Mercurial > repos > galaxyp > peptideshaker

annotate peptide_shaker.xml @ 29:78fad25eff17 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 4256c7c6fde06722b66f433f5913c2e707bc930f-dirty
author galaxyp
date Fri, 10 Jun 2016 09:58:03 -0400
parents 432140bcc7fe
children ad60446b1e93
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
29
78fad25eff17 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 4256c7c6fde06722b66f433f5913c2e707bc930f-dirty
galaxyp
parents: 28
diff changeset
1 <tool id="peptide_shaker" name="Peptide Shaker" version="1.11.0">
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>
29
78fad25eff17 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 4256c7c6fde06722b66f433f5913c2e707bc930f-dirty
galaxyp
parents: 28
diff changeset
9 <requirement type="package" version="1.11">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 $temp_stderr = "peptideshaker_stderr"
18
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
18
22
e3be595c0bf5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 5ca27ef280bee8b65fd3d0d2cd5ff280a2cebb3d
iracooke
parents: 21
diff changeset
19
18
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
20 mkdir output_reports;
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
21 cwd=`pwd`;
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
22
22
e3be595c0bf5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 5ca27ef280bee8b65fd3d0d2cd5ff280a2cebb3d
iracooke
parents: 21
diff changeset
23 cp -r "\${PEPTIDESHAKER_JAR_PATH%/*}" bin;
e3be595c0bf5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 5ca27ef280bee8b65fd3d0d2cd5ff280a2cebb3d
iracooke
parents: 21
diff changeset
24 tmp_peptideshaker_jar_path=`echo "\$cwd/bin/\${PEPTIDESHAKER_JAR_PATH\#\#/*/}"`;
e3be595c0bf5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 5ca27ef280bee8b65fd3d0d2cd5ff280a2cebb3d
iracooke
parents: 21
diff changeset
25
20
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
iracooke
parents: 18
diff changeset
26 ln -s '$searchgui_input' searchgui_input.zip &&
18
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
27 ######################
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
28 ## PeptideShakerCLI ##
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
29 ######################
22
e3be595c0bf5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 5ca27ef280bee8b65fd3d0d2cd5ff280a2cebb3d
iracooke
parents: 21
diff changeset
30 (java -cp \$tmp_peptideshaker_jar_path eu.isas.peptideshaker.cmd.PeptideShakerCLI
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
24
815f93bb3e1b Uploaded
galaxyp
parents: 22
diff changeset
36 -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
37 -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
38
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
iracooke
parents: 18
diff changeset
39 -threads "\${GALAXY_SLOTS:-12}"
18
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
40
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
41 ##Optional gene annotation parameter
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
42 #if $species_type.species_type_selector != 'no_species_type':
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
43 -species_type "${species_type.species_type_selector}"
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
44 -species "${species_type.species}"
20
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
iracooke
parents: 18
diff changeset
45 -species_update 1
18
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
46 #end if
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
47
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
48 ##Optional processing parameters:
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
49 #if $processing_options.processing_options_selector == "yes"
26
3ef5a7dd1a36 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6dcfe37e286523588aa2738599af8d3273290f28-dirty
galaxyp
parents: 25
diff changeset
50 -protein_fdr "${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
51 -peptide_fdr "${processing_options.peptide_fdr}"
3ef5a7dd1a36 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6dcfe37e286523588aa2738599af8d3273290f28-dirty
galaxyp
parents: 25
diff changeset
52 -psm_fdr "${processing_options.psm_fdr}"
18
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
53 -ptm_score "${processing_options.ptm_score.ptm_score_selector}"
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
54 #if $processing_options.ptm_score.ptm_score_selector == 1
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
55 -score_neutral_losses "${processing_options.ptm_score.neutral_losses}"
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
56 #if str($processing_options.ptm_score.ptm_threshold) != ''
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
57 -ptm_threshold "${processing_options.ptm_score.ptm_threshold}"
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
58 #end if
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
59 #end if
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
60 -protein_fraction_mw_confidence "${processing_options.protein_fraction_mw_confidence}"
29
78fad25eff17 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 4256c7c6fde06722b66f433f5913c2e707bc930f-dirty
galaxyp
parents: 28
diff changeset
61 -ptm_alignment "${processing_options.ptm_alignment}"
18
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
62 #end if
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
63
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
64 ##Optional filtering parameters:
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
65 #if $filtering_options.filtering_options_selector == "yes":
26
3ef5a7dd1a36 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6dcfe37e286523588aa2738599af8d3273290f28-dirty
galaxyp
parents: 25
diff changeset
66 -import_peptide_length_min "${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
67 -import_peptide_length_max "${filtering_options.max_peptide_length}"
3ef5a7dd1a36 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6dcfe37e286523588aa2738599af8d3273290f28-dirty
galaxyp
parents: 25
diff changeset
68 -import_precurosor_mz "${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
69 -import_precurosor_mz_ppm "${filtering_options.max_precursor_error_type}"
20
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
iracooke
parents: 18
diff changeset
70 ##-max_xtandem_e "${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
71 ##-max_omssa_e "${filtering_options.max_omssa_e}"
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
iracooke
parents: 18
diff changeset
72 ##-max_mascot_e "${filtering_options.max_mascot_e}"
18
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
73 -exclude_unknown_ptms "${filtering_options.exclude_unknown_ptms}"
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
74 #end if
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
75
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
76 2>> $temp_stderr)
20
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
iracooke
parents: 18
diff changeset
77
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
iracooke
parents: 18
diff changeset
78 &&
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
iracooke
parents: 18
diff changeset
79
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
iracooke
parents: 18
diff changeset
80 echo "Running Reports";
18
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
81
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
82 ##################################
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
83 ## PeptideShaker Report options ##
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
84 ##################################
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
85
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
86 #if 'mzidentML' in str($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
87 echo "Generating mzIdentML";
22
e3be595c0bf5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 5ca27ef280bee8b65fd3d0d2cd5ff280a2cebb3d
iracooke
parents: 21
diff changeset
88 (java -cp \$tmp_peptideshaker_jar_path eu.isas.peptideshaker.cmd.MzidCLI
20
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
iracooke
parents: 18
diff changeset
89 -in \$cwd/peptideshaker_output.zip
18
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
90 -output_file output.mzid
20
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
iracooke
parents: 18
diff changeset
91 -contact_first_name "Proteomics"
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
iracooke
parents: 18
diff changeset
92 -contact_last_name "Galaxy"
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
iracooke
parents: 18
diff changeset
93 -contact_email "galaxyp@umn.edu"
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
iracooke
parents: 18
diff changeset
94 -contact_address "galaxyp@umn.edu"
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
iracooke
parents: 18
diff changeset
95 -organization_name "University of Minnesota"
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
iracooke
parents: 18
diff changeset
96 -organization_email "galaxyp@umn.edu"
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
iracooke
parents: 18
diff changeset
97 -organization_address "Minneapolis, MN 55455, Vereinigte Staaten"
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
iracooke
parents: 18
diff changeset
98 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
99 &&
18
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
100 #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
101
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
iracooke
parents: 18
diff changeset
102 ## 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
103 ## '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
104 ## 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
105 #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
106
22
e3be595c0bf5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 5ca27ef280bee8b65fd3d0d2cd5ff280a2cebb3d
iracooke
parents: 21
diff changeset
107 (java -cp \$tmp_peptideshaker_jar_path eu.isas.peptideshaker.cmd.ReportCLI
20
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
iracooke
parents: 18
diff changeset
108 -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
109 -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
110 -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
111 #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
112 #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
113 #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
114 #end if
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
iracooke
parents: 18
diff changeset
115 #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
116 #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
117 #end if
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
iracooke
parents: 18
diff changeset
118 #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
119 #silent $cleaned_list.remove('zip')
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
iracooke
parents: 18
diff changeset
120 #end if
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
iracooke
parents: 18
diff changeset
121 ## Only numbers are left over. These corresponds to different reports.
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
iracooke
parents: 18
diff changeset
122 -reports #echo ','.join($cleaned_list)#
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
iracooke
parents: 18
diff changeset
123
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
iracooke
parents: 18
diff changeset
124 2>> $temp_stderr)
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
iracooke
parents: 18
diff changeset
125 &&
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
iracooke
parents: 18
diff changeset
126 #end if
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
iracooke
parents: 18
diff changeset
127
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
iracooke
parents: 18
diff changeset
128
18
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
129 #if '0' in str($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
130 find \$cwd/output_reports -name '*Certificate_of_Analysis*' -exec bash -c 'mv "$0" "certificate.txt"' {} \;
18
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
131 ;
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
132 #end if
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
133 #if '1' in str($outputs).split(','):
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
134 find \$cwd/output_reports -name '*Hierarchical*' -exec bash -c 'mv "$0" "hierarchical.txt"' {} \;
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
135 ;
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
136 #end if
20
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
iracooke
parents: 18
diff changeset
137 #if '2' in str($outputs).split(','):
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
iracooke
parents: 18
diff changeset
138 find \$cwd/output_reports -name '*PSM_Phosphorylation_Report*' -exec bash -c 'mv "$0" "psm_phospho.txt"' {} \;
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
iracooke
parents: 18
diff changeset
139 ;
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
iracooke
parents: 18
diff changeset
140 #end if
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
iracooke
parents: 18
diff changeset
141 #if '3' in str($outputs).split(','):
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
iracooke
parents: 18
diff changeset
142 find \$cwd/output_reports -name '*PSM_Report*' -exec bash -c 'mv "$0" "psm.txt"' {} \;
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
iracooke
parents: 18
diff changeset
143 ;
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
iracooke
parents: 18
diff changeset
144 #end if
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
iracooke
parents: 18
diff changeset
145 #if '4' in str($outputs).split(','):
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
iracooke
parents: 18
diff changeset
146 find \$cwd/output_reports -name '*Peptide_Phosphorylation_Report*' -exec bash -c 'mv "$0" "peptides_phospho.txt"' {} \;
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
iracooke
parents: 18
diff changeset
147 ;
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
iracooke
parents: 18
diff changeset
148 #end if
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
iracooke
parents: 18
diff changeset
149 #if '5' in str($outputs).split(','):
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
iracooke
parents: 18
diff changeset
150 find \$cwd/output_reports -name '*Peptide_Report*' -exec bash -c 'mv "$0" "peptides.txt"' {} \;
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
iracooke
parents: 18
diff changeset
151 ;
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
iracooke
parents: 18
diff changeset
152 #end if
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
iracooke
parents: 18
diff changeset
153 #if '6' in str($outputs).split(','):
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
iracooke
parents: 18
diff changeset
154 find \$cwd/output_reports -name '*Protein_Phosphorylation_Report*' -exec bash -c 'mv "$0" "proteins_phospho.txt"' {} \;
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
iracooke
parents: 18
diff changeset
155 ;
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
iracooke
parents: 18
diff changeset
156 #end if
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
iracooke
parents: 18
diff changeset
157 #if '7' in str($outputs).split(','):
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
iracooke
parents: 18
diff changeset
158 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
159 ;
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
iracooke
parents: 18
diff changeset
160 #end if
18
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
161
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
162 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
163 cat $temp_stderr 2>&1;
18
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
164 (exit \$exit_code_for_galaxy)
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
165
20
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
iracooke
parents: 18
diff changeset
166 ]]>
18
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
167 </command>
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
168 <inputs>
21
dfaea053e32f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 327a3944f2f56668d607c3d6cb08ae7d588e208c
iracooke
parents: 20
diff changeset
169 <param name="searchgui_input" format="searchgui_archive" type="data" label="Compressed SearchGUI results"
24
815f93bb3e1b Uploaded
galaxyp
parents: 22
diff changeset
170 help="SearchGUI Results from History">
815f93bb3e1b Uploaded
galaxyp
parents: 22
diff changeset
171 <options options_filter_attribute="metadata.searchgui_major_version" >
815f93bb3e1b Uploaded
galaxyp
parents: 22
diff changeset
172 <filter type="add_value" value="@SEARCHGUI_MAJOR_VERSION@" />
815f93bb3e1b Uploaded
galaxyp
parents: 22
diff changeset
173 </options>
815f93bb3e1b Uploaded
galaxyp
parents: 22
diff changeset
174 </param>
18
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
175
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
176 <conditional name="species_type">
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
177 <param name="species_type_selector" type="select" optional="true" label="The species type to use for the gene annotation"
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
178 help="(Optional) If your species is supported under one of the groups, selecting it will allow GO annotations and other information to be included in the results">
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
179 <option value="Fungi">Fungi</option>
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
180 <option value="Plants">Plants</option>
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
181 <option value="Metazoa">Metazoa</option>
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
182 <option value="Vertebrates">Vertebrates</option>
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
183 <option value="Protists">Protists</option>
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
184 <option value="no_species_type" selected="true">No species restriction</option>
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
185 </param>
24
815f93bb3e1b Uploaded
galaxyp
parents: 22
diff changeset
186 <when value="no_species_type"/>
18
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
187 <when value="Protists">
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
188 <param name="species" type="select" label="The species to use for the gene annotation"
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
189 help="">
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
190 <option value="Albugo laibachii">Albugo laibachii</option>
20
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
iracooke
parents: 18
diff changeset
191 <option value="Bigelowiella natans">Bigelowiella natans</option>
18
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
192 <option value="Dictyostelium discoideum">Dictyostelium discoideum</option>
20
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
iracooke
parents: 18
diff changeset
193 <option value="Emiliania huxleyi">Emiliania huxleyi</option>
18
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
194 <option value="Entamoeba histolytica">Entamoeba histolytica</option>
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
195 <option value="Giardia lamblia">Giardia lamblia</option>
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
196 <option value="Guillardia theta CCMP2712">Guillardia theta CCMP2712</option>
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
197 <option value="Hyaloperonospora arabidopsidis">Hyaloperonospora arabidopsidis</option>
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
198 <option value="Leishmania major">Leishmania major</option>
20
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
iracooke
parents: 18
diff changeset
199 <option value="Paramecium tetraurelia">Paramecium tetraurelia</option>
18
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
200 <option value="Phaeodactylum tricornutum">Phaeodactylum tricornutum</option>
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
201 <option value="Phytophthora infestans">Phytophthora infestans</option>
20
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
iracooke
parents: 18
diff changeset
202 <option value="Phytophthora kernoviae">Phytophthora kernoviae</option>
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
iracooke
parents: 18
diff changeset
203 <option value="Phytophthora lateralis">Phytophthora lateralis</option>
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
iracooke
parents: 18
diff changeset
204 <option value="Phytophthora parasitica">Phytophthora parasitica</option>
18
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
205 <option value="Phytophthora ramorum">Phytophthora ramorum</option>
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
206 <option value="Phytophthora sojae">Phytophthora sojae</option>
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
207 <option value="Plasmodium berghei">Plasmodium berghei</option>
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
208 <option value="Plasmodium chabaudi">Plasmodium chabaudi</option>
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
209 <option value="Plasmodium falciparum">Plasmodium falciparum</option>
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
210 <option value="Plasmodium knowlesi">Plasmodium knowlesi</option>
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
211 <option value="Plasmodium vivax">Plasmodium vivax</option>
20
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
iracooke
parents: 18
diff changeset
212 <option value="Pythium aphanidermatum">Pythium aphanidermatum</option>
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
iracooke
parents: 18
diff changeset
213 <option value="Pythium arrhenomanes">Pythium arrhenomanes</option>
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
iracooke
parents: 18
diff changeset
214 <option value="Pythium irregulare">Pythium irregulare</option>
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
iracooke
parents: 18
diff changeset
215 <option value="Pythium iwayamai">Pythium iwayamai</option>
18
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
216 <option value="Pythium ultimum">Pythium ultimum</option>
20
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
iracooke
parents: 18
diff changeset
217 <option value="Pythium vexans">Pythium vexans</option>
18
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
218 <option value="Tetrahymena thermophila">Tetrahymena thermophila</option>
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
219 <option value="Thalassiosira pseudonana">Thalassiosira pseudonana</option>
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
220 <option value="Toxoplasma gondii">Toxoplasma gondii</option>
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
221 <option value="Trypanosoma brucei">Trypanosoma brucei</option>
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
222 </param>
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
223 </when>
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
224 <when value="Plants">
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
225 <param name="species" type="select" label="The species to use for the gene annotation"
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
226 help="">
20
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
iracooke
parents: 18
diff changeset
227 <option value="Amborella (Amborella trichopoda)">Amborella (Amborella trichopoda)</option>
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
iracooke
parents: 18
diff changeset
228 <option value="Arabidopsis lyrata (Lyrate rockcress)">Arabidopsis lyrata (Lyrate rockcress)</option>
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
iracooke
parents: 18
diff changeset
229 <option value="Arabidopsis thaliana (Thale-cress)">Arabidopsis thaliana (Thale-cress)</option>
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
iracooke
parents: 18
diff changeset
230 <option value="Brachypodium distachyon (False brome)">Brachypodium distachyon (False brome)</option>
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
iracooke
parents: 18
diff changeset
231 <option value="Brassica oleracea">Brassica oleracea</option>
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
iracooke
parents: 18
diff changeset
232 <option value="Brassica rapa genes (Field mustard)">Brassica rapa genes (Field mustard)</option>
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
iracooke
parents: 18
diff changeset
233 <option value="Chlamydomonas reinhardtii (Green algae)">Chlamydomonas reinhardtii (Green algae)</option>
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
iracooke
parents: 18
diff changeset
234 <option value="Cyanidioschyzon merolae (Red algae)">Cyanidioschyzon merolae (Red algae)</option>
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
iracooke
parents: 18
diff changeset
235 <option value="Glycine max (Soybean)">Glycine max (Soybean)</option>
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
iracooke
parents: 18
diff changeset
236 <option value="Hordeum vulgare (Barley)">Hordeum vulgare (Barley)</option>
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
iracooke
parents: 18
diff changeset
237 <option value="Leersia perrieri (Leersia)">Leersia perrieri (Leersia)</option>
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
iracooke
parents: 18
diff changeset
238 <option value="Medicago truncatula (Barrel medic)">Medicago truncatula (Barrel medic)</option>
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
iracooke
parents: 18
diff changeset
239 <option value="Musa acuminata (Banana)">Musa acuminata (Banana)</option>
18
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
240 <option value="Oryza brachyantha">Oryza brachyantha</option>
20
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
iracooke
parents: 18
diff changeset
241 <option value="Oryza glumaepatula">Oryza glumaepatula</option>
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
iracooke
parents: 18
diff changeset
242 <option value="Oryza meridionalis">Oryza meridionalis</option>
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
iracooke
parents: 18
diff changeset
243 <option value="Oryza nivara">Oryza nivara</option>
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
iracooke
parents: 18
diff changeset
244 <option value="Oryza punctata">Oryza punctata</option>
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
iracooke
parents: 18
diff changeset
245 <option value="Oryza rufipogon (Common wild rice)">Oryza rufipogon (Common wild rice)</option>
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
iracooke
parents: 18
diff changeset
246 <option value="Oryza sativa (Indica rice)">Oryza sativa (Indica rice)</option>
18
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
247 <option value="Oryza sativa Indica Group">Oryza sativa Indica Group</option>
20
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
iracooke
parents: 18
diff changeset
248 <option value="Oryza sativa Japonica (Japonica rice)">Oryza sativa Japonica (Japonica rice)</option>
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
iracooke
parents: 18
diff changeset
249 <option value="Ostreococcus lucimarinus (Green algae)">Ostreococcus lucimarinus (Green algae)</option>
18
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
250 <option value="Physcomitrella patens">Physcomitrella patens</option>
20
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
iracooke
parents: 18
diff changeset
251 <option value="Physcomitrella patens (Moss)">Physcomitrella patens (Moss)</option>
18
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
252 <option value="Populus trichocarpa">Populus trichocarpa</option>
20
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
iracooke
parents: 18
diff changeset
253 <option value="Populus trichocarpa (Western balsam poplar)">Populus trichocarpa (Western balsam poplar)</option>
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
iracooke
parents: 18
diff changeset
254 <option value="Prunus persica (Peach)">Prunus persica (Peach)</option>
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
iracooke
parents: 18
diff changeset
255 <option value="Selaginella moellendorffii (Spike moss)">Selaginella moellendorffii (Spike moss)</option>
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
iracooke
parents: 18
diff changeset
256 <option value="Setaria italica (Foxtail millet)">Setaria italica (Foxtail millet)</option>
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
iracooke
parents: 18
diff changeset
257 <option value="Solanum lycopersicum (Tomato)">Solanum lycopersicum (Tomato)</option>
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
iracooke
parents: 18
diff changeset
258 <option value="Solanum tuberosum (Potato)">Solanum tuberosum (Potato)</option>
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
iracooke
parents: 18
diff changeset
259 <option value="Sorghum bicolor (Sorghum)">Sorghum bicolor (Sorghum)</option>
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
iracooke
parents: 18
diff changeset
260 <option value="Theobroma cacao (Cocoa)">Theobroma cacao (Cocoa)</option>
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
iracooke
parents: 18
diff changeset
261 <option value="Triticum aestivum (Bread wheat)">Triticum aestivum (Bread wheat)</option>
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
iracooke
parents: 18
diff changeset
262 <option value="Triticum urartu (Einkorn)">Triticum urartu (Einkorn)</option>
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
iracooke
parents: 18
diff changeset
263 <option value="Vitis vinifera (Wine grape)">Vitis vinifera (Wine grape)</option>
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
iracooke
parents: 18
diff changeset
264 <option value="Zea mays (Maize)">Zea mays (Maize)</option>
18
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
265 </param>
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
266 </when>
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
267 <when value="Metazoa">
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
268 <param name="species" type="select" label="The species to use for the gene annotation"
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
269 help="">
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
270 <option value="Acyrthosiphon pisum">Acyrthosiphon pisum</option>
20
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
iracooke
parents: 18
diff changeset
271 <option value="Aedes aegypti (Yellow fever mosquito)">Aedes aegypti (Yellow fever mosquito)</option>
18
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
272 <option value="Amphimedon queenslandica">Amphimedon queenslandica</option>
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
273 <option value="Anopheles darlingi">Anopheles darlingi</option>
20
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
iracooke
parents: 18
diff changeset
274 <option value="Anopheles gambiae (African malaria mosquito) ">Anopheles gambiae (African malaria mosquito) </option>
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
iracooke
parents: 18
diff changeset
275 <option value="Apis mellifera ">Apis mellifera </option>
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
iracooke
parents: 18
diff changeset
276 <option value="Atta cephalotes ">Atta cephalotes </option>
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
iracooke
parents: 18
diff changeset
277 <option value="Bombyx mori ">Bombyx mori </option>
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
iracooke
parents: 18
diff changeset
278 <option value="Brugia malayi ">Brugia malayi </option>
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
iracooke
parents: 18
diff changeset
279 <option value="Caenorhabditis brenneri ">Caenorhabditis brenneri </option>
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="Caenorhabditis briggsae ">Caenorhabditis briggsae </option>
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
iracooke
parents: 18
diff changeset
281 <option value="Caenorhabditis elegans ">Caenorhabditis elegans </option>
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
iracooke
parents: 18
diff changeset
282 <option value="Caenorhabditis japonica ">Caenorhabditis japonica </option>
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
iracooke
parents: 18
diff changeset
283 <option value="Caenorhabditis remanei ">Caenorhabditis remanei </option>
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="Culex quinquefasciatus (Southern house mosquito) ">Culex quinquefasciatus (Southern house mosquito) </option>
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
iracooke
parents: 18
diff changeset
285 <option value="Danaus plexippus ">Danaus plexippus </option>
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
iracooke
parents: 18
diff changeset
286 <option value="Daphnia pulex ">Daphnia pulex </option>
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
iracooke
parents: 18
diff changeset
287 <option value="Dendroctonus ponderosae">Dendroctonus ponderosae</option>
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
iracooke
parents: 18
diff changeset
288 <option value="Drosophila ananassae ">Drosophila ananassae </option>
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
iracooke
parents: 18
diff changeset
289 <option value="Drosophila erecta ">Drosophila erecta </option>
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
iracooke
parents: 18
diff changeset
290 <option value="Drosophila grimshawi ">Drosophila grimshawi </option>
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
iracooke
parents: 18
diff changeset
291 <option value="Drosophila melanogaster (Fruit fly) ">Drosophila melanogaster (Fruit fly) </option>
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
iracooke
parents: 18
diff changeset
292 <option value="Drosophila mojavensis ">Drosophila mojavensis </option>
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
iracooke
parents: 18
diff changeset
293 <option value="Drosophila persimilis ">Drosophila persimilis </option>
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
iracooke
parents: 18
diff changeset
294 <option value="Drosophila pseudoobscura ">Drosophila pseudoobscura </option>
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
iracooke
parents: 18
diff changeset
295 <option value="Drosophila sechellia ">Drosophila sechellia </option>
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
iracooke
parents: 18
diff changeset
296 <option value="Drosophila simulans ">Drosophila simulans </option>
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
iracooke
parents: 18
diff changeset
297 <option value="Drosophila virilis ">Drosophila virilis </option>
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
iracooke
parents: 18
diff changeset
298 <option value="Drosophila willistoni ">Drosophila willistoni </option>
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
iracooke
parents: 18
diff changeset
299 <option value="Drosophila yakuba ">Drosophila yakuba </option>
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
iracooke
parents: 18
diff changeset
300 <option value="Heliconius melpomene ">Heliconius melpomene </option>
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
iracooke
parents: 18
diff changeset
301 <option value="Helobdella robusta">Helobdella robusta</option>
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
iracooke
parents: 18
diff changeset
302 <option value="Ixodes scapularis (Black-legged tick) ">Ixodes scapularis (Black-legged tick) </option>
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
iracooke
parents: 18
diff changeset
303 <option value="Loa loa ">Loa loa </option>
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
iracooke
parents: 18
diff changeset
304 <option value="Lottia gigantea">Lottia gigantea</option>
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
iracooke
parents: 18
diff changeset
305 <option value="Megaselia scalaris ">Megaselia scalaris </option>
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
iracooke
parents: 18
diff changeset
306 <option value="Melitaea cinxia">Melitaea cinxia</option>
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
iracooke
parents: 18
diff changeset
307 <option value="Mnemiopsis leidyi">Mnemiopsis leidyi</option>
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
iracooke
parents: 18
diff changeset
308 <option value="Nasonia vitripennis ">Nasonia vitripennis </option>
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
iracooke
parents: 18
diff changeset
309 <option value="Nematostella vectensis ">Nematostella vectensis </option>
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
iracooke
parents: 18
diff changeset
310 <option value="Onchocerca volvulus">Onchocerca volvulus</option>
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
iracooke
parents: 18
diff changeset
311 <option value="Pediculus humanus (Human louse) ">Pediculus humanus (Human louse) </option>
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
iracooke
parents: 18
diff changeset
312 <option value="Pristionchus pacificus ">Pristionchus pacificus </option>
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
iracooke
parents: 18
diff changeset
313 <option value="Rhodnius prolixus">Rhodnius prolixus</option>
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
iracooke
parents: 18
diff changeset
314 <option value="Schistosoma mansoni ">Schistosoma mansoni </option>
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
iracooke
parents: 18
diff changeset
315 <option value="Solenopsis invicta (Red fire ant)">Solenopsis invicta (Red fire ant)</option>
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
iracooke
parents: 18
diff changeset
316 <option value="Strigamia maritima ">Strigamia maritima </option>
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
iracooke
parents: 18
diff changeset
317 <option value="Strongylocentrotus purpuratus ">Strongylocentrotus purpuratus </option>
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
iracooke
parents: 18
diff changeset
318 <option value="Tetranychus urticae">Tetranychus urticae</option>
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
iracooke
parents: 18
diff changeset
319 <option value="Tribolium castaneum (red flour beetle) ">Tribolium castaneum (red flour beetle) </option>
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
iracooke
parents: 18
diff changeset
320 <option value="Trichinella spiralis ">Trichinella spiralis </option>
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
iracooke
parents: 18
diff changeset
321 <option value="Trichoplax adhaerens ">Trichoplax adhaerens </option>
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
iracooke
parents: 18
diff changeset
322 <option value="Zootermopsis nevadensis">Zootermopsis nevadensis</option>
18
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
323 </param>
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
324 </when>
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
325 <when value="Fungi">
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
326 <param name="species" type="select" label="The species to use for the gene annotation"
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
327 help="">
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
328 <option value="Ashbya gossypii">Ashbya gossypii</option>
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
329 <option value="Aspergillus clavatus">Aspergillus clavatus</option>
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
330 <option value="Aspergillus flavus">Aspergillus flavus</option>
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
331 <option value="Aspergillus fumigatus">Aspergillus fumigatus</option>
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
332 <option value="Aspergillus fumigatusa1163">Aspergillus fumigatusa1163</option>
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
333 <option value="Aspergillus nidulans">Aspergillus nidulans</option>
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
334 <option value="Aspergillus niger">Aspergillus niger</option>
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
335 <option value="Aspergillus oryzae">Aspergillus oryzae</option>
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
336 <option value="Aspergillus terreus">Aspergillus terreus</option>
20
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
iracooke
parents: 18
diff changeset
337 <option value="Blumeria graminis">Blumeria graminis</option>
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
iracooke
parents: 18
diff changeset
338 <option value="Botrytis cinerea">Botrytis cinerea</option>
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
iracooke
parents: 18
diff changeset
339 <option value="Colletotrichum gloeosporioides">Colletotrichum gloeosporioides</option>
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
iracooke
parents: 18
diff changeset
340 <option value="Colletotrichum higginsianum">Colletotrichum higginsianum</option>
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
iracooke
parents: 18
diff changeset
341 <option value="Colletotrichum orbiculare">Colletotrichum orbiculare</option>
18
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
342 <option value="Cryptococcus neoformans">Cryptococcus neoformans</option>
20
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
iracooke
parents: 18
diff changeset
343 <option value="Dothistroma septosporum">Dothistroma septosporum</option>
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
iracooke
parents: 18
diff changeset
344 <option value="Fusarium fujikuroi">Fusarium fujikuroi</option>
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
iracooke
parents: 18
diff changeset
345 <option value="Fusarium graminearum">Fusarium graminearum</option>
18
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
346 <option value="Fusarium oxysporum">Fusarium oxysporum</option>
20
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
iracooke
parents: 18
diff changeset
347 <option value="Fusarium pseudograminearum">Fusarium pseudograminearum</option>
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
iracooke
parents: 18
diff changeset
348 <option value="Fusarium solani">Fusarium solani</option>
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
iracooke
parents: 18
diff changeset
349 <option value="Fusarium verticillioides">Fusarium verticillioides</option>
18
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
350 <option value="Gaeumannomyces graminis">Gaeumannomyces graminis</option>
20
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
iracooke
parents: 18
diff changeset
351 <option value="Colletotrichum graminicola">Colletotrichum graminicola</option>
18
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
352 <option value="Komagataella pastoris">Komagataella pastoris</option>
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
353 <option value="Leptosphaeria maculans">Leptosphaeria maculans</option>
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
354 <option value="Magnaporthe oryzae">Magnaporthe oryzae</option>
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
355 <option value="Magnaporthe poae">Magnaporthe poae</option>
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
356 <option value="Melampsora larici-populina">Melampsora larici-populina</option>
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
357 <option value="Neosartorya fischeri">Neosartorya fischeri</option>
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
358 <option value="Neurospora crassa">Neurospora crassa</option>
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
359 <option value="Phaeosphaeria nodorum">Phaeosphaeria nodorum</option>
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
360 <option value="Puccinia graminis">Puccinia graminis</option>
20
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
iracooke
parents: 18
diff changeset
361 <option value="Puccinia graminis Ug99">Puccinia graminis Ug99</option>
18
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
362 <option value="Puccinia triticina">Puccinia triticina</option>
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
363 <option value="Pyrenophora teres">Pyrenophora teres</option>
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
364 <option value="Pyrenophora tritici-repentis">Pyrenophora tritici-repentis</option>
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
365 <option value="Saccharomyces cerevisiae">Saccharomyces cerevisiae</option>
20
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
iracooke
parents: 18
diff changeset
366 <option value="Schizosaccharomyces cryophilus">Schizosaccharomyces cryophilus</option>
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
iracooke
parents: 18
diff changeset
367 <option value="Schizosaccharomyces japonicus">Schizosaccharomyces japonicus</option>
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
iracooke
parents: 18
diff changeset
368 <option value="Schizosaccharomyces octosporus">Schizosaccharomyces octosporus</option>
18
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
369 <option value="Schizosaccharomyces pombe">Schizosaccharomyces pombe</option>
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
370 <option value="Sclerotinia sclerotiorum">Sclerotinia sclerotiorum</option>
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
371 <option value="Sporisorium reilianum">Sporisorium reilianum</option>
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
372 <option value="Trichoderma reesei">Trichoderma reesei</option>
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
373 <option value="Trichoderma virens">Trichoderma virens</option>
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
374 <option value="Tuber melanosporum">Tuber melanosporum</option>
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
375 <option value="Ustilago maydis">Ustilago maydis</option>
20
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
iracooke
parents: 18
diff changeset
376 <option value="Verticillium dahliae JR2">Verticillium dahliae JR2</option>
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
iracooke
parents: 18
diff changeset
377 <option value="Verticillium dahliae">Verticillium dahliae</option>
18
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
378 <option value="Yarrowia lipolytica">Yarrowia lipolytica</option>
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
379 <option value="Zymoseptoria tritici">Zymoseptoria tritici</option>
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
380 </param>
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
381 </when>
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
382 <when value="Vertebrates">
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
383 <param name="species" type="select" label="The species to use for the gene annotation"
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
384 help="">
20
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
iracooke
parents: 18
diff changeset
385 <option value="Alpaca (Vicugna pacos)">Alpaca (Vicugna pacos)</option>
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
iracooke
parents: 18
diff changeset
386 <option value="Amazon molly (Poecilia formosa)">Amazon molly (Poecilia formosa)</option>
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
iracooke
parents: 18
diff changeset
387 <option value="Anole lizard (Anolis carolinensis)">Anole lizard (Anolis carolinensis)</option>
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
iracooke
parents: 18
diff changeset
388 <option value="Armadillo (Dasypus novemcinctus)">Armadillo (Dasypus novemcinctus)</option>
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
iracooke
parents: 18
diff changeset
389 <option value="Bushbaby (Otolemur garnettii)">Bushbaby (Otolemur garnettii)</option>
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
iracooke
parents: 18
diff changeset
390 <option value="C. elegans (Caenorhabditis elegans)">C. elegans (Caenorhabditis elegans)</option>
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
iracooke
parents: 18
diff changeset
391 <option value="C.intestinalis (Ciona intestinalis)">C.intestinalis (Ciona intestinalis)</option>
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
iracooke
parents: 18
diff changeset
392 <option value="C.savignyi (Ciona savignyi)">C.savignyi (Ciona savignyi)</option>
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
iracooke
parents: 18
diff changeset
393 <option value="Cat (Felis catus)">Cat (Felis catus)</option>
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
iracooke
parents: 18
diff changeset
394 <option value="Cave fish (Astyanax mexicanus)">Cave fish (Astyanax mexicanus)</option>
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
iracooke
parents: 18
diff changeset
395 <option value="Chicken (Gallus gallus)">Chicken (Gallus gallus)</option>
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
iracooke
parents: 18
diff changeset
396 <option value="Chimpanzee (Pan troglodytes)">Chimpanzee (Pan troglodytes)</option>
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
iracooke
parents: 18
diff changeset
397 <option value="Chinese softshell turtle (Pelodiscus sinensis)">Chinese softshell turtle (Pelodiscus sinensis)</option>
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
iracooke
parents: 18
diff changeset
398 <option value="Cod (Gadus morhua)">Cod (Gadus morhua)</option>
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
iracooke
parents: 18
diff changeset
399 <option value="Coelacanth (Latimeria chalumnae)">Coelacanth (Latimeria chalumnae)</option>
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
iracooke
parents: 18
diff changeset
400 <option value="Cow (Bos taurus)">Cow (Bos taurus)</option>
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
iracooke
parents: 18
diff changeset
401 <option value="Dog (Canis lupus familiaris)">Dog (Canis lupus familiaris)</option>
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
iracooke
parents: 18
diff changeset
402 <option value="Dolphin (Tursiops truncatus)">Dolphin (Tursiops truncatus)</option>
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
iracooke
parents: 18
diff changeset
403 <option value="Duck (Anas platyrhynchos)">Duck (Anas platyrhynchos)</option>
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
iracooke
parents: 18
diff changeset
404 <option value="Elephant (Loxodonta africana)">Elephant (Loxodonta africana)</option>
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
iracooke
parents: 18
diff changeset
405 <option value="Ferret (Mustela putorius furo)">Ferret (Mustela putorius furo)</option>
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
iracooke
parents: 18
diff changeset
406 <option value="Flycatcher (Ficedula albicollis)">Flycatcher (Ficedula albicollis)</option>
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
iracooke
parents: 18
diff changeset
407 <option value="Fruitfly (Drosophila melanogaster)">Fruitfly (Drosophila melanogaster)</option>
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
iracooke
parents: 18
diff changeset
408 <option value="Fugu (Takifugu rubripes)">Fugu (Takifugu rubripes)</option>
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
iracooke
parents: 18
diff changeset
409 <option value="Gibbon (Nomascus leucogenys)">Gibbon (Nomascus leucogenys)</option>
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
iracooke
parents: 18
diff changeset
410 <option value="Gorilla (Gorilla gorilla gorilla)">Gorilla (Gorilla gorilla gorilla)</option>
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
iracooke
parents: 18
diff changeset
411 <option value="Guinea Pig (Cavia porcellus)">Guinea Pig (Cavia porcellus)</option>
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
iracooke
parents: 18
diff changeset
412 <option value="Hedgehog (Erinaceus europaeus)">Hedgehog (Erinaceus europaeus)</option>
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
iracooke
parents: 18
diff changeset
413 <option value="Horse (Equus caballus)">Horse (Equus caballus)</option>
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
iracooke
parents: 18
diff changeset
414 <option value="Human (Homo sapiens)">Human (Homo sapiens)</option>
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
iracooke
parents: 18
diff changeset
415 <option value="Hyrax (Procavia capensis)">Hyrax (Procavia capensis)</option>
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
iracooke
parents: 18
diff changeset
416 <option value="Kangaroo rat (Dipodomys ordii)">Kangaroo rat (Dipodomys ordii)</option>
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
iracooke
parents: 18
diff changeset
417 <option value="Lamprey (Petromyzon marinus)">Lamprey (Petromyzon marinus)</option>
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
iracooke
parents: 18
diff changeset
418 <option value="Lesser hedgehog tenrec (Echinops telfairi)">Lesser hedgehog tenrec (Echinops telfairi)</option>
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
iracooke
parents: 18
diff changeset
419 <option value="Macaque (Macaca mulatta)">Macaque (Macaca mulatta)</option>
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
iracooke
parents: 18
diff changeset
420 <option value="Marmoset (Callithrix jacchus)">Marmoset (Callithrix jacchus)</option>
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
iracooke
parents: 18
diff changeset
421 <option value="Medaka (Oryzias latipes)">Medaka (Oryzias latipes)</option>
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
iracooke
parents: 18
diff changeset
422 <option value="Megabat (Pteropus vampyrus)">Megabat (Pteropus vampyrus)</option>
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
iracooke
parents: 18
diff changeset
423 <option value="Microbat (Myotis lucifugus)">Microbat (Myotis lucifugus)</option>
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
iracooke
parents: 18
diff changeset
424 <option value="Mouse (Mus musculus)">Mouse (Mus musculus)</option>
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
iracooke
parents: 18
diff changeset
425 <option value="Mouse Lemur (Microcebus murinus)">Mouse Lemur (Microcebus murinus)</option>
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
iracooke
parents: 18
diff changeset
426 <option value="Opossum (Monodelphis domestica)">Opossum (Monodelphis domestica)</option>
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
iracooke
parents: 18
diff changeset
427 <option value="Orangutan (Pongo abelii)">Orangutan (Pongo abelii)</option>
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
iracooke
parents: 18
diff changeset
428 <option value="Panda (Ailuropoda melanoleuca)">Panda (Ailuropoda melanoleuca)</option>
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
iracooke
parents: 18
diff changeset
429 <option value="Pig (Sus scrofa)">Pig (Sus scrofa)</option>
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
iracooke
parents: 18
diff changeset
430 <option value="Pika (Ochotona princeps)">Pika (Ochotona princeps)</option>
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
iracooke
parents: 18
diff changeset
431 <option value="Platyfish (Xiphophorus maculatus)">Platyfish (Xiphophorus maculatus)</option>
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
iracooke
parents: 18
diff changeset
432 <option value="Platypus (Ornithorhynchus anatinus)">Platypus (Ornithorhynchus anatinus)</option>
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
iracooke
parents: 18
diff changeset
433 <option value="Rabbit (Oryctolagus cuniculus)">Rabbit (Oryctolagus cuniculus)</option>
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
iracooke
parents: 18
diff changeset
434 <option value="Rat (Rattus norvegicus)">Rat (Rattus norvegicus)</option>
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
iracooke
parents: 18
diff changeset
435 <option value="S. cerevisiae (Saccharomyces cerevisiae)">S. cerevisiae (Saccharomyces cerevisiae)</option>
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
iracooke
parents: 18
diff changeset
436 <option value="Sheep (Ovis aries)">Sheep (Ovis aries)</option>
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
iracooke
parents: 18
diff changeset
437 <option value="Shrew (Sorex araneus)">Shrew (Sorex araneus)</option>
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
iracooke
parents: 18
diff changeset
438 <option value="Sloth (Choloepus hoffmanni)">Sloth (Choloepus hoffmanni)</option>
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
iracooke
parents: 18
diff changeset
439 <option value="Spotted gar (Lepisosteus oculatus)">Spotted gar (Lepisosteus oculatus)</option>
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
iracooke
parents: 18
diff changeset
440 <option value="Squirrel (Ictidomys tridecemlineatus)">Squirrel (Ictidomys tridecemlineatus)</option>
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
iracooke
parents: 18
diff changeset
441 <option value="Stickleback (Gasterosteus aculeatus)">Stickleback (Gasterosteus aculeatus)</option>
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
iracooke
parents: 18
diff changeset
442 <option value="Tarsier (Tarsius syrichta)">Tarsier (Tarsius syrichta)</option>
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
iracooke
parents: 18
diff changeset
443 <option value="Tasmanian devil (Sarcophilus harrisii)">Tasmanian devil (Sarcophilus harrisii)</option>
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
iracooke
parents: 18
diff changeset
444 <option value="Tetraodon (Tetraodon nigroviridis)">Tetraodon (Tetraodon nigroviridis)</option>
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
iracooke
parents: 18
diff changeset
445 <option value="Tilapia (Oreochromis niloticus)">Tilapia (Oreochromis niloticus)</option>
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
iracooke
parents: 18
diff changeset
446 <option value="Tree Shrew (Tupaia belangeri)">Tree Shrew (Tupaia belangeri)</option>
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
iracooke
parents: 18
diff changeset
447 <option value="Turkey (Meleagris gallopavo)">Turkey (Meleagris gallopavo)</option>
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
iracooke
parents: 18
diff changeset
448 <option value="Vervet-AGM (Chlorocebus sabaeus)">Vervet-AGM (Chlorocebus sabaeus)</option>
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
iracooke
parents: 18
diff changeset
449 <option value="Wallaby (Macropus eugenii)">Wallaby (Macropus eugenii)</option>
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
iracooke
parents: 18
diff changeset
450 <option value="Xenopus (Xenopus tropicalis)">Xenopus (Xenopus tropicalis)</option>
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
iracooke
parents: 18
diff changeset
451 <option value="Zebra Finch (Taeniopygia guttata)">Zebra Finch (Taeniopygia guttata)</option>
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
iracooke
parents: 18
diff changeset
452 <option value="Zebrafish (Danio rerio)">Zebrafish (Danio rerio)</option>
18
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
453 </param>
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
454 </when>
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
455 </conditional>
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
456 <conditional name="processing_options">
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
457 <param name="processing_options_selector" type="select" label="Specify Advanced PeptideShaker Processing Options">
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
458 <option value="no" selected="True">Default Processing Options</option>
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
459 <option value="yes">Advanced Processing Options</option>
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
460 </param>
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
461 <when value="no" />
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
462 <when value="yes">
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
463 <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
464 <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
465 <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
466 <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
467 help="default 95%: '95.0'" />
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
468 <conditional name="ptm_score">
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
469 <param name="ptm_score_selector" type="select" label="The PTM probabilistic score to use for PTM localization">
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
470 <option value="0" selected="True">A-score</option>
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
471 <option value="1">PhosphoRS</option>
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
472 </param>
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
473 <when value="0" />
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
474 <when value="1">
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
475 <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
476 <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
477 help="Automatic mode will be used if not set" />
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
478 </when>
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
479 </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
480 <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
481 <!-- SKIPPING -protein_fraction_mw_confidence ${processing_options.protein_fraction_mw_confidence} -->
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
482 </when>
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
483 </conditional>
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
484 <conditional name="filtering_options">
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
485 <param name="filtering_options_selector" type="select" label="Specify Advanced Filtering Options"
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
486 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
487 <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
488 <option value="yes">Advanced Filtering Options</option>
18
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
489 </param>
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
490 <when value="no" />
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
491 <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
492 <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
493 <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
494 <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
495 help="Next option specifies units (Da or ppm)" />
18
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
496 <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
497 <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
498 <option value="0">Daltons</option>
18
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
499 </param>
20
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
iracooke
parents: 18
diff changeset
500 <!--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
501 <!--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
502 <!--param name="max_mascot_e" label="Maximum Mascot e-value filter" value="100" type="float" help="" /-->
18
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
503 <param name="exclude_unknown_ptms" label="Exclude Unknown PTMs" type="boolean" truevalue="1" falsevalue="0" checked="true" />
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
504 </when>
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
505 </conditional>
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
506 <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
507 <option value="zip">Zip File for import to Desktop App</option>
18
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
508 <option value="mzidentML" selected="True">mzidentML File</option>
20
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
iracooke
parents: 18
diff changeset
509 <option value="3" >PSM Report</option>
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
iracooke
parents: 18
diff changeset
510 <option value="4" >Peptide Phosphorylation Report</option>
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
iracooke
parents: 18
diff changeset
511 <option value="5" >Peptide Report</option>
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
iracooke
parents: 18
diff changeset
512 <option value="6" >Protein Phosphorylation Report</option>
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
iracooke
parents: 18
diff changeset
513 <option value="7" >Protein Report</option>
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
iracooke
parents: 18
diff changeset
514 <option value="2">PSM Phosphorylation Report</option>
18
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
515 <option value="0">Certificate of Analysis</option>
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
516 <option value="1">Hierarchical Report</option>
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
517 <option value="cps">CPS file</option>
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
518 <validator type="no_options" message="Please select at least one output file" />
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
519 </param>
20
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
iracooke
parents: 18
diff changeset
520
18
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
521 </inputs>
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
522 <outputs>
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
523 <data format="mzid" name="mzidentML" from_work_dir="output.mzid" label="${tool.name} on ${on_string}: mzidentML file">
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
524 <filter>'mzidentML' in outputs</filter>
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
525 </data>
20
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
iracooke
parents: 18
diff changeset
526 <data format="peptideshaker_archive" name="output_cps" from_work_dir="peptideshaker_output.cps" label="${tool.name} on ${on_string}: CPS file">
18
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
527 <filter>'cps' in outputs</filter>
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
528 </data>
20
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
iracooke
parents: 18
diff changeset
529 <data format="zip" name="output_zip" from_work_dir="peptideshaker_output.zip" label="${tool.name} on ${on_string}: Archive">
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
iracooke
parents: 18
diff changeset
530 <filter>'zip' in outputs</filter>
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
iracooke
parents: 18
diff changeset
531 </data>
18
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
532 <data format="txt" name="output_certificate" from_work_dir="certificate.txt" label="${tool.name} on ${on_string}: Parameters">
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
533 <filter>'0' in outputs</filter>
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
534 </data>
20
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
iracooke
parents: 18
diff changeset
535 <data format="tabular" name="output_hierarchical" from_work_dir="hierarchical.txt" label="${tool.name} on ${on_string}: Hierarchical Report">
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
iracooke
parents: 18
diff changeset
536 <filter>'1' in outputs</filter>
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
iracooke
parents: 18
diff changeset
537 </data>
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
iracooke
parents: 18
diff changeset
538 <data format="tabular" name="output_psm_phosphorylation" from_work_dir="psm_phospho.txt" label="${tool.name} on ${on_string}: PSM Phosphorylation Report">
18
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
539 <filter>'2' in outputs</filter>
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
540 </data>
20
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
iracooke
parents: 18
diff changeset
541 <data format="tabular" name="output_psm" from_work_dir="psm.txt" label="${tool.name} on ${on_string}: PSM Report">
18
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
542 <filter>'3' in outputs</filter>
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
543 </data>
20
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
iracooke
parents: 18
diff changeset
544 <data format="tabular" name="output_peptides_phosphorylation" from_work_dir="peptides_phospho.txt" label="${tool.name} on ${on_string}: Peptide Phosphorylation Report">
18
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
545 <filter>'4' in outputs</filter>
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
546 </data>
20
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
iracooke
parents: 18
diff changeset
547 <data format="tabular" name="output_peptides" from_work_dir="peptides.txt" label="${tool.name} on ${on_string}: Peptide Report">
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
iracooke
parents: 18
diff changeset
548 <filter>'5' in outputs</filter>
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
iracooke
parents: 18
diff changeset
549 </data>
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
iracooke
parents: 18
diff changeset
550 <data format="tabular" name="output_proteins_phosphorylation" from_work_dir="proteins_phospho.txt" label="${tool.name} on ${on_string}: Protein Phosphorylation Report">
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
iracooke
parents: 18
diff changeset
551 <filter>'6' in outputs</filter>
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
iracooke
parents: 18
diff changeset
552 </data>
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
iracooke
parents: 18
diff changeset
553 <data format="tabular" name="output_proteins" from_work_dir="proteins.txt" label="${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
554 <filter>'7' in outputs</filter>
18
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
555 </data>
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
556 </outputs>
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
557 <tests>
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
558 <test>
21
dfaea053e32f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 327a3944f2f56668d607c3d6cb08ae7d588e208c
iracooke
parents: 20
diff changeset
559 <param name="searchgui_input" value="tiny_searchgui_result1.zip" ftype="searchgui_archive"/>
18
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
560 <param name="species_type_selector" value="no_species_type"/>
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
561 <param name="processing_options_selector" value="no"/>
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
562 <param name="filtering_options_selector" value="no"/>
20
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
iracooke
parents: 18
diff changeset
563 <param name="outputs" value="zip,cps,3"/>
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
iracooke
parents: 18
diff changeset
564 <output name="output_zip" file="peptide_shaker_result1.zip" ftype="zip" compare="sim_size" delta="600" />
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
iracooke
parents: 18
diff changeset
565 <output name="output_cps" file="peptide_shaker_result1.cps" ftype="peptideshaker_archive" compare="sim_size" delta="600" />
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
iracooke
parents: 18
diff changeset
566 <output name="output_psm" file="peptide_shaker_psm_result1.tabular" ftype="tabular" />
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
iracooke
parents: 18
diff changeset
567 </test>
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
iracooke
parents: 18
diff changeset
568 <test>
21
dfaea053e32f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 327a3944f2f56668d607c3d6cb08ae7d588e208c
iracooke
parents: 20
diff changeset
569 <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
570 <param name="species_type_selector" value="no_species_type"/>
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
iracooke
parents: 18
diff changeset
571 <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
572 <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
573 <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
574 <param name="outputs" value="0,1,2,3,4,5,6,7"/>
21
dfaea053e32f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 327a3944f2f56668d607c3d6cb08ae7d588e208c
iracooke
parents: 20
diff changeset
575 <output name="output_certificate" file="peptide_shaker_certificate_result2.txt" ftype="txt" lines_diff="6"/>
20
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
iracooke
parents: 18
diff changeset
576 <output name="output_hierarchical" file="peptide_shaker_hierarchical_result2.tabular" ftype="tabular" />
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
iracooke
parents: 18
diff changeset
577 <output name="output_psm" file="peptide_shaker_psm_result2.tabular" ftype="tabular" />
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
iracooke
parents: 18
diff changeset
578 <output name="output_psm_phosphorylation" file="peptide_shaker_psm_phoshorylation_result2.tabular" ftype="tabular" />
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
iracooke
parents: 18
diff changeset
579 <output name="output_peptides" file="peptide_shaker_peptides_result2.tabular" ftype="tabular" />
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
iracooke
parents: 18
diff changeset
580 <output name="output_peptides_phosphorylation" file="peptide_shaker_peptides_phoshorylation_result2.tabular" ftype="tabular" />
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
iracooke
parents: 18
diff changeset
581 <output name="output_proteins" file="peptide_shaker_proteins_result2.tabular" ftype="tabular" />
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
iracooke
parents: 18
diff changeset
582 <output name="output_proteins_phosphorylation" file="peptide_shaker_proteins_phoshorylation_result2.tabular" ftype="tabular" />
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
iracooke
parents: 18
diff changeset
583 </test>
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
iracooke
parents: 18
diff changeset
584 <test>
21
dfaea053e32f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 327a3944f2f56668d607c3d6cb08ae7d588e208c
iracooke
parents: 20
diff changeset
585 <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
586 <param name="species_type_selector" value="Vertebrates"/>
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
iracooke
parents: 18
diff changeset
587 <param name="species" value="Human (Homo sapiens)"/>
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
iracooke
parents: 18
diff changeset
588 <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
589 <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
590 <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
591 <param name="outputs" value="5"/>
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
iracooke
parents: 18
diff changeset
592 <output name="output_peptides" file="peptide_shaker_peptides_result3.tabular" ftype="tabular" />
18
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
593 </test>
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
594 </tests>
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
595 <help>
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
596 **What it does**
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
597
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
598 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
599
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
600 https://code.google.com/p/peptide-shaker/
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
601
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
602 https://code.google.com/p/searchgui/
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
603
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
604 ----
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
605
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
606 Reports
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
607 =======
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
608
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
609
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
610 PSM Report
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
611 ----------
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
612
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
613 * 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
614 * 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
615 * Variable Modifications: The variable modifications
18
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
616 * D-score: D-score for variable PTM localization
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
617 * probabilistic PTM score: The probabilistic score (e.g. A-score or PhosphoRS) used for variable PTM localization.
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
618 * Localization Confidence: The confidence in variable PTM localization.
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
619 * Fixed Modifications: The fixed modifications.
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
620 * Spectrum File: The spectrum file.
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
621 * Spectrum Title: The title of the spectrum.
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
622 * Spectrum Scan Number: The spectrum scan number.
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
623 * RT: Retention time
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
624 * m/z: Measured m/z
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
625 * Measured Charge: The charge as given in the spectrum file.
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
626 * Identification Charge: The charge as inferred by the search engine.
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
627 * Theoretical Mass: The theoretical mass of the peptide.
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
628 * Isotope Number: The isotope number targetted by the instrument.
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
629 * Precursor m/z Error: The precursor m/z matching error.
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
630 * Score: Score of the retained peptide as a combination of the algorithm scores (used to rank PSMs).
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
631 * Confidence: Confidence in percent associated to the retained PSM.
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
632 * Decoy: Indicates whether the peptide is a decoy (1: yes, 0: no).
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
633 * Validation: Indicates the validation level of the protein group.
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
634
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
635
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
636 Protein Report
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
637 --------------
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
638
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
639 * Main Accession: Main accession of the protein group.
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
640 * Description: Description of the protein designed by the main accession.
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
641 * Gene Name: The gene names of the Ensembl gene ID associated to the main accession.
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
642 * Chromosome: The chromosome of the Ensembl gene ID associated to the main accession.
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
643 * PI: Protein Inference status of the protein group.
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
644 * Secondary Accessions: Other accessions in the protein group (alphabetical order).
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
645 * Protein Group: The complete protein group (alphabetical order).
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
646 * #Peptides: Total number of peptides.
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
647 * #Validated Peptides: Number of validated peptides.
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
648 * #Unique: Total number of peptides unique to this protein group.
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
649 * #PSMs: Number of PSMs
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
650 * #Validated PSMs: Number of validated PSMs
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
651 * Coverage (%): Sequence coverage in percent of the protein designed by the main accession.
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
652 * 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
653 * MW (kDa): Molecular Weight.
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
654 * Spectrum Counting NSAF: Normalized Spectrum Abundance Factor (NSAF)
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
655 * Spectrum Counting emPAI: exponentially modified Protein Abundance Index (emPAI)
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
656 * 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
657 * 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
658 * Score: Score of the protein group.
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
659 * Confidence: Confidence in percent associated to the protein group.
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
660 * Decoy: Indicates whether the protein group is a decoy (1: yes, 0: no).
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
661 * Validation: Indicates the validation level of the protein group.
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
662
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
663
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
664 Peptide Report
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
665 --------------
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
666
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
667
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
668 * Protein(s): Protein(s) to which this peptide can be attached.
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
669 * AAs Before: The amino-acids before the sequence.
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
670 * Sequence: Sequence of the peptide.
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
671 * AAs After: The amino-acids after the sequence.
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
672 * Modified Sequence: The peptide sequence annotated with variable modifications.
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
673 * Variable Modifications: The variable modifications.
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
674 * Localization Confidence: The confidence in PTMs localization.
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
675 * Fixed Modifications: The fixed modifications.
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
676 * #Validated PSMs: Number of validated PSMs.
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
677 * #PSMs: Number of PSMs.
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
678 * Score: Score of the peptide.
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
679 * Confidence: Confidence in percent associated to the peptide.
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
680 * Decoy: Indicates whether the peptide is a decoy (1: yes, 0: no).
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
681 * Validation: Indicates the validation level of the protein group.
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
682
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
683
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
684 Hierachical Report
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
685 ------------------
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
686
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
687 * Main Accession: Main accession of the protein group.
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
688 * Description: Description of the protein designed by the main accession.
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
689 * PI: Protein Inference status of the protein group.
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
690 * Secondary Accessions: Other accessions in the protein group (alphabetical order).
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
691 * Protein Group: The complete protein group (alphabetical order).
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
692 * #Peptides: Total number of peptides.
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
693 * #Validated Peptides: Number of validated peptides.
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
694 * #Unique: Total number of peptides unique to this protein group.
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
695 * #PSMs: Number of PSMs
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
696 * #Validated PSMs: Number of validated PSMs
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
697 * Coverage (%): Sequence coverage in percent of the protein designed by the main accession.
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
698 * 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
699 * MW (kDa): Molecular Weight.
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
700 * Spectrum Counting NSAF: Normalized Spectrum Abundance Factor (NSAF)
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
701 * Spectrum Counting emPAI: exponentially modified Protein Abundance Index (emPAI)
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
702 * Confident Modification Sites: # Confident Modification Sites List of the sites where a variable modification was confidently localized.
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
703 * Other Modification Sites: # Other Modification Sites List of the non-confident sites where a variable modification was localized.
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
704 * Score: Score of the protein group.
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
705 * Confidence: Confidence in percent associated to the protein group.
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
706 * Decoy: Indicates whether the protein group is a decoy (1: yes, 0: no).
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
707 * Validation: Indicates the validation level of the protein group.
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
708 * Protein(s): Protein(s) to which this peptide can be attached.
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
709 * AAs Before: The amino-acids before the sequence.
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
710 * Sequence: Sequence of the peptide.
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
711 * AAs After: The amino-acids after the sequence.
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
712 * Variable Modifications: The variable modifications.
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
713 * Localization Confidence: The confidence in PTMs localization.
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
714 * Fixed Modifications: The fixed modifications.
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
715 * #Validated PSMs: Number of validated PSMs.
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
716 * #PSMs: Number of PSMs.
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
717 * Score: Score of the peptide.
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
718 * Confidence: Confidence in percent associated to the peptide.
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
719 * Decoy: Indicates whether the peptide is a decoy (1: yes, 0: no).
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
720 * Validation: Indicates the validation level of the protein group.
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
721 * Protein(s): Protein(s) to which the peptide can be attached.
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
722 * Sequence: Sequence of the peptide.
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
723 * Modified Sequence: The peptide sequence annotated with variable modifications.
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
724 * Variable Modifications: The variable modifications.
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
725 * D-score: D-score for variable PTM localization.
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
726 * probabilistic PTM score: The probabilistic score (e.g. A-score or PhosphoRS) used for variable PTM localization.
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
727 * Localization Confidence: The confidence in variable PTM localization.
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
728 * Fixed Modifications: The fixed modifications.
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
729 * Spectrum File: The spectrum file.
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
730 * Spectrum Title: The title of the spectrum.
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
731 * Spectrum Scan Number: The spectrum scan number.
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
732 * RT: Retention time
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
733 * m/z: Measured m/z
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
734 * Measured Charge: The charge as given in the spectrum file.
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
735 * Identification Charge: The charge as inferred by the search engine.
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
736 * Theoretical Mass: The theoretical mass of the peptide.
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
737 * Isotope Number: The isotope number targetted by the instrument.
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
738 * Precursor m/z Error: The precursor m/z matching error.
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
739 * Score: Score of the retained peptide as a combination of the algorithm scores (used to rank PSMs).
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
740 * Confidence: Confidence in percent associated to the retained PSM.
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
741 * Decoy: Indicates whether the peptide is a decoy (1: yes, 0: no).
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
742 * Validation: Indicates the validation level of the protein group.
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
743
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
744
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
745 ------
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
746
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
747 **Citation**
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
748
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
749 To cite the underlying tools (PeptideShaker and SearchGUI) please refer to the list of papers at http://peptide-shaker.googlecode.com
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
750
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
751 If you use this tool in Galaxy, please cite Chilton J, Ira Cooke, Bjoern Gruening et al. https://bitbucket.org/galaxyp/peptideshaker
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
752 </help>
20
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
iracooke
parents: 18
diff changeset
753 <expand macro="citations" />
18
a5f9b959d5d1 Uploaded
iracooke
parents:
diff changeset
754 </tool>