>
18
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
289 <option value="0">Certificate of Analysis</option>
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
290 <option value="1">Hierarchical Report</option>
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
291 <option value="cps">CPS file</option>
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
292 <validator type="no_options" message="Please select at least one output file" />
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
293 </param>
20
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
iracooke
parents: 18
diff changeset
294
18
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
295 </inputs>
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
296 <outputs>
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
297 <data format="mzid" name="mzidentML" from_work_dir="output.mzid" label="${tool.name} on ${on_string}: mzidentML file">
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
298 <filter>'mzidentML' in outputs</filter>
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
299 </data>
20
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
iracooke
parents: 18
diff changeset
300 <data format="peptideshaker_archive" name="output_cps" from_work_dir="peptideshaker_output.cps" label="${tool.name} on ${on_string}: CPS file">
18
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
301 <filter>'cps' in outputs</filter>
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
302 </data>
20
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
iracooke
parents: 18
diff changeset
303 <data format="zip" name="output_zip" from_work_dir="peptideshaker_output.zip" label="${tool.name} on ${on_string}: Archive">
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
iracooke
parents: 18
diff changeset
304 <filter>'zip' in outputs</filter>
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
iracooke
parents: 18
diff changeset
305 </data>
18
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
306 <data format="txt" name="output_certificate" from_work_dir="certificate.txt" label="${tool.name} on ${on_string}: Parameters">
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
307 <filter>'0' in outputs</filter>
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
308 </data>
20
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
iracooke
parents: 18
diff changeset
309 <data format="tabular" name="output_hierarchical" from_work_dir="hierarchical.txt" label="${tool.name} on ${on_string}: Hierarchical Report">
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
iracooke
parents: 18
diff changeset
310 <filter>'1' in outputs</filter>
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
iracooke
parents: 18
diff changeset
311 </data>
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
iracooke
parents: 18
diff changeset
312 <data format="tabular" name="output_psm_phosphorylation" from_work_dir="psm_phospho.txt" label="${tool.name} on ${on_string}: PSM Phosphorylation Report">
18
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
313 <filter>'2' in outputs</filter>
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
314 </data>
20
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
iracooke
parents: 18
diff changeset
315 <data format="tabular" name="output_psm" from_work_dir="psm.txt" label="${tool.name} on ${on_string}: PSM Report">
18
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
316 <filter>'3' in outputs</filter>
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
317 </data>
30
ad60446b1e93 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit bdb5ee12705a3494eee96d1963f16f68bbe41d5c
galaxyp
parents: 29
diff changeset
318 <data format="tabular" name="output_extended_psm" from_work_dir="psmx.txt" label="${tool.name} on ${on_string}: Extended PSM Report">
ad60446b1e93 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit bdb5ee12705a3494eee96d1963f16f68bbe41d5c
galaxyp
parents: 29
diff changeset
319 <filter>'8' in outputs</filter>
ad60446b1e93 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit bdb5ee12705a3494eee96d1963f16f68bbe41d5c
galaxyp
parents: 29
diff changeset
320 </data>
20
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
iracooke
parents: 18
diff changeset
321 <data format="tabular" name="output_peptides_phosphorylation" from_work_dir="peptides_phospho.txt" label="${tool.name} on ${on_string}: Peptide Phosphorylation Report">
18
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
322 <filter>'4' in outputs</filter>
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
323 </data>
20
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
iracooke
parents: 18
diff changeset
324 <data format="tabular" name="output_peptides" from_work_dir="peptides.txt" label="${tool.name} on ${on_string}: Peptide Report">
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
iracooke
parents: 18
diff changeset
325 <filter>'5' in outputs</filter>
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
iracooke
parents: 18
diff changeset
326 </data>
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
iracooke
parents: 18
diff changeset
327 <data format="tabular" name="output_proteins_phosphorylation" from_work_dir="proteins_phospho.txt" label="${tool.name} on ${on_string}: Protein Phosphorylation Report">
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
iracooke
parents: 18
diff changeset
328 <filter>'6' in outputs</filter>
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
iracooke
parents: 18
diff changeset
329 </data>
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
iracooke
parents: 18
diff changeset
330 <data format="tabular" name="output_proteins" from_work_dir="proteins.txt" label="${tool.name} on ${on_string}: Protein Report">
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
iracooke
parents: 18
diff changeset
331 <filter>'7' in outputs</filter>
18
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
332 </data>
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
333 </outputs>
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
334 <tests>
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
335 <test>
21
dfaea053e32f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 327a3944f2f56668d607c3d6cb08ae7d588e208c
iracooke
parents: 20
diff changeset
336 <param name="searchgui_input" value="tiny_searchgui_result1.zip" ftype="searchgui_archive"/>
18
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
337 <param name="processing_options_selector" value="no"/>
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
338 <param name="filtering_options_selector" value="no"/>
30
ad60446b1e93 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit bdb5ee12705a3494eee96d1963f16f68bbe41d5c
galaxyp
parents: 29
diff changeset
339 <param name="outputs" value="zip,3"/>
33
bce45e9e6d70 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 32
diff changeset
340 <output name="output_zip" file="peptide_shaker_result1.zip" ftype="zip" compare="sim_size" delta="3000" />
32
ff592231f118 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 047efcfa1e9f45648e6e81d3776a1a93e2cfe46d
galaxyp
parents: 30
diff changeset
341 <output name="output_psm">
ff592231f118 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 047efcfa1e9f45648e6e81d3776a1a93e2cfe46d
galaxyp
parents: 30
diff changeset
342 <assert_contents>
ff592231f118 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 047efcfa1e9f45648e6e81d3776a1a93e2cfe46d
galaxyp
parents: 30
diff changeset
343 <has_text text="cds.comp41779_c0_seq1" />
ff592231f118 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 047efcfa1e9f45648e6e81d3776a1a93e2cfe46d
galaxyp
parents: 30
diff changeset
344 </assert_contents>
ff592231f118 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 047efcfa1e9f45648e6e81d3776a1a93e2cfe46d
galaxyp
parents: 30
diff changeset
345 </output>
20
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
iracooke
parents: 18
diff changeset
346 </test>
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
iracooke
parents: 18
diff changeset
347 <test>
21
dfaea053e32f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 327a3944f2f56668d607c3d6cb08ae7d588e208c
iracooke
parents: 20
diff changeset
348 <param name="searchgui_input" value="tiny_searchgui_result1.zip" ftype="searchgui_archive"/>
20
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
iracooke
parents: 18
diff changeset
349 <param name="processing_options_selector" value="no"/>
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
iracooke
parents: 18
diff changeset
350 <param name="filtering_options_selector" value="yes"/>
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
iracooke
parents: 18
diff changeset
351 <param name="min_peptide_length" value="1"/>
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
iracooke
parents: 18
diff changeset
352 <param name="outputs" value="0,1,2,3,4,5,6,7"/>
32
ff592231f118 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 047efcfa1e9f45648e6e81d3776a1a93e2cfe46d
galaxyp
parents: 30
diff changeset
353 <output name="output_certificate">
ff592231f118 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 047efcfa1e9f45648e6e81d3776a1a93e2cfe46d
galaxyp
parents: 30
diff changeset
354 <assert_contents>
ff592231f118 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 047efcfa1e9f45648e6e81d3776a1a93e2cfe46d
galaxyp
parents: 30
diff changeset
355 <has_text text="Tolerance: 100" />
ff592231f118 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 047efcfa1e9f45648e6e81d3776a1a93e2cfe46d
galaxyp
parents: 30
diff changeset
356 <has_text text="Carbamidomethylation of C" />
ff592231f118 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 047efcfa1e9f45648e6e81d3776a1a93e2cfe46d
galaxyp
parents: 30
diff changeset
357 </assert_contents>
ff592231f118 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 047efcfa1e9f45648e6e81d3776a1a93e2cfe46d
galaxyp
parents: 30
diff changeset
358 </output>
ff592231f118 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 047efcfa1e9f45648e6e81d3776a1a93e2cfe46d
galaxyp
parents: 30
diff changeset
359 <output name="output_hierarchical">
ff592231f118 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 047efcfa1e9f45648e6e81d3776a1a93e2cfe46d
galaxyp
parents: 30
diff changeset
360 <assert_contents>
33
bce45e9e6d70 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 32
diff changeset
361 <has_text_matching expression="1.1\tcds.comp" />
32
ff592231f118 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 047efcfa1e9f45648e6e81d3776a1a93e2cfe46d
galaxyp
parents: 30
diff changeset
362 </assert_contents>
ff592231f118 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 047efcfa1e9f45648e6e81d3776a1a93e2cfe46d
galaxyp
parents: 30
diff changeset
363 </output>
ff592231f118 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 047efcfa1e9f45648e6e81d3776a1a93e2cfe46d
galaxyp
parents: 30
diff changeset
364 <output name="output_psm">
ff592231f118 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 047efcfa1e9f45648e6e81d3776a1a93e2cfe46d
galaxyp
parents: 30
diff changeset
365 <assert_contents>
ff592231f118 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 047efcfa1e9f45648e6e81d3776a1a93e2cfe46d
galaxyp
parents: 30
diff changeset
366 <not_has_text text="Phosphosite" />
ff592231f118 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 047efcfa1e9f45648e6e81d3776a1a93e2cfe46d
galaxyp
parents: 30
diff changeset
367 <has_text text="cds.comp41779_c0_seq1" />
ff592231f118 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 047efcfa1e9f45648e6e81d3776a1a93e2cfe46d
galaxyp
parents: 30
diff changeset
368 </assert_contents>
ff592231f118 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 047efcfa1e9f45648e6e81d3776a1a93e2cfe46d
galaxyp
parents: 30
diff changeset
369 </output>
ff592231f118 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 047efcfa1e9f45648e6e81d3776a1a93e2cfe46d
galaxyp
parents: 30
diff changeset
370 <output name="output_psm_phosphorylation">
ff592231f118 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 047efcfa1e9f45648e6e81d3776a1a93e2cfe46d
galaxyp
parents: 30
diff changeset
371 <assert_contents>
ff592231f118 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 047efcfa1e9f45648e6e81d3776a1a93e2cfe46d
galaxyp
parents: 30
diff changeset
372 <has_text text="Phosphosite" />
ff592231f118 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 047efcfa1e9f45648e6e81d3776a1a93e2cfe46d
galaxyp
parents: 30
diff changeset
373 <has_text text="cds.comp41779_c0_seq1" />
ff592231f118 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 047efcfa1e9f45648e6e81d3776a1a93e2cfe46d
galaxyp
parents: 30
diff changeset
374 </assert_contents>
ff592231f118 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 047efcfa1e9f45648e6e81d3776a1a93e2cfe46d
galaxyp
parents: 30
diff changeset
375 </output>
ff592231f118 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 047efcfa1e9f45648e6e81d3776a1a93e2cfe46d
galaxyp
parents: 30
diff changeset
376 <output name="output_peptides">
ff592231f118 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 047efcfa1e9f45648e6e81d3776a1a93e2cfe46d
galaxyp
parents: 30
diff changeset
377 <assert_contents>
ff592231f118 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 047efcfa1e9f45648e6e81d3776a1a93e2cfe46d
galaxyp
parents: 30
diff changeset
378 <has_text text="Modification" />
ff592231f118 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 047efcfa1e9f45648e6e81d3776a1a93e2cfe46d
galaxyp
parents: 30
diff changeset
379 <has_text text="cds.comp41779_c0_seq1" />
ff592231f118 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 047efcfa1e9f45648e6e81d3776a1a93e2cfe46d
galaxyp
parents: 30
diff changeset
380 </assert_contents>
ff592231f118 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 047efcfa1e9f45648e6e81d3776a1a93e2cfe46d
galaxyp
parents: 30
diff changeset
381 </output>
ff592231f118 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 047efcfa1e9f45648e6e81d3776a1a93e2cfe46d
galaxyp
parents: 30
diff changeset
382 <output name="output_peptides_phosphorylation">
ff592231f118 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 047efcfa1e9f45648e6e81d3776a1a93e2cfe46d
galaxyp
parents: 30
diff changeset
383 <assert_contents>
ff592231f118 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 047efcfa1e9f45648e6e81d3776a1a93e2cfe46d
galaxyp
parents: 30
diff changeset
384 <has_text text="Phosphosite" />
ff592231f118 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 047efcfa1e9f45648e6e81d3776a1a93e2cfe46d
galaxyp
parents: 30
diff changeset
385 <has_text text="cds.comp41779_c0_seq1" />
ff592231f118 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 047efcfa1e9f45648e6e81d3776a1a93e2cfe46d
galaxyp
parents: 30
diff changeset
386 </assert_contents>
ff592231f118 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 047efcfa1e9f45648e6e81d3776a1a93e2cfe46d
galaxyp
parents: 30
diff changeset
387 </output>
ff592231f118 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 047efcfa1e9f45648e6e81d3776a1a93e2cfe46d
galaxyp
parents: 30
diff changeset
388 <output name="output_proteins">
ff592231f118 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 047efcfa1e9f45648e6e81d3776a1a93e2cfe46d
galaxyp
parents: 30
diff changeset
389 <assert_contents>
ff592231f118 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 047efcfa1e9f45648e6e81d3776a1a93e2cfe46d
galaxyp
parents: 30
diff changeset
390 <has_text text="Modification" />
ff592231f118 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 047efcfa1e9f45648e6e81d3776a1a93e2cfe46d
galaxyp
parents: 30
diff changeset
391 <has_text text="cds.comp41779_c0_seq1" />
ff592231f118 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 047efcfa1e9f45648e6e81d3776a1a93e2cfe46d
galaxyp
parents: 30
diff changeset
392 </assert_contents>
ff592231f118 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 047efcfa1e9f45648e6e81d3776a1a93e2cfe46d
galaxyp
parents: 30
diff changeset
393 </output>
ff592231f118 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 047efcfa1e9f45648e6e81d3776a1a93e2cfe46d
galaxyp
parents: 30
diff changeset
394 <output name="output_proteins_phosphorylation">
ff592231f118 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 047efcfa1e9f45648e6e81d3776a1a93e2cfe46d
galaxyp
parents: 30
diff changeset
395 <assert_contents>
ff592231f118 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 047efcfa1e9f45648e6e81d3776a1a93e2cfe46d
galaxyp
parents: 30
diff changeset
396 <has_text text="Phosphosite" />
ff592231f118 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 047efcfa1e9f45648e6e81d3776a1a93e2cfe46d
galaxyp
parents: 30
diff changeset
397 <has_text text="cds.comp41779_c0_seq1" />
ff592231f118 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 047efcfa1e9f45648e6e81d3776a1a93e2cfe46d
galaxyp
parents: 30
diff changeset
398 </assert_contents>
ff592231f118 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 047efcfa1e9f45648e6e81d3776a1a93e2cfe46d
galaxyp
parents: 30
diff changeset
399 </output>
20
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
iracooke
parents: 18
diff changeset
400 </test>
18
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
401 </tests>
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
402 <help>
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
403 **What it does**
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
404
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
405 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.
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
406
30
ad60446b1e93 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit bdb5ee12705a3494eee96d1963f16f68bbe41d5c
galaxyp
parents: 29
diff changeset
407 http://compomics.github.io/projects/peptide-shaker.html
ad60446b1e93 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit bdb5ee12705a3494eee96d1963f16f68bbe41d5c
galaxyp
parents: 29
diff changeset
408 http://compomics.github.io/projects/searchgui.html
18
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
409
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
410 ----
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
411
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
412 Reports
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
413 =======
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
414
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
415
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
416 PSM Report
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
417 ----------
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
418
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
419 * Protein(s): Protein(s) to which the peptide can be attached
20
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
iracooke
parents: 18
diff changeset
420 * Sequence: Sequence of the peptide
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
iracooke
parents: 18
diff changeset
421 * Variable Modifications: The variable modifications
18
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
422 * D-score: D-score for variable PTM localization
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
423 * probabilistic PTM score: The probabilistic score (e.g. A-score or PhosphoRS) used for variable PTM localization.
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
424 * Localization Confidence: The confidence in variable PTM localization.
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
425 * Fixed Modifications: The fixed modifications.
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
426 * Spectrum File: The spectrum file.
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
427 * Spectrum Title: The title of the spectrum.
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
428 * Spectrum Scan Number: The spectrum scan number.
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
429 * RT: Retention time
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
430 * m/z: Measured m/z
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
431 * Measured Charge: The charge as given in the spectrum file.
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
432 * Identification Charge: The charge as inferred by the search engine.
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
433 * Theoretical Mass: The theoretical mass of the peptide.
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
434 * Isotope Number: The isotope number targetted by the instrument.
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
435 * Precursor m/z Error: The precursor m/z matching error.
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
436 * Score: Score of the retained peptide as a combination of the algorithm scores (used to rank PSMs).
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
437 * Confidence: Confidence in percent associated to the retained PSM.
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
438 * Decoy: Indicates whether the peptide is a decoy (1: yes, 0: no).
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
439 * Validation: Indicates the validation level of the protein group.
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
440
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
441
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
442 Protein Report
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
443 --------------
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
444
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
445 * Main Accession: Main accession of the protein group.
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
446 * Description: Description of the protein designed by the main accession.
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
447 * Gene Name: The gene names of the Ensembl gene ID associated to the main accession.
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
448 * Chromosome: The chromosome of the Ensembl gene ID associated to the main accession.
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
449 * PI: Protein Inference status of the protein group.
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
450 * Secondary Accessions: Other accessions in the protein group (alphabetical order).
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
451 * Protein Group: The complete protein group (alphabetical order).
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
452 * #Peptides: Total number of peptides.
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
453 * #Validated Peptides: Number of validated peptides.
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
454 * #Unique: Total number of peptides unique to this protein group.
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
455 * #PSMs: Number of PSMs
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
456 * #Validated PSMs: Number of validated PSMs
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
457 * Coverage (%): Sequence coverage in percent of the protein designed by the main accession.
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
458 * Possible Coverage (%): Possible sequence coverage in percent of the protein designed by the main accession according to the search settings.
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
459 * MW (kDa): Molecular Weight.
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
460 * Spectrum Counting NSAF: Normalized Spectrum Abundance Factor (NSAF)
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
461 * Spectrum Counting emPAI: exponentially modified Protein Abundance Index (emPAI)
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
462 * Confident Modification Sites: Number of Confident Modification Sites List of the sites where a variable modification was confidently localized.
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
463 * Other Modification Sites: Number of other Modification Sites List of the non*confident sites where a variable modification was localized.
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
464 * Score: Score of the protein group.
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
465 * Confidence: Confidence in percent associated to the protein group.
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
466 * Decoy: Indicates whether the protein group is a decoy (1: yes, 0: no).
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
467 * Validation: Indicates the validation level of the protein group.
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
468
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
469
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
470 Peptide Report
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
471 --------------
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
472
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
473
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
474 * Protein(s): Protein(s) to which this peptide can be attached.
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
475 * AAs Before: The amino-acids before the sequence.
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
476 * Sequence: Sequence of the peptide.
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
477 * AAs After: The amino-acids after the sequence.
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
478 * Modified Sequence: The peptide sequence annotated with variable modifications.
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
479 * Variable Modifications: The variable modifications.
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
480 * Localization Confidence: The confidence in PTMs localization.
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
481 * Fixed Modifications: The fixed modifications.
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
482 * #Validated PSMs: Number of validated PSMs.
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
483 * #PSMs: Number of PSMs.
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
484 * Score: Score of the peptide.
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
485 * Confidence: Confidence in percent associated to the peptide.
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
486 * Decoy: Indicates whether the peptide is a decoy (1: yes, 0: no).
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
487 * Validation: Indicates the validation level of the protein group.
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
488
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
489
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
490 Hierachical Report
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
491 ------------------
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
492
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
493 * Main Accession: Main accession of the protein group.
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
494 * Description: Description of the protein designed by the main accession.
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
495 * PI: Protein Inference status of the protein group.
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
496 * Secondary Accessions: Other accessions in the protein group (alphabetical order).
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
497 * Protein Group: The complete protein group (alphabetical order).
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
498 * #Peptides: Total number of peptides.
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
499 * #Validated Peptides: Number of validated peptides.
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
500 * #Unique: Total number of peptides unique to this protein group.
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
501 * #PSMs: Number of PSMs
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
502 * #Validated PSMs: Number of validated PSMs
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
503 * Coverage (%): Sequence coverage in percent of the protein designed by the main accession.
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
504 * Possible Coverage (%): Possible sequence coverage in percent of the protein designed by the main accession according to the search settings.
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
505 * MW (kDa): Molecular Weight.
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
506 * Spectrum Counting NSAF: Normalized Spectrum Abundance Factor (NSAF)
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
507 * Spectrum Counting emPAI: exponentially modified Protein Abundance Index (emPAI)
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
508 * Confident Modification Sites: # Confident Modification Sites List of the sites where a variable modification was confidently localized.
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
509 * Other Modification Sites: # Other Modification Sites List of the non-confident sites where a variable modification was localized.
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
510 * Score: Score of the protein group.
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
511 * Confidence: Confidence in percent associated to the protein group.
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
512 * Decoy: Indicates whether the protein group is a decoy (1: yes, 0: no).
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
513 * Validation: Indicates the validation level of the protein group.
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
514 * Protein(s): Protein(s) to which this peptide can be attached.
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
515 * AAs Before: The amino-acids before the sequence.
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
516 * Sequence: Sequence of the peptide.
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
517 * AAs After: The amino-acids after the sequence.
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
518 * Variable Modifications: The variable modifications.
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
519 * Localization Confidence: The confidence in PTMs localization.
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
520 * Fixed Modifications: The fixed modifications.
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
521 * #Validated PSMs: Number of validated PSMs.
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
522 * #PSMs: Number of PSMs.
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
523 * Score: Score of the peptide.
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
524 * Confidence: Confidence in percent associated to the peptide.
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
525 * Decoy: Indicates whether the peptide is a decoy (1: yes, 0: no).
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
526 * Validation: Indicates the validation level of the protein group.
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
527 * Protein(s): Protein(s) to which the peptide can be attached.
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
528 * Sequence: Sequence of the peptide.
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
529 * Modified Sequence: The peptide sequence annotated with variable modifications.
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
530 * Variable Modifications: The variable modifications.
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
531 * D-score: D-score for variable PTM localization.
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
532 * probabilistic PTM score: The probabilistic score (e.g. A-score or PhosphoRS) used for variable PTM localization.
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
533 * Localization Confidence: The confidence in variable PTM localization.
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
534 * Fixed Modifications: The fixed modifications.
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
535 * Spectrum File: The spectrum file.
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
536 * Spectrum Title: The title of the spectrum.
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
537 * Spectrum Scan Number: The spectrum scan number.
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
538 * RT: Retention time
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
539 * m/z: Measured m/z
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
540 * Measured Charge: The charge as given in the spectrum file.
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
541 * Identification Charge: The charge as inferred by the search engine.
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
542 * Theoretical Mass: The theoretical mass of the peptide.
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
543 * Isotope Number: The isotope number targetted by the instrument.
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
544 * Precursor m/z Error: The precursor m/z matching error.
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
545 * Score: Score of the retained peptide as a combination of the algorithm scores (used to rank PSMs).
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
546 * Confidence: Confidence in percent associated to the retained PSM.
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
547 * Decoy: Indicates whether the peptide is a decoy (1: yes, 0: no).
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
548 * Validation: Indicates the validation level of the protein group.
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
549
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
550
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
551 ------
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
552
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
553 **Citation**
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
554
30
ad60446b1e93 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit bdb5ee12705a3494eee96d1963f16f68bbe41d5c
galaxyp
parents: 29
diff changeset
555 To cite the underlying tools (PeptideShaker and SearchGUI) please refer to the list of papers at http://compomics.github.io
18
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
556
30
ad60446b1e93 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit bdb5ee12705a3494eee96d1963f16f68bbe41d5c
galaxyp
parents: 29
diff changeset
557 If you use this tool in Galaxy, please cite Chilton J, Ira Cooke, Bjoern Gruening et al.
18
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
558 </help>
20
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
iracooke
parents: 18
diff changeset
559 <expand macro="citations" />
18
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
560 </tool>