peptideshaker: peptide_shaker.xml annotate

annotate peptide_shaker.xml @ 45:5fa8b409599e draft

planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 62699d7e79ddbe3374ed28dfeb9002e8efa4c544

author	galaxyp
date	Mon, 30 Apr 2018 04:41:50 -0400
parents	f35bb9d0c93e
children	baeced706dbc

rev	line source
45 5fa8b409599e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 62699d7e79ddbe3374ed28dfeb9002e8efa4c544 galaxyp parents: 44 diff changeset	1 <tool id="peptide_shaker" name="Peptide Shaker" version="1.16.20">
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>
45 5fa8b409599e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 62699d7e79ddbe3374ed28dfeb9002e8efa4c544 galaxyp parents: 44 diff changeset	9 <requirement type="package" version="1.16.20">peptide-shaker</requirement>
21 dfaea053e32f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 327a3944f2f56668d607c3d6cb08ae7d588e208c iracooke parents: 20 diff changeset	10 </requirements>
20 2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b iracooke parents: 18 diff changeset	11 <expand macro="stdio" />
18 a5f9b959d5d1 Uploaded iracooke parents: diff changeset	12 <command>
20 2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b iracooke parents: 18 diff changeset	13 <![CDATA[
18 a5f9b959d5d1 Uploaded iracooke parents: diff changeset	14 #from datetime import datetime
a5f9b959d5d1 Uploaded iracooke parents: diff changeset	15 #set $exp_str = "Galaxy_Experiment_%s" % datetime.now().strftime("%Y%m%d%H%M%s")
a5f9b959d5d1 Uploaded iracooke parents: diff changeset	16 #set $samp_str = "Sample_%s" % datetime.now().strftime("%Y%m%d%H%M%s")
20 2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b iracooke parents: 18 diff changeset	17 #set $temp_stderr = "peptideshaker_stderr"
30 ad60446b1e93 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit bdb5ee12705a3494eee96d1963f16f68bbe41d5c galaxyp parents: 29 diff changeset	18 #set $bin_dir = "bin"
18 a5f9b959d5d1 Uploaded iracooke parents: diff changeset	19
22 e3be595c0bf5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 5ca27ef280bee8b65fd3d0d2cd5ff280a2cebb3d iracooke parents: 21 diff changeset	20
18 a5f9b959d5d1 Uploaded iracooke parents: diff changeset	21 mkdir output_reports;
a5f9b959d5d1 Uploaded iracooke parents: diff changeset	22 cwd=`pwd`;
a5f9b959d5d1 Uploaded iracooke parents: diff changeset	23
20 2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b iracooke parents: 18 diff changeset	24 ln -s '$searchgui_input' searchgui_input.zip &&
30 ad60446b1e93 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit bdb5ee12705a3494eee96d1963f16f68bbe41d5c galaxyp parents: 29 diff changeset	25 jar xvf searchgui_input.zip SEARCHGUI_IdentificationParameters.par &&
18 a5f9b959d5d1 Uploaded iracooke parents: diff changeset	26 ######################
a5f9b959d5d1 Uploaded iracooke parents: diff changeset	27 ## PeptideShakerCLI ##
a5f9b959d5d1 Uploaded iracooke parents: diff changeset	28 ######################
30 ad60446b1e93 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit bdb5ee12705a3494eee96d1963f16f68bbe41d5c galaxyp parents: 29 diff changeset	29 (peptide-shaker eu.isas.peptideshaker.cmd.PeptideShakerCLI
ad60446b1e93 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit bdb5ee12705a3494eee96d1963f16f68bbe41d5c galaxyp parents: 29 diff changeset	30 --exec_dir="\$cwd/${bin_dir}"
20 2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b iracooke parents: 18 diff changeset	31 -temp_folder \$cwd/PeptideShakerCLI
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b iracooke parents: 18 diff changeset	32 -experiment '$exp_str'
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b iracooke parents: 18 diff changeset	33 -sample '$samp_str'
18 a5f9b959d5d1 Uploaded iracooke parents: diff changeset	34 -replicate 1
20 2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b iracooke parents: 18 diff changeset	35 -identification_files \$cwd/searchgui_input.zip
30 ad60446b1e93 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit bdb5ee12705a3494eee96d1963f16f68bbe41d5c galaxyp parents: 29 diff changeset	36 -id_params \$cwd/SEARCHGUI_IdentificationParameters.par
24 815f93bb3e1b Uploaded galaxyp parents: 22 diff changeset	37 -out \$cwd/peptideshaker_output.cpsx
20 2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b iracooke parents: 18 diff changeset	38 -zip \$cwd/peptideshaker_output.zip
44 f35bb9d0c93e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 981be1bde91d6d565693cd691553f77465e653bb galaxyp parents: 38 diff changeset	39 #set $cleaned_list = str($outputs).split(',')
f35bb9d0c93e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 981be1bde91d6d565693cd691553f77465e653bb galaxyp parents: 38 diff changeset	40 #if 'cps' in $cleaned_list:
f35bb9d0c93e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 981be1bde91d6d565693cd691553f77465e653bb galaxyp parents: 38 diff changeset	41 #silent $cleaned_list.remove('cps')
f35bb9d0c93e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 981be1bde91d6d565693cd691553f77465e653bb galaxyp parents: 38 diff changeset	42 #end if
f35bb9d0c93e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 981be1bde91d6d565693cd691553f77465e653bb galaxyp parents: 38 diff changeset	43 #if 'mzidentML' in $cleaned_list:
f35bb9d0c93e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 981be1bde91d6d565693cd691553f77465e653bb galaxyp parents: 38 diff changeset	44 #silent $cleaned_list.remove('mzidentML')
f35bb9d0c93e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 981be1bde91d6d565693cd691553f77465e653bb galaxyp parents: 38 diff changeset	45 #end if
f35bb9d0c93e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 981be1bde91d6d565693cd691553f77465e653bb galaxyp parents: 38 diff changeset	46 #if 'zip' in $cleaned_list:
f35bb9d0c93e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 981be1bde91d6d565693cd691553f77465e653bb galaxyp parents: 38 diff changeset	47 #silent $cleaned_list.remove('zip')
f35bb9d0c93e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 981be1bde91d6d565693cd691553f77465e653bb galaxyp parents: 38 diff changeset	48 #end if
f35bb9d0c93e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 981be1bde91d6d565693cd691553f77465e653bb galaxyp parents: 38 diff changeset	49 #if len($cleaned_list) > 0
f35bb9d0c93e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 981be1bde91d6d565693cd691553f77465e653bb galaxyp parents: 38 diff changeset	50 ## Only numbers are left over. These corresponds to different reports.
f35bb9d0c93e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 981be1bde91d6d565693cd691553f77465e653bb galaxyp parents: 38 diff changeset	51 -reports #echo ','.join($cleaned_list)#
f35bb9d0c93e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 981be1bde91d6d565693cd691553f77465e653bb galaxyp parents: 38 diff changeset	52 #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	53
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b iracooke parents: 18 diff changeset	54 -threads "\${GALAXY_SLOTS:-12}"
18 a5f9b959d5d1 Uploaded iracooke parents: diff changeset	55
a5f9b959d5d1 Uploaded iracooke parents: diff changeset	56 ##Optional processing parameters:
a5f9b959d5d1 Uploaded iracooke parents: diff changeset	57 #if $processing_options.processing_options_selector == "yes"
26 3ef5a7dd1a36 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6dcfe37e286523588aa2738599af8d3273290f28-dirty galaxyp parents: 25 diff changeset	58 -protein_fdr "${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	59 -peptide_fdr "${processing_options.peptide_fdr}"
3ef5a7dd1a36 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6dcfe37e286523588aa2738599af8d3273290f28-dirty galaxyp parents: 25 diff changeset	60 -psm_fdr "${processing_options.psm_fdr}"
18 a5f9b959d5d1 Uploaded iracooke parents: diff changeset	61 -ptm_score "${processing_options.ptm_score.ptm_score_selector}"
a5f9b959d5d1 Uploaded iracooke parents: diff changeset	62 #if $processing_options.ptm_score.ptm_score_selector == 1
a5f9b959d5d1 Uploaded iracooke parents: diff changeset	63 -score_neutral_losses "${processing_options.ptm_score.neutral_losses}"
a5f9b959d5d1 Uploaded iracooke parents: diff changeset	64 #if str($processing_options.ptm_score.ptm_threshold) != ''
a5f9b959d5d1 Uploaded iracooke parents: diff changeset	65 -ptm_threshold "${processing_options.ptm_score.ptm_threshold}"
a5f9b959d5d1 Uploaded iracooke parents: diff changeset	66 #end if
a5f9b959d5d1 Uploaded iracooke parents: diff changeset	67 #end if
38 79e37eff006d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 48984afa5f3d1b80ecbbff2847645c15acd81fe6 galaxyp parents: 37 diff changeset	68 -ptm_alignment "${processing_options.ptm_alignment}"
79e37eff006d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 48984afa5f3d1b80ecbbff2847645c15acd81fe6 galaxyp parents: 37 diff changeset	69 -ptm_sequence_matching_type "${processing_options.ptm_sequence_matching_type}"
18 a5f9b959d5d1 Uploaded iracooke parents: diff changeset	70 -protein_fraction_mw_confidence "${processing_options.protein_fraction_mw_confidence}"
a5f9b959d5d1 Uploaded iracooke parents: diff changeset	71 #end if
a5f9b959d5d1 Uploaded iracooke parents: diff changeset	72
a5f9b959d5d1 Uploaded iracooke parents: diff changeset	73 ##Optional filtering parameters:
a5f9b959d5d1 Uploaded iracooke parents: diff changeset	74 #if $filtering_options.filtering_options_selector == "yes":
26 3ef5a7dd1a36 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6dcfe37e286523588aa2738599af8d3273290f28-dirty galaxyp parents: 25 diff changeset	75 -import_peptide_length_min "${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	76 -import_peptide_length_max "${filtering_options.max_peptide_length}"
3ef5a7dd1a36 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6dcfe37e286523588aa2738599af8d3273290f28-dirty galaxyp parents: 25 diff changeset	77 -import_precurosor_mz "${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	78 -import_precurosor_mz_ppm "${filtering_options.max_precursor_error_type}"
20 2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b iracooke parents: 18 diff changeset	79 ##-max_xtandem_e "${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	80 ##-max_omssa_e "${filtering_options.max_omssa_e}"
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b iracooke parents: 18 diff changeset	81 ##-max_mascot_e "${filtering_options.max_mascot_e}"
18 a5f9b959d5d1 Uploaded iracooke parents: diff changeset	82 -exclude_unknown_ptms "${filtering_options.exclude_unknown_ptms}"
a5f9b959d5d1 Uploaded iracooke parents: diff changeset	83 #end if
a5f9b959d5d1 Uploaded iracooke parents: diff changeset	84
a5f9b959d5d1 Uploaded iracooke parents: diff changeset	85 2>> $temp_stderr)
20 2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b iracooke parents: 18 diff changeset	86
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b iracooke parents: 18 diff changeset	87 &&
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b iracooke parents: 18 diff changeset	88
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b iracooke parents: 18 diff changeset	89 echo "Running Reports";
18 a5f9b959d5d1 Uploaded iracooke parents: diff changeset	90
a5f9b959d5d1 Uploaded iracooke parents: diff changeset	91 ##################################
a5f9b959d5d1 Uploaded iracooke parents: diff changeset	92 ## PeptideShaker Report options ##
a5f9b959d5d1 Uploaded iracooke parents: diff changeset	93 ##################################
a5f9b959d5d1 Uploaded iracooke parents: diff changeset	94
a5f9b959d5d1 Uploaded iracooke parents: diff changeset	95 #if 'mzidentML' in str($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	96 echo "Generating mzIdentML";
30 ad60446b1e93 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit bdb5ee12705a3494eee96d1963f16f68bbe41d5c galaxyp parents: 29 diff changeset	97 (peptide-shaker eu.isas.peptideshaker.cmd.MzidCLI
ad60446b1e93 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit bdb5ee12705a3494eee96d1963f16f68bbe41d5c galaxyp parents: 29 diff changeset	98 --exec_dir="\$cwd/${bin_dir}"
20 2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b iracooke parents: 18 diff changeset	99 -in \$cwd/peptideshaker_output.zip
33 bce45e9e6d70 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312 galaxyp parents: 32 diff changeset	100 -output_file \$cwd/output.mzid
30 ad60446b1e93 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit bdb5ee12705a3494eee96d1963f16f68bbe41d5c galaxyp parents: 29 diff changeset	101 #if $contact_options.contact_options_selector == "yes":
ad60446b1e93 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit bdb5ee12705a3494eee96d1963f16f68bbe41d5c galaxyp parents: 29 diff changeset	102 -contact_first_name "$contact_options.contact_first_name"
ad60446b1e93 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit bdb5ee12705a3494eee96d1963f16f68bbe41d5c galaxyp parents: 29 diff changeset	103 -contact_last_name "$contact_options.contact_last_name"
ad60446b1e93 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit bdb5ee12705a3494eee96d1963f16f68bbe41d5c galaxyp parents: 29 diff changeset	104 -contact_email "$contact_options.contact_email"
ad60446b1e93 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit bdb5ee12705a3494eee96d1963f16f68bbe41d5c galaxyp parents: 29 diff changeset	105 -contact_address "$contact_options.contact_address"
ad60446b1e93 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit bdb5ee12705a3494eee96d1963f16f68bbe41d5c galaxyp parents: 29 diff changeset	106 #if str($contact_options.contact_url).strip() != '':
ad60446b1e93 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit bdb5ee12705a3494eee96d1963f16f68bbe41d5c galaxyp parents: 29 diff changeset	107 -contact_url = "$contact_options.contact_url"
ad60446b1e93 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit bdb5ee12705a3494eee96d1963f16f68bbe41d5c galaxyp parents: 29 diff changeset	108 #end if
ad60446b1e93 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit bdb5ee12705a3494eee96d1963f16f68bbe41d5c galaxyp parents: 29 diff changeset	109 -organization_name "$contact_options.organization_name"
ad60446b1e93 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit bdb5ee12705a3494eee96d1963f16f68bbe41d5c galaxyp parents: 29 diff changeset	110 -organization_email "$contact_options.organization_email"
ad60446b1e93 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit bdb5ee12705a3494eee96d1963f16f68bbe41d5c galaxyp parents: 29 diff changeset	111 -organization_address "$contact_options.organization_address"
ad60446b1e93 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit bdb5ee12705a3494eee96d1963f16f68bbe41d5c galaxyp parents: 29 diff changeset	112 #if str($contact_options.organization_url).strip() != '':
ad60446b1e93 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit bdb5ee12705a3494eee96d1963f16f68bbe41d5c galaxyp parents: 29 diff changeset	113 -organization_url = "$contact_options.organization_url"
ad60446b1e93 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit bdb5ee12705a3494eee96d1963f16f68bbe41d5c galaxyp parents: 29 diff changeset	114 #end if
ad60446b1e93 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit bdb5ee12705a3494eee96d1963f16f68bbe41d5c galaxyp parents: 29 diff changeset	115 #else:
ad60446b1e93 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit bdb5ee12705a3494eee96d1963f16f68bbe41d5c galaxyp parents: 29 diff changeset	116 -contact_first_name "Proteomics"
ad60446b1e93 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit bdb5ee12705a3494eee96d1963f16f68bbe41d5c galaxyp parents: 29 diff changeset	117 -contact_last_name "Galaxy"
ad60446b1e93 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit bdb5ee12705a3494eee96d1963f16f68bbe41d5c galaxyp parents: 29 diff changeset	118 -contact_email "galaxyp@umn.edu"
ad60446b1e93 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit bdb5ee12705a3494eee96d1963f16f68bbe41d5c galaxyp parents: 29 diff changeset	119 -contact_address "galaxyp@umn.edu"
ad60446b1e93 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit bdb5ee12705a3494eee96d1963f16f68bbe41d5c galaxyp parents: 29 diff changeset	120 -organization_name "University of Minnesota"
ad60446b1e93 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit bdb5ee12705a3494eee96d1963f16f68bbe41d5c galaxyp parents: 29 diff changeset	121 -organization_email "galaxyp@umn.edu"
ad60446b1e93 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit bdb5ee12705a3494eee96d1963f16f68bbe41d5c galaxyp parents: 29 diff changeset	122 -organization_address "Minneapolis, MN 55455, Vereinigte Staaten"
ad60446b1e93 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit bdb5ee12705a3494eee96d1963f16f68bbe41d5c galaxyp parents: 29 diff changeset	123 #end if
44 f35bb9d0c93e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 981be1bde91d6d565693cd691553f77465e653bb galaxyp parents: 38 diff changeset	124 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	125 &&
18 a5f9b959d5d1 Uploaded iracooke parents: diff changeset	126 #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	127
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b iracooke parents: 18 diff changeset	128 ## Generate Reports if the user has selected one of the 8 additional reports
44 f35bb9d0c93e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 981be1bde91d6d565693cd691553f77465e653bb galaxyp parents: 38 diff changeset	129 ## 'cps', 'mzidentML' and 'zip' are not valid options for PeptideShaker
20 2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b iracooke parents: 18 diff changeset	130 ## 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	131 #if set(["0","1","2","3","4","5","6","7"]).intersection( set( str( $outputs ).split(',') ) ):
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b iracooke parents: 18 diff changeset	132
30 ad60446b1e93 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit bdb5ee12705a3494eee96d1963f16f68bbe41d5c galaxyp parents: 29 diff changeset	133 (peptide-shaker eu.isas.peptideshaker.cmd.ReportCLI
ad60446b1e93 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit bdb5ee12705a3494eee96d1963f16f68bbe41d5c galaxyp parents: 29 diff changeset	134 --exec_dir="\$cwd/${bin_dir}"
20 2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b iracooke parents: 18 diff changeset	135 -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	136 -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	137 -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	138 #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	139 #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	140 #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	141 #end if
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b iracooke parents: 18 diff changeset	142 #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	143 #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	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 '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	146 #silent $cleaned_list.remove('zip')
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b iracooke parents: 18 diff changeset	147 #end if
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b iracooke parents: 18 diff changeset	148 ## Only numbers are left over. These corresponds to different reports.
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b iracooke parents: 18 diff changeset	149 -reports #echo ','.join($cleaned_list)#
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b iracooke parents: 18 diff changeset	150
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b iracooke parents: 18 diff changeset	151 2>> $temp_stderr)
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b iracooke parents: 18 diff changeset	152 &&
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b iracooke parents: 18 diff changeset	153 #end if
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b iracooke parents: 18 diff changeset	154
30 ad60446b1e93 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit bdb5ee12705a3494eee96d1963f16f68bbe41d5c galaxyp parents: 29 diff changeset	155 ## # ls -l \$cwd/output_reports/* ;
20 2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b iracooke parents: 18 diff changeset	156
18 a5f9b959d5d1 Uploaded iracooke parents: diff changeset	157 #if '0' in str($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	158 find \$cwd/output_reports -name 'Certificate_of_Analysis' -exec bash -c 'mv "$0" "certificate.txt"' {} \;
18 a5f9b959d5d1 Uploaded iracooke parents: diff changeset	159 ;
a5f9b959d5d1 Uploaded iracooke parents: diff changeset	160 #end if
a5f9b959d5d1 Uploaded iracooke parents: diff changeset	161 #if '1' in str($outputs).split(','):
a5f9b959d5d1 Uploaded iracooke parents: diff changeset	162 find \$cwd/output_reports -name 'Hierarchical' -exec bash -c 'mv "$0" "hierarchical.txt"' {} \;
a5f9b959d5d1 Uploaded iracooke parents: diff changeset	163 ;
a5f9b959d5d1 Uploaded iracooke parents: diff changeset	164 #end if
20 2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b iracooke parents: 18 diff changeset	165 #if '2' in str($outputs).split(','):
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b iracooke parents: 18 diff changeset	166 find \$cwd/output_reports -name 'PSM_Phosphorylation_Report' -exec bash -c 'mv "$0" "psm_phospho.txt"' {} \;
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b iracooke parents: 18 diff changeset	167 ;
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b iracooke parents: 18 diff changeset	168 #end if
30 ad60446b1e93 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit bdb5ee12705a3494eee96d1963f16f68bbe41d5c galaxyp parents: 29 diff changeset	169 #if '8' in str($outputs).split(','):
ad60446b1e93 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit bdb5ee12705a3494eee96d1963f16f68bbe41d5c galaxyp parents: 29 diff changeset	170 find \$cwd/output_reports -name 'Extended_PSM_Report' -exec bash -c 'mv "$0" "psmx.txt"' {} \;
ad60446b1e93 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit bdb5ee12705a3494eee96d1963f16f68bbe41d5c galaxyp parents: 29 diff changeset	171 ;
ad60446b1e93 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit bdb5ee12705a3494eee96d1963f16f68bbe41d5c galaxyp parents: 29 diff changeset	172 #end if
20 2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b iracooke parents: 18 diff changeset	173 #if '3' in str($outputs).split(','):
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b iracooke parents: 18 diff changeset	174 find \$cwd/output_reports -name 'PSM_Report' -exec bash -c 'mv "$0" "psm.txt"' {} \;
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b iracooke parents: 18 diff changeset	175 ;
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b iracooke parents: 18 diff changeset	176 #end if
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b iracooke parents: 18 diff changeset	177 #if '4' in str($outputs).split(','):
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b iracooke parents: 18 diff changeset	178 find \$cwd/output_reports -name 'Peptide_Phosphorylation_Report' -exec bash -c 'mv "$0" "peptides_phospho.txt"' {} \;
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b iracooke parents: 18 diff changeset	179 ;
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b iracooke parents: 18 diff changeset	180 #end if
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b iracooke parents: 18 diff changeset	181 #if '5' in str($outputs).split(','):
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b iracooke parents: 18 diff changeset	182 find \$cwd/output_reports -name 'Peptide_Report' -exec bash -c 'mv "$0" "peptides.txt"' {} \;
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b iracooke parents: 18 diff changeset	183 ;
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b iracooke parents: 18 diff changeset	184 #end if
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b iracooke parents: 18 diff changeset	185 #if '6' in str($outputs).split(','):
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b iracooke parents: 18 diff changeset	186 find \$cwd/output_reports -name 'Protein_Phosphorylation_Report' -exec bash -c 'mv "$0" "proteins_phospho.txt"' {} \;
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b iracooke parents: 18 diff changeset	187 ;
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b iracooke parents: 18 diff changeset	188 #end if
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b iracooke parents: 18 diff changeset	189 #if '7' in str($outputs).split(','):
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b iracooke parents: 18 diff changeset	190 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	191 ;
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b iracooke parents: 18 diff changeset	192 #end if
18 a5f9b959d5d1 Uploaded iracooke parents: diff changeset	193
a5f9b959d5d1 Uploaded iracooke parents: diff changeset	194 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	195 cat $temp_stderr 2>&1;
18 a5f9b959d5d1 Uploaded iracooke parents: diff changeset	196 (exit \$exit_code_for_galaxy)
a5f9b959d5d1 Uploaded iracooke parents: diff changeset	197
20 2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b iracooke parents: 18 diff changeset	198 ]]>
18 a5f9b959d5d1 Uploaded iracooke parents: diff changeset	199 </command>
a5f9b959d5d1 Uploaded iracooke parents: diff changeset	200 <inputs>
21 dfaea053e32f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 327a3944f2f56668d607c3d6cb08ae7d588e208c iracooke parents: 20 diff changeset	201 <param name="searchgui_input" format="searchgui_archive" type="data" label="Compressed SearchGUI results"
24 815f93bb3e1b Uploaded galaxyp parents: 22 diff changeset	202 help="SearchGUI Results from History">
815f93bb3e1b Uploaded galaxyp parents: 22 diff changeset	203 <options options_filter_attribute="metadata.searchgui_major_version" >
815f93bb3e1b Uploaded galaxyp parents: 22 diff changeset	204 <filter type="add_value" value="@SEARCHGUI_MAJOR_VERSION@" />
815f93bb3e1b Uploaded galaxyp parents: 22 diff changeset	205 </options>
815f93bb3e1b Uploaded galaxyp parents: 22 diff changeset	206 </param>
18 a5f9b959d5d1 Uploaded iracooke parents: diff changeset	207 <conditional name="processing_options">
a5f9b959d5d1 Uploaded iracooke parents: diff changeset	208 <param name="processing_options_selector" type="select" label="Specify Advanced PeptideShaker Processing Options">
a5f9b959d5d1 Uploaded iracooke parents: diff changeset	209 <option value="no" selected="True">Default Processing Options</option>
a5f9b959d5d1 Uploaded iracooke parents: diff changeset	210 <option value="yes">Advanced Processing Options</option>
a5f9b959d5d1 Uploaded iracooke parents: diff changeset	211 </param>
a5f9b959d5d1 Uploaded iracooke parents: diff changeset	212 <when value="no" />
a5f9b959d5d1 Uploaded iracooke parents: diff changeset	213 <when value="yes">
a5f9b959d5d1 Uploaded iracooke parents: diff changeset	214 <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	215 <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	216 <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	217 <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	218 help="default 95%: '95.0'" />
a5f9b959d5d1 Uploaded iracooke parents: diff changeset	219 <conditional name="ptm_score">
a5f9b959d5d1 Uploaded iracooke parents: diff changeset	220 <param name="ptm_score_selector" type="select" label="The PTM probabilistic score to use for PTM localization">
a5f9b959d5d1 Uploaded iracooke parents: diff changeset	221 <option value="0" selected="True">A-score</option>
a5f9b959d5d1 Uploaded iracooke parents: diff changeset	222 <option value="1">PhosphoRS</option>
38 79e37eff006d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 48984afa5f3d1b80ecbbff2847645c15acd81fe6 galaxyp parents: 37 diff changeset	223 <option value="2">None</option>
18 a5f9b959d5d1 Uploaded iracooke parents: diff changeset	224 </param>
a5f9b959d5d1 Uploaded iracooke parents: diff changeset	225 <when value="0" />
a5f9b959d5d1 Uploaded iracooke parents: diff changeset	226 <when value="1">
a5f9b959d5d1 Uploaded iracooke parents: diff changeset	227 <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	228 <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	229 help="Automatic mode will be used if not set" />
a5f9b959d5d1 Uploaded iracooke parents: diff changeset	230 </when>
38 79e37eff006d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 48984afa5f3d1b80ecbbff2847645c15acd81fe6 galaxyp parents: 37 diff changeset	231 <when value="2" />
18 a5f9b959d5d1 Uploaded iracooke parents: diff changeset	232 </conditional>
38 79e37eff006d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 48984afa5f3d1b80ecbbff2847645c15acd81fe6 galaxyp parents: 37 diff changeset	233 <param name="ptm_sequence_matching_type" type="select" label="The PTM to peptide sequence matching type">
79e37eff006d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 48984afa5f3d1b80ecbbff2847645c15acd81fe6 galaxyp parents: 37 diff changeset	234 <option value="0">Character Sequence</option>
79e37eff006d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 48984afa5f3d1b80ecbbff2847645c15acd81fe6 galaxyp parents: 37 diff changeset	235 <option value="1" selected="true">Amino Acids</option>
79e37eff006d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 48984afa5f3d1b80ecbbff2847645c15acd81fe6 galaxyp parents: 37 diff changeset	236 <option value="2">Indistinguishable Amino Acids</option>
79e37eff006d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 48984afa5f3d1b80ecbbff2847645c15acd81fe6 galaxyp parents: 37 diff changeset	237 </param>
29 78fad25eff17 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 4256c7c6fde06722b66f433f5913c2e707bc930f-dirty galaxyp parents: 28 diff changeset	238 <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	239 <!-- SKIPPING -protein_fraction_mw_confidence ${processing_options.protein_fraction_mw_confidence} -->
a5f9b959d5d1 Uploaded iracooke parents: diff changeset	240 </when>
a5f9b959d5d1 Uploaded iracooke parents: diff changeset	241 </conditional>
a5f9b959d5d1 Uploaded iracooke parents: diff changeset	242 <conditional name="filtering_options">
a5f9b959d5d1 Uploaded iracooke parents: diff changeset	243 <param name="filtering_options_selector" type="select" label="Specify Advanced Filtering Options"
a5f9b959d5d1 Uploaded iracooke parents: diff changeset	244 help="Filter based on peptide lengths, precursor mass error, E value errors from X! Tandem and OMSSA, and include/exclude unknown PTM’s">
a5f9b959d5d1 Uploaded iracooke parents: diff changeset	245 <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	246 <option value="yes">Advanced Filtering Options</option>
18 a5f9b959d5d1 Uploaded iracooke parents: diff changeset	247 </param>
a5f9b959d5d1 Uploaded iracooke parents: diff changeset	248 <when value="no" />
a5f9b959d5d1 Uploaded iracooke parents: diff changeset	249 <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	250 <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	251 <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	252 <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	253 help="Next option specifies units (Da or ppm)" />
18 a5f9b959d5d1 Uploaded iracooke parents: diff changeset	254 <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	255 <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	256 <option value="0">Daltons</option>
18 a5f9b959d5d1 Uploaded iracooke parents: diff changeset	257 </param>
20 2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b iracooke parents: 18 diff changeset	258 <!--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	259 <!--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	260 <!--param name="max_mascot_e" label="Maximum Mascot e-value filter" value="100" type="float" help="" /-->
18 a5f9b959d5d1 Uploaded iracooke parents: diff changeset	261 <param name="exclude_unknown_ptms" label="Exclude Unknown PTMs" type="boolean" truevalue="1" falsevalue="0" checked="true" />
a5f9b959d5d1 Uploaded iracooke parents: diff changeset	262 </when>
a5f9b959d5d1 Uploaded iracooke parents: diff changeset	263 </conditional>
30 ad60446b1e93 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit bdb5ee12705a3494eee96d1963f16f68bbe41d5c galaxyp parents: 29 diff changeset	264 <conditional name="contact_options">
ad60446b1e93 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit bdb5ee12705a3494eee96d1963f16f68bbe41d5c galaxyp parents: 29 diff changeset	265 <param name="contact_options_selector" type="select" label="Specify Contact Information for mzIdendML"
ad60446b1e93 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit bdb5ee12705a3494eee96d1963f16f68bbe41d5c galaxyp parents: 29 diff changeset	266 help="Create a Galaxy workflow to save these values">
ad60446b1e93 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit bdb5ee12705a3494eee96d1963f16f68bbe41d5c galaxyp parents: 29 diff changeset	267 <option value="no" selected="True">GalaxyP Project contact (Not suitable for PRIDE submission)</option>
ad60446b1e93 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit bdb5ee12705a3494eee96d1963f16f68bbe41d5c galaxyp parents: 29 diff changeset	268 <option value="yes">Specify Contact Information</option>
ad60446b1e93 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit bdb5ee12705a3494eee96d1963f16f68bbe41d5c galaxyp parents: 29 diff changeset	269 </param>
ad60446b1e93 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit bdb5ee12705a3494eee96d1963f16f68bbe41d5c galaxyp parents: 29 diff changeset	270 <when value="no" />
ad60446b1e93 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit bdb5ee12705a3494eee96d1963f16f68bbe41d5c galaxyp parents: 29 diff changeset	271 <when value="yes">
ad60446b1e93 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit bdb5ee12705a3494eee96d1963f16f68bbe41d5c galaxyp parents: 29 diff changeset	272 <param name="contact_first_name" type="text" value="" label="Contact first name.">
ad60446b1e93 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit bdb5ee12705a3494eee96d1963f16f68bbe41d5c galaxyp parents: 29 diff changeset	273 <validator type="regex" message="">\S+.*</validator>
ad60446b1e93 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit bdb5ee12705a3494eee96d1963f16f68bbe41d5c galaxyp parents: 29 diff changeset	274 </param>
ad60446b1e93 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit bdb5ee12705a3494eee96d1963f16f68bbe41d5c galaxyp parents: 29 diff changeset	275 <param name="contact_last_name" type="text" value="" label="Contact last name.">
ad60446b1e93 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit bdb5ee12705a3494eee96d1963f16f68bbe41d5c galaxyp parents: 29 diff changeset	276 <validator type="regex" message="">\S+.*</validator>
ad60446b1e93 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit bdb5ee12705a3494eee96d1963f16f68bbe41d5c galaxyp parents: 29 diff changeset	277 </param>
ad60446b1e93 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit bdb5ee12705a3494eee96d1963f16f68bbe41d5c galaxyp parents: 29 diff changeset	278 <param name="contact_email" type="text" value="" label="Contact e-mail.">
ad60446b1e93 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit bdb5ee12705a3494eee96d1963f16f68bbe41d5c galaxyp parents: 29 diff changeset	279 <validator type="regex" message="">\S+@\S+</validator>
ad60446b1e93 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit bdb5ee12705a3494eee96d1963f16f68bbe41d5c galaxyp parents: 29 diff changeset	280 </param>
ad60446b1e93 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit bdb5ee12705a3494eee96d1963f16f68bbe41d5c galaxyp parents: 29 diff changeset	281 <param name="contact_address" type="text" value="" label="Contact address.">
ad60446b1e93 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit bdb5ee12705a3494eee96d1963f16f68bbe41d5c galaxyp parents: 29 diff changeset	282 <validator type="regex" message="">\S+.*</validator>
ad60446b1e93 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit bdb5ee12705a3494eee96d1963f16f68bbe41d5c galaxyp parents: 29 diff changeset	283 </param>
ad60446b1e93 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit bdb5ee12705a3494eee96d1963f16f68bbe41d5c galaxyp parents: 29 diff changeset	284 <param name="contact_url" type="text" value="" optional="true" label="Contact URL.">
ad60446b1e93 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit bdb5ee12705a3494eee96d1963f16f68bbe41d5c galaxyp parents: 29 diff changeset	285 </param>
ad60446b1e93 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit bdb5ee12705a3494eee96d1963f16f68bbe41d5c galaxyp parents: 29 diff changeset	286 <param name="organization_name" type="text" value="" label="Organization name.">
ad60446b1e93 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit bdb5ee12705a3494eee96d1963f16f68bbe41d5c galaxyp parents: 29 diff changeset	287 <validator type="regex" message="">\S+.*</validator>
ad60446b1e93 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit bdb5ee12705a3494eee96d1963f16f68bbe41d5c galaxyp parents: 29 diff changeset	288 </param>
ad60446b1e93 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit bdb5ee12705a3494eee96d1963f16f68bbe41d5c galaxyp parents: 29 diff changeset	289 <param name="organization_email" type="text" value="" label="Organization e-mail.">
ad60446b1e93 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit bdb5ee12705a3494eee96d1963f16f68bbe41d5c galaxyp parents: 29 diff changeset	290 <validator type="regex" message="">\S+@\S+</validator>
ad60446b1e93 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit bdb5ee12705a3494eee96d1963f16f68bbe41d5c galaxyp parents: 29 diff changeset	291 </param>
ad60446b1e93 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit bdb5ee12705a3494eee96d1963f16f68bbe41d5c galaxyp parents: 29 diff changeset	292 <param name="organization_address" type="text" value="" label="Organization address.">
ad60446b1e93 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit bdb5ee12705a3494eee96d1963f16f68bbe41d5c galaxyp parents: 29 diff changeset	293 <validator type="regex" message="">\S+.*</validator>
ad60446b1e93 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit bdb5ee12705a3494eee96d1963f16f68bbe41d5c galaxyp parents: 29 diff changeset	294 </param>
ad60446b1e93 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit bdb5ee12705a3494eee96d1963f16f68bbe41d5c galaxyp parents: 29 diff changeset	295 <param name="organization_url" type="text" value="" optional="true" label="Organization URL.">
ad60446b1e93 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit bdb5ee12705a3494eee96d1963f16f68bbe41d5c galaxyp parents: 29 diff changeset	296 </param>
ad60446b1e93 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit bdb5ee12705a3494eee96d1963f16f68bbe41d5c galaxyp parents: 29 diff changeset	297 </when>
ad60446b1e93 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit bdb5ee12705a3494eee96d1963f16f68bbe41d5c galaxyp parents: 29 diff changeset	298 </conditional>
ad60446b1e93 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit bdb5ee12705a3494eee96d1963f16f68bbe41d5c galaxyp parents: 29 diff changeset	299
ad60446b1e93 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit bdb5ee12705a3494eee96d1963f16f68bbe41d5c galaxyp parents: 29 diff changeset	300 <param name="include_sequences" type="boolean" truevalue="1" falsevalue="0" checked="false" label="Include the protein sequences in mzIdentML" />
18 a5f9b959d5d1 Uploaded iracooke parents: diff changeset	301 <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	302 <option value="zip">Zip File for import to Desktop App</option>
18 a5f9b959d5d1 Uploaded iracooke parents: diff changeset	303 <option value="mzidentML" selected="True">mzidentML File</option>
30 ad60446b1e93 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit bdb5ee12705a3494eee96d1963f16f68bbe41d5c galaxyp parents: 29 diff changeset	304 <option value="3">PSM Report</option>
ad60446b1e93 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit bdb5ee12705a3494eee96d1963f16f68bbe41d5c galaxyp parents: 29 diff changeset	305 <option value="8">Extended PSM Report</option>
20 2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b iracooke parents: 18 diff changeset	306 <option value="2">PSM Phosphorylation Report</option>
30 ad60446b1e93 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit bdb5ee12705a3494eee96d1963f16f68bbe41d5c galaxyp parents: 29 diff changeset	307 <option value="5">Peptide Report</option>
ad60446b1e93 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit bdb5ee12705a3494eee96d1963f16f68bbe41d5c galaxyp parents: 29 diff changeset	308 <option value="4">Peptide Phosphorylation Report</option>
ad60446b1e93 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit bdb5ee12705a3494eee96d1963f16f68bbe41d5c galaxyp parents: 29 diff changeset	309 <option value="7">Protein Report</option>
ad60446b1e93 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit bdb5ee12705a3494eee96d1963f16f68bbe41d5c galaxyp parents: 29 diff changeset	310 <option value="6">Protein Phosphorylation Report</option>
18 a5f9b959d5d1 Uploaded iracooke parents: diff changeset	311 <option value="0">Certificate of Analysis</option>
a5f9b959d5d1 Uploaded iracooke parents: diff changeset	312 <option value="1">Hierarchical Report</option>
a5f9b959d5d1 Uploaded iracooke parents: diff changeset	313 <option value="cps">CPS file</option>
a5f9b959d5d1 Uploaded iracooke parents: diff changeset	314 <validator type="no_options" message="Please select at least one output file" />
a5f9b959d5d1 Uploaded iracooke parents: diff changeset	315 </param>
20 2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b iracooke parents: 18 diff changeset	316
18 a5f9b959d5d1 Uploaded iracooke parents: diff changeset	317 </inputs>
a5f9b959d5d1 Uploaded iracooke parents: diff changeset	318 <outputs>
a5f9b959d5d1 Uploaded iracooke parents: diff changeset	319 <data format="mzid" name="mzidentML" from_work_dir="output.mzid" label="${tool.name} on ${on_string}: mzidentML file">
a5f9b959d5d1 Uploaded iracooke parents: diff changeset	320 <filter>'mzidentML' in outputs</filter>
a5f9b959d5d1 Uploaded iracooke parents: diff changeset	321 </data>
44 f35bb9d0c93e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 981be1bde91d6d565693cd691553f77465e653bb galaxyp parents: 38 diff changeset	322 <data format="peptideshaker_archive" name="output_cps" from_work_dir="peptideshaker_output.cpsx" label="${tool.name} on ${on_string}: CPS file">
18 a5f9b959d5d1 Uploaded iracooke parents: diff changeset	323 <filter>'cps' in outputs</filter>
a5f9b959d5d1 Uploaded iracooke parents: diff changeset	324 </data>
20 2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b iracooke parents: 18 diff changeset	325 <data format="zip" name="output_zip" from_work_dir="peptideshaker_output.zip" label="${tool.name} on ${on_string}: Archive">
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b iracooke parents: 18 diff changeset	326 <filter>'zip' in outputs</filter>
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b iracooke parents: 18 diff changeset	327 </data>
18 a5f9b959d5d1 Uploaded iracooke parents: diff changeset	328 <data format="txt" name="output_certificate" from_work_dir="certificate.txt" label="${tool.name} on ${on_string}: Parameters">
a5f9b959d5d1 Uploaded iracooke parents: diff changeset	329 <filter>'0' in outputs</filter>
a5f9b959d5d1 Uploaded iracooke parents: diff changeset	330 </data>
20 2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b iracooke parents: 18 diff changeset	331 <data format="tabular" name="output_hierarchical" from_work_dir="hierarchical.txt" label="${tool.name} on ${on_string}: Hierarchical Report">
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b iracooke parents: 18 diff changeset	332 <filter>'1' in outputs</filter>
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b iracooke parents: 18 diff changeset	333 </data>
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b iracooke parents: 18 diff changeset	334 <data format="tabular" name="output_psm_phosphorylation" from_work_dir="psm_phospho.txt" label="${tool.name} on ${on_string}: PSM Phosphorylation Report">
18 a5f9b959d5d1 Uploaded iracooke parents: diff changeset	335 <filter>'2' in outputs</filter>
a5f9b959d5d1 Uploaded iracooke parents: diff changeset	336 </data>
20 2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b iracooke parents: 18 diff changeset	337 <data format="tabular" name="output_psm" from_work_dir="psm.txt" label="${tool.name} on ${on_string}: PSM Report">
18 a5f9b959d5d1 Uploaded iracooke parents: diff changeset	338 <filter>'3' in outputs</filter>
a5f9b959d5d1 Uploaded iracooke parents: diff changeset	339 </data>
30 ad60446b1e93 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit bdb5ee12705a3494eee96d1963f16f68bbe41d5c galaxyp parents: 29 diff changeset	340 <data format="tabular" name="output_extended_psm" from_work_dir="psmx.txt" label="${tool.name} on ${on_string}: Extended PSM Report">
ad60446b1e93 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit bdb5ee12705a3494eee96d1963f16f68bbe41d5c galaxyp parents: 29 diff changeset	341 <filter>'8' in outputs</filter>
ad60446b1e93 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit bdb5ee12705a3494eee96d1963f16f68bbe41d5c galaxyp parents: 29 diff changeset	342 </data>
20 2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b iracooke parents: 18 diff changeset	343 <data format="tabular" name="output_peptides_phosphorylation" from_work_dir="peptides_phospho.txt" label="${tool.name} on ${on_string}: Peptide Phosphorylation Report">
18 a5f9b959d5d1 Uploaded iracooke parents: diff changeset	344 <filter>'4' in outputs</filter>
a5f9b959d5d1 Uploaded iracooke parents: diff changeset	345 </data>
20 2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b iracooke parents: 18 diff changeset	346 <data format="tabular" name="output_peptides" from_work_dir="peptides.txt" label="${tool.name} on ${on_string}: Peptide Report">
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b iracooke parents: 18 diff changeset	347 <filter>'5' in outputs</filter>
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b iracooke parents: 18 diff changeset	348 </data>
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b iracooke parents: 18 diff changeset	349 <data format="tabular" name="output_proteins_phosphorylation" from_work_dir="proteins_phospho.txt" label="${tool.name} on ${on_string}: Protein Phosphorylation Report">
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b iracooke parents: 18 diff changeset	350 <filter>'6' in outputs</filter>
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b iracooke parents: 18 diff changeset	351 </data>
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b iracooke parents: 18 diff changeset	352 <data format="tabular" name="output_proteins" from_work_dir="proteins.txt" label="${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	353 <filter>'7' in outputs</filter>
18 a5f9b959d5d1 Uploaded iracooke parents: diff changeset	354 </data>
a5f9b959d5d1 Uploaded iracooke parents: diff changeset	355 </outputs>
a5f9b959d5d1 Uploaded iracooke parents: diff changeset	356 <tests>
a5f9b959d5d1 Uploaded iracooke parents: diff changeset	357 <test>
21 dfaea053e32f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 327a3944f2f56668d607c3d6cb08ae7d588e208c iracooke parents: 20 diff changeset	358 <param name="searchgui_input" value="tiny_searchgui_result1.zip" ftype="searchgui_archive"/>
18 a5f9b959d5d1 Uploaded iracooke parents: diff changeset	359 <param name="processing_options_selector" value="no"/>
a5f9b959d5d1 Uploaded iracooke parents: diff changeset	360 <param name="filtering_options_selector" value="no"/>
30 ad60446b1e93 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit bdb5ee12705a3494eee96d1963f16f68bbe41d5c galaxyp parents: 29 diff changeset	361 <param name="outputs" value="zip,3"/>
33 bce45e9e6d70 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312 galaxyp parents: 32 diff changeset	362 <output name="output_zip" file="peptide_shaker_result1.zip" ftype="zip" compare="sim_size" delta="3000" />
32 ff592231f118 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 047efcfa1e9f45648e6e81d3776a1a93e2cfe46d galaxyp parents: 30 diff changeset	363 <output name="output_psm">
ff592231f118 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 047efcfa1e9f45648e6e81d3776a1a93e2cfe46d galaxyp parents: 30 diff changeset	364 <assert_contents>
ff592231f118 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 047efcfa1e9f45648e6e81d3776a1a93e2cfe46d galaxyp parents: 30 diff changeset	365 <has_text text="cds.comp41779_c0_seq1" />
ff592231f118 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 047efcfa1e9f45648e6e81d3776a1a93e2cfe46d galaxyp parents: 30 diff changeset	366 </assert_contents>
ff592231f118 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 047efcfa1e9f45648e6e81d3776a1a93e2cfe46d galaxyp parents: 30 diff changeset	367 </output>
20 2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b iracooke parents: 18 diff changeset	368 </test>
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b iracooke parents: 18 diff changeset	369 <test>
21 dfaea053e32f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 327a3944f2f56668d607c3d6cb08ae7d588e208c iracooke parents: 20 diff changeset	370 <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	371 <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	372 <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	373 <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	374 <param name="outputs" value="0,1,2,3,4,5,6,7"/>
32 ff592231f118 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 047efcfa1e9f45648e6e81d3776a1a93e2cfe46d galaxyp parents: 30 diff changeset	375 <output name="output_certificate">
ff592231f118 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 047efcfa1e9f45648e6e81d3776a1a93e2cfe46d galaxyp parents: 30 diff changeset	376 <assert_contents>
ff592231f118 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 047efcfa1e9f45648e6e81d3776a1a93e2cfe46d galaxyp parents: 30 diff changeset	377 <has_text text="Tolerance: 100" />
ff592231f118 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 047efcfa1e9f45648e6e81d3776a1a93e2cfe46d galaxyp parents: 30 diff changeset	378 <has_text text="Carbamidomethylation of C" />
ff592231f118 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 047efcfa1e9f45648e6e81d3776a1a93e2cfe46d galaxyp parents: 30 diff changeset	379 </assert_contents>
ff592231f118 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 047efcfa1e9f45648e6e81d3776a1a93e2cfe46d galaxyp parents: 30 diff changeset	380 </output>
ff592231f118 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 047efcfa1e9f45648e6e81d3776a1a93e2cfe46d galaxyp parents: 30 diff changeset	381 <output name="output_hierarchical">
ff592231f118 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 047efcfa1e9f45648e6e81d3776a1a93e2cfe46d galaxyp parents: 30 diff changeset	382 <assert_contents>
33 bce45e9e6d70 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312 galaxyp parents: 32 diff changeset	383 <has_text_matching expression="1.1\tcds.comp" />
32 ff592231f118 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 047efcfa1e9f45648e6e81d3776a1a93e2cfe46d galaxyp parents: 30 diff changeset	384 </assert_contents>
ff592231f118 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 047efcfa1e9f45648e6e81d3776a1a93e2cfe46d galaxyp parents: 30 diff changeset	385 </output>
ff592231f118 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 047efcfa1e9f45648e6e81d3776a1a93e2cfe46d galaxyp parents: 30 diff changeset	386 <output name="output_psm">
ff592231f118 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 047efcfa1e9f45648e6e81d3776a1a93e2cfe46d galaxyp parents: 30 diff changeset	387 <assert_contents>
ff592231f118 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 047efcfa1e9f45648e6e81d3776a1a93e2cfe46d galaxyp parents: 30 diff changeset	388 <not_has_text text="Phosphosite" />
ff592231f118 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 047efcfa1e9f45648e6e81d3776a1a93e2cfe46d galaxyp parents: 30 diff changeset	389 <has_text text="cds.comp41779_c0_seq1" />
ff592231f118 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 047efcfa1e9f45648e6e81d3776a1a93e2cfe46d galaxyp parents: 30 diff changeset	390 </assert_contents>
ff592231f118 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 047efcfa1e9f45648e6e81d3776a1a93e2cfe46d galaxyp parents: 30 diff changeset	391 </output>
ff592231f118 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 047efcfa1e9f45648e6e81d3776a1a93e2cfe46d galaxyp parents: 30 diff changeset	392 <output name="output_psm_phosphorylation">
ff592231f118 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 047efcfa1e9f45648e6e81d3776a1a93e2cfe46d galaxyp parents: 30 diff changeset	393 <assert_contents>
ff592231f118 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 047efcfa1e9f45648e6e81d3776a1a93e2cfe46d galaxyp parents: 30 diff changeset	394 <has_text text="Phosphosite" />
ff592231f118 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 047efcfa1e9f45648e6e81d3776a1a93e2cfe46d galaxyp parents: 30 diff changeset	395 <has_text text="cds.comp41779_c0_seq1" />
ff592231f118 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 047efcfa1e9f45648e6e81d3776a1a93e2cfe46d galaxyp parents: 30 diff changeset	396 </assert_contents>
ff592231f118 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 047efcfa1e9f45648e6e81d3776a1a93e2cfe46d galaxyp parents: 30 diff changeset	397 </output>
ff592231f118 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 047efcfa1e9f45648e6e81d3776a1a93e2cfe46d galaxyp parents: 30 diff changeset	398 <output name="output_peptides">
ff592231f118 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 047efcfa1e9f45648e6e81d3776a1a93e2cfe46d galaxyp parents: 30 diff changeset	399 <assert_contents>
ff592231f118 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 047efcfa1e9f45648e6e81d3776a1a93e2cfe46d galaxyp parents: 30 diff changeset	400 <has_text text="Modification" />
ff592231f118 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 047efcfa1e9f45648e6e81d3776a1a93e2cfe46d galaxyp parents: 30 diff changeset	401 <has_text text="cds.comp41779_c0_seq1" />
ff592231f118 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 047efcfa1e9f45648e6e81d3776a1a93e2cfe46d galaxyp parents: 30 diff changeset	402 </assert_contents>
ff592231f118 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 047efcfa1e9f45648e6e81d3776a1a93e2cfe46d galaxyp parents: 30 diff changeset	403 </output>
ff592231f118 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 047efcfa1e9f45648e6e81d3776a1a93e2cfe46d galaxyp parents: 30 diff changeset	404 <output name="output_peptides_phosphorylation">
ff592231f118 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 047efcfa1e9f45648e6e81d3776a1a93e2cfe46d galaxyp parents: 30 diff changeset	405 <assert_contents>
ff592231f118 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 047efcfa1e9f45648e6e81d3776a1a93e2cfe46d galaxyp parents: 30 diff changeset	406 <has_text text="Phosphosite" />
ff592231f118 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 047efcfa1e9f45648e6e81d3776a1a93e2cfe46d galaxyp parents: 30 diff changeset	407 <has_text text="cds.comp41779_c0_seq1" />
ff592231f118 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 047efcfa1e9f45648e6e81d3776a1a93e2cfe46d galaxyp parents: 30 diff changeset	408 </assert_contents>
ff592231f118 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 047efcfa1e9f45648e6e81d3776a1a93e2cfe46d galaxyp parents: 30 diff changeset	409 </output>
ff592231f118 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 047efcfa1e9f45648e6e81d3776a1a93e2cfe46d galaxyp parents: 30 diff changeset	410 <output name="output_proteins">
ff592231f118 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 047efcfa1e9f45648e6e81d3776a1a93e2cfe46d galaxyp parents: 30 diff changeset	411 <assert_contents>
ff592231f118 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 047efcfa1e9f45648e6e81d3776a1a93e2cfe46d galaxyp parents: 30 diff changeset	412 <has_text text="Modification" />
ff592231f118 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 047efcfa1e9f45648e6e81d3776a1a93e2cfe46d galaxyp parents: 30 diff changeset	413 <has_text text="cds.comp41779_c0_seq1" />
ff592231f118 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 047efcfa1e9f45648e6e81d3776a1a93e2cfe46d galaxyp parents: 30 diff changeset	414 </assert_contents>
ff592231f118 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 047efcfa1e9f45648e6e81d3776a1a93e2cfe46d galaxyp parents: 30 diff changeset	415 </output>
ff592231f118 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 047efcfa1e9f45648e6e81d3776a1a93e2cfe46d galaxyp parents: 30 diff changeset	416 <output name="output_proteins_phosphorylation">
ff592231f118 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 047efcfa1e9f45648e6e81d3776a1a93e2cfe46d galaxyp parents: 30 diff changeset	417 <assert_contents>
ff592231f118 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 047efcfa1e9f45648e6e81d3776a1a93e2cfe46d galaxyp parents: 30 diff changeset	418 <has_text text="Phosphosite" />
ff592231f118 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 047efcfa1e9f45648e6e81d3776a1a93e2cfe46d galaxyp parents: 30 diff changeset	419 <has_text text="cds.comp41779_c0_seq1" />
ff592231f118 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 047efcfa1e9f45648e6e81d3776a1a93e2cfe46d galaxyp parents: 30 diff changeset	420 </assert_contents>
ff592231f118 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 047efcfa1e9f45648e6e81d3776a1a93e2cfe46d galaxyp parents: 30 diff changeset	421 </output>
20 2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b iracooke parents: 18 diff changeset	422 </test>
44 f35bb9d0c93e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 981be1bde91d6d565693cd691553f77465e653bb galaxyp parents: 38 diff changeset	423 <test>
f35bb9d0c93e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 981be1bde91d6d565693cd691553f77465e653bb galaxyp parents: 38 diff changeset	424 <param name="searchgui_input" value="tiny_searchgui_result1.zip" ftype="searchgui_archive"/>
f35bb9d0c93e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 981be1bde91d6d565693cd691553f77465e653bb galaxyp parents: 38 diff changeset	425 <param name="processing_options_selector" value="no"/>
f35bb9d0c93e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 981be1bde91d6d565693cd691553f77465e653bb galaxyp parents: 38 diff changeset	426 <param name="filtering_options_selector" value="no"/>
f35bb9d0c93e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 981be1bde91d6d565693cd691553f77465e653bb galaxyp parents: 38 diff changeset	427 <param name="outputs" value="3,cps"/>
f35bb9d0c93e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 981be1bde91d6d565693cd691553f77465e653bb galaxyp parents: 38 diff changeset	428 <output name="output_cps" file="peptide_shaker_result1.cpsx" ftype="peptideshaker_archive" compare="sim_size" delta="3000"/>
f35bb9d0c93e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 981be1bde91d6d565693cd691553f77465e653bb galaxyp parents: 38 diff changeset	429 <output name="output_psm">
f35bb9d0c93e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 981be1bde91d6d565693cd691553f77465e653bb galaxyp parents: 38 diff changeset	430 <assert_contents>
f35bb9d0c93e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 981be1bde91d6d565693cd691553f77465e653bb galaxyp parents: 38 diff changeset	431 <has_text text="cds.comp41779_c0_seq1" />
f35bb9d0c93e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 981be1bde91d6d565693cd691553f77465e653bb galaxyp parents: 38 diff changeset	432 </assert_contents>
f35bb9d0c93e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 981be1bde91d6d565693cd691553f77465e653bb galaxyp parents: 38 diff changeset	433 </output>
f35bb9d0c93e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 981be1bde91d6d565693cd691553f77465e653bb galaxyp parents: 38 diff changeset	434 </test>
18 a5f9b959d5d1 Uploaded iracooke parents: diff changeset	435 </tests>
a5f9b959d5d1 Uploaded iracooke parents: diff changeset	436 <help>
a5f9b959d5d1 Uploaded iracooke parents: diff changeset	437 What it does
a5f9b959d5d1 Uploaded iracooke parents: diff changeset	438
a5f9b959d5d1 Uploaded iracooke parents: diff changeset	439 Runs multiple search engines (X! Tandem, OMSSA and MS-GF+) on any number of MGF peak lists using the SearchGUI application and combines the results.
a5f9b959d5d1 Uploaded iracooke parents: diff changeset	440
30 ad60446b1e93 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit bdb5ee12705a3494eee96d1963f16f68bbe41d5c galaxyp parents: 29 diff changeset	441 http://compomics.github.io/projects/peptide-shaker.html
ad60446b1e93 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit bdb5ee12705a3494eee96d1963f16f68bbe41d5c galaxyp parents: 29 diff changeset	442 http://compomics.github.io/projects/searchgui.html
18 a5f9b959d5d1 Uploaded iracooke parents: diff changeset	443
a5f9b959d5d1 Uploaded iracooke parents: diff changeset	444 ----
a5f9b959d5d1 Uploaded iracooke parents: diff changeset	445
a5f9b959d5d1 Uploaded iracooke parents: diff changeset	446 Reports
a5f9b959d5d1 Uploaded iracooke parents: diff changeset	447 =======
a5f9b959d5d1 Uploaded iracooke parents: diff changeset	448
a5f9b959d5d1 Uploaded iracooke parents: diff changeset	449
a5f9b959d5d1 Uploaded iracooke parents: diff changeset	450 PSM Report
a5f9b959d5d1 Uploaded iracooke parents: diff changeset	451 ----------
a5f9b959d5d1 Uploaded iracooke parents: diff changeset	452
a5f9b959d5d1 Uploaded iracooke parents: diff changeset	453 * 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	454 * 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	455 * Variable Modifications: The variable modifications
18 a5f9b959d5d1 Uploaded iracooke parents: diff changeset	456 * D-score: D-score for variable PTM localization
a5f9b959d5d1 Uploaded iracooke parents: diff changeset	457 * probabilistic PTM score: The probabilistic score (e.g. A-score or PhosphoRS) used for variable PTM localization.
a5f9b959d5d1 Uploaded iracooke parents: diff changeset	458 * Localization Confidence: The confidence in variable PTM localization.
a5f9b959d5d1 Uploaded iracooke parents: diff changeset	459 * Fixed Modifications: The fixed modifications.
a5f9b959d5d1 Uploaded iracooke parents: diff changeset	460 * Spectrum File: The spectrum file.
a5f9b959d5d1 Uploaded iracooke parents: diff changeset	461 * Spectrum Title: The title of the spectrum.
a5f9b959d5d1 Uploaded iracooke parents: diff changeset	462 * Spectrum Scan Number: The spectrum scan number.
a5f9b959d5d1 Uploaded iracooke parents: diff changeset	463 * RT: Retention time
a5f9b959d5d1 Uploaded iracooke parents: diff changeset	464 * m/z: Measured m/z
a5f9b959d5d1 Uploaded iracooke parents: diff changeset	465 * Measured Charge: The charge as given in the spectrum file.
a5f9b959d5d1 Uploaded iracooke parents: diff changeset	466 * Identification Charge: The charge as inferred by the search engine.
a5f9b959d5d1 Uploaded iracooke parents: diff changeset	467 * Theoretical Mass: The theoretical mass of the peptide.
a5f9b959d5d1 Uploaded iracooke parents: diff changeset	468 * Isotope Number: The isotope number targetted by the instrument.
a5f9b959d5d1 Uploaded iracooke parents: diff changeset	469 * Precursor m/z Error: The precursor m/z matching error.
a5f9b959d5d1 Uploaded iracooke parents: diff changeset	470 * Score: Score of the retained peptide as a combination of the algorithm scores (used to rank PSMs).
a5f9b959d5d1 Uploaded iracooke parents: diff changeset	471 * Confidence: Confidence in percent associated to the retained PSM.
a5f9b959d5d1 Uploaded iracooke parents: diff changeset	472 * Decoy: Indicates whether the peptide is a decoy (1: yes, 0: no).
a5f9b959d5d1 Uploaded iracooke parents: diff changeset	473 * Validation: Indicates the validation level of the protein group.
a5f9b959d5d1 Uploaded iracooke parents: diff changeset	474
a5f9b959d5d1 Uploaded iracooke parents: diff changeset	475
a5f9b959d5d1 Uploaded iracooke parents: diff changeset	476 Protein Report
a5f9b959d5d1 Uploaded iracooke parents: diff changeset	477 --------------
a5f9b959d5d1 Uploaded iracooke parents: diff changeset	478
a5f9b959d5d1 Uploaded iracooke parents: diff changeset	479 * Main Accession: Main accession of the protein group.
a5f9b959d5d1 Uploaded iracooke parents: diff changeset	480 * Description: Description of the protein designed by the main accession.
a5f9b959d5d1 Uploaded iracooke parents: diff changeset	481 * Gene Name: The gene names of the Ensembl gene ID associated to the main accession.
a5f9b959d5d1 Uploaded iracooke parents: diff changeset	482 * Chromosome: The chromosome of the Ensembl gene ID associated to the main accession.
a5f9b959d5d1 Uploaded iracooke parents: diff changeset	483 * PI: Protein Inference status of the protein group.
a5f9b959d5d1 Uploaded iracooke parents: diff changeset	484 * Secondary Accessions: Other accessions in the protein group (alphabetical order).
a5f9b959d5d1 Uploaded iracooke parents: diff changeset	485 * Protein Group: The complete protein group (alphabetical order).
a5f9b959d5d1 Uploaded iracooke parents: diff changeset	486 * #Peptides: Total number of peptides.
a5f9b959d5d1 Uploaded iracooke parents: diff changeset	487 * #Validated Peptides: Number of validated peptides.
a5f9b959d5d1 Uploaded iracooke parents: diff changeset	488 * #Unique: Total number of peptides unique to this protein group.
a5f9b959d5d1 Uploaded iracooke parents: diff changeset	489 * #PSMs: Number of PSMs
a5f9b959d5d1 Uploaded iracooke parents: diff changeset	490 * #Validated PSMs: Number of validated PSMs
a5f9b959d5d1 Uploaded iracooke parents: diff changeset	491 * Coverage (%): Sequence coverage in percent of the protein designed by the main accession.
a5f9b959d5d1 Uploaded iracooke parents: diff changeset	492 * 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	493 * MW (kDa): Molecular Weight.
a5f9b959d5d1 Uploaded iracooke parents: diff changeset	494 * Spectrum Counting NSAF: Normalized Spectrum Abundance Factor (NSAF)
a5f9b959d5d1 Uploaded iracooke parents: diff changeset	495 * Spectrum Counting emPAI: exponentially modified Protein Abundance Index (emPAI)
a5f9b959d5d1 Uploaded iracooke parents: diff changeset	496 * 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	497 * 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	498 * Score: Score of the protein group.
a5f9b959d5d1 Uploaded iracooke parents: diff changeset	499 * Confidence: Confidence in percent associated to the protein group.
a5f9b959d5d1 Uploaded iracooke parents: diff changeset	500 * Decoy: Indicates whether the protein group is a decoy (1: yes, 0: no).
a5f9b959d5d1 Uploaded iracooke parents: diff changeset	501 * Validation: Indicates the validation level of the protein group.
a5f9b959d5d1 Uploaded iracooke parents: diff changeset	502
a5f9b959d5d1 Uploaded iracooke parents: diff changeset	503
a5f9b959d5d1 Uploaded iracooke parents: diff changeset	504 Peptide Report
a5f9b959d5d1 Uploaded iracooke parents: diff changeset	505 --------------
a5f9b959d5d1 Uploaded iracooke parents: diff changeset	506
a5f9b959d5d1 Uploaded iracooke parents: diff changeset	507
a5f9b959d5d1 Uploaded iracooke parents: diff changeset	508 * Protein(s): Protein(s) to which this peptide can be attached.
a5f9b959d5d1 Uploaded iracooke parents: diff changeset	509 * AAs Before: The amino-acids before the sequence.
a5f9b959d5d1 Uploaded iracooke parents: diff changeset	510 * Sequence: Sequence of the peptide.
a5f9b959d5d1 Uploaded iracooke parents: diff changeset	511 * AAs After: The amino-acids after the sequence.
a5f9b959d5d1 Uploaded iracooke parents: diff changeset	512 * Modified Sequence: The peptide sequence annotated with variable modifications.
a5f9b959d5d1 Uploaded iracooke parents: diff changeset	513 * Variable Modifications: The variable modifications.
a5f9b959d5d1 Uploaded iracooke parents: diff changeset	514 * Localization Confidence: The confidence in PTMs localization.
a5f9b959d5d1 Uploaded iracooke parents: diff changeset	515 * Fixed Modifications: The fixed modifications.
a5f9b959d5d1 Uploaded iracooke parents: diff changeset	516 * #Validated PSMs: Number of validated PSMs.
a5f9b959d5d1 Uploaded iracooke parents: diff changeset	517 * #PSMs: Number of PSMs.
a5f9b959d5d1 Uploaded iracooke parents: diff changeset	518 * Score: Score of the peptide.
a5f9b959d5d1 Uploaded iracooke parents: diff changeset	519 * Confidence: Confidence in percent associated to the peptide.
a5f9b959d5d1 Uploaded iracooke parents: diff changeset	520 * Decoy: Indicates whether the peptide is a decoy (1: yes, 0: no).
a5f9b959d5d1 Uploaded iracooke parents: diff changeset	521 * Validation: Indicates the validation level of the protein group.
a5f9b959d5d1 Uploaded iracooke parents: diff changeset	522
a5f9b959d5d1 Uploaded iracooke parents: diff changeset	523
a5f9b959d5d1 Uploaded iracooke parents: diff changeset	524 Hierachical Report
a5f9b959d5d1 Uploaded iracooke parents: diff changeset	525 ------------------
a5f9b959d5d1 Uploaded iracooke parents: diff changeset	526
a5f9b959d5d1 Uploaded iracooke parents: diff changeset	527 * Main Accession: Main accession of the protein group.
a5f9b959d5d1 Uploaded iracooke parents: diff changeset	528 * Description: Description of the protein designed by the main accession.
a5f9b959d5d1 Uploaded iracooke parents: diff changeset	529 * PI: Protein Inference status of the protein group.
a5f9b959d5d1 Uploaded iracooke parents: diff changeset	530 * Secondary Accessions: Other accessions in the protein group (alphabetical order).
a5f9b959d5d1 Uploaded iracooke parents: diff changeset	531 * Protein Group: The complete protein group (alphabetical order).
a5f9b959d5d1 Uploaded iracooke parents: diff changeset	532 * #Peptides: Total number of peptides.
a5f9b959d5d1 Uploaded iracooke parents: diff changeset	533 * #Validated Peptides: Number of validated peptides.
a5f9b959d5d1 Uploaded iracooke parents: diff changeset	534 * #Unique: Total number of peptides unique to this protein group.
a5f9b959d5d1 Uploaded iracooke parents: diff changeset	535 * #PSMs: Number of PSMs
a5f9b959d5d1 Uploaded iracooke parents: diff changeset	536 * #Validated PSMs: Number of validated PSMs
a5f9b959d5d1 Uploaded iracooke parents: diff changeset	537 * Coverage (%): Sequence coverage in percent of the protein designed by the main accession.
a5f9b959d5d1 Uploaded iracooke parents: diff changeset	538 * 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	539 * MW (kDa): Molecular Weight.
a5f9b959d5d1 Uploaded iracooke parents: diff changeset	540 * Spectrum Counting NSAF: Normalized Spectrum Abundance Factor (NSAF)
a5f9b959d5d1 Uploaded iracooke parents: diff changeset	541 * Spectrum Counting emPAI: exponentially modified Protein Abundance Index (emPAI)
a5f9b959d5d1 Uploaded iracooke parents: diff changeset	542 * Confident Modification Sites: # Confident Modification Sites List of the sites where a variable modification was confidently localized.
a5f9b959d5d1 Uploaded iracooke parents: diff changeset	543 * Other Modification Sites: # Other Modification Sites List of the non-confident sites where a variable modification was localized.
a5f9b959d5d1 Uploaded iracooke parents: diff changeset	544 * Score: Score of the protein group.
a5f9b959d5d1 Uploaded iracooke parents: diff changeset	545 * Confidence: Confidence in percent associated to the protein group.
a5f9b959d5d1 Uploaded iracooke parents: diff changeset	546 * Decoy: Indicates whether the protein group is a decoy (1: yes, 0: no).
a5f9b959d5d1 Uploaded iracooke parents: diff changeset	547 * Validation: Indicates the validation level of the protein group.
a5f9b959d5d1 Uploaded iracooke parents: diff changeset	548 * Protein(s): Protein(s) to which this peptide can be attached.
a5f9b959d5d1 Uploaded iracooke parents: diff changeset	549 * AAs Before: The amino-acids before the sequence.
a5f9b959d5d1 Uploaded iracooke parents: diff changeset	550 * Sequence: Sequence of the peptide.
a5f9b959d5d1 Uploaded iracooke parents: diff changeset	551 * AAs After: The amino-acids after the sequence.
a5f9b959d5d1 Uploaded iracooke parents: diff changeset	552 * Variable Modifications: The variable modifications.
a5f9b959d5d1 Uploaded iracooke parents: diff changeset	553 * Localization Confidence: The confidence in PTMs localization.
a5f9b959d5d1 Uploaded iracooke parents: diff changeset	554 * Fixed Modifications: The fixed modifications.
a5f9b959d5d1 Uploaded iracooke parents: diff changeset	555 * #Validated PSMs: Number of validated PSMs.
a5f9b959d5d1 Uploaded iracooke parents: diff changeset	556 * #PSMs: Number of PSMs.
a5f9b959d5d1 Uploaded iracooke parents: diff changeset	557 * Score: Score of the peptide.
a5f9b959d5d1 Uploaded iracooke parents: diff changeset	558 * Confidence: Confidence in percent associated to the peptide.
a5f9b959d5d1 Uploaded iracooke parents: diff changeset	559 * Decoy: Indicates whether the peptide is a decoy (1: yes, 0: no).
a5f9b959d5d1 Uploaded iracooke parents: diff changeset	560 * Validation: Indicates the validation level of the protein group.
a5f9b959d5d1 Uploaded iracooke parents: diff changeset	561 * Protein(s): Protein(s) to which the peptide can be attached.
a5f9b959d5d1 Uploaded iracooke parents: diff changeset	562 * Sequence: Sequence of the peptide.
a5f9b959d5d1 Uploaded iracooke parents: diff changeset	563 * Modified Sequence: The peptide sequence annotated with variable modifications.
a5f9b959d5d1 Uploaded iracooke parents: diff changeset	564 * Variable Modifications: The variable modifications.
a5f9b959d5d1 Uploaded iracooke parents: diff changeset	565 * D-score: D-score for variable PTM localization.
a5f9b959d5d1 Uploaded iracooke parents: diff changeset	566 * probabilistic PTM score: The probabilistic score (e.g. A-score or PhosphoRS) used for variable PTM localization.
a5f9b959d5d1 Uploaded iracooke parents: diff changeset	567 * Localization Confidence: The confidence in variable PTM localization.
a5f9b959d5d1 Uploaded iracooke parents: diff changeset	568 * Fixed Modifications: The fixed modifications.
a5f9b959d5d1 Uploaded iracooke parents: diff changeset	569 * Spectrum File: The spectrum file.
a5f9b959d5d1 Uploaded iracooke parents: diff changeset	570 * Spectrum Title: The title of the spectrum.
a5f9b959d5d1 Uploaded iracooke parents: diff changeset	571 * Spectrum Scan Number: The spectrum scan number.
a5f9b959d5d1 Uploaded iracooke parents: diff changeset	572 * RT: Retention time
a5f9b959d5d1 Uploaded iracooke parents: diff changeset	573 * m/z: Measured m/z
a5f9b959d5d1 Uploaded iracooke parents: diff changeset	574 * Measured Charge: The charge as given in the spectrum file.
a5f9b959d5d1 Uploaded iracooke parents: diff changeset	575 * Identification Charge: The charge as inferred by the search engine.
a5f9b959d5d1 Uploaded iracooke parents: diff changeset	576 * Theoretical Mass: The theoretical mass of the peptide.
a5f9b959d5d1 Uploaded iracooke parents: diff changeset	577 * Isotope Number: The isotope number targetted by the instrument.
a5f9b959d5d1 Uploaded iracooke parents: diff changeset	578 * Precursor m/z Error: The precursor m/z matching error.
a5f9b959d5d1 Uploaded iracooke parents: diff changeset	579 * Score: Score of the retained peptide as a combination of the algorithm scores (used to rank PSMs).
a5f9b959d5d1 Uploaded iracooke parents: diff changeset	580 * Confidence: Confidence in percent associated to the retained PSM.
a5f9b959d5d1 Uploaded iracooke parents: diff changeset	581 * Decoy: Indicates whether the peptide is a decoy (1: yes, 0: no).
a5f9b959d5d1 Uploaded iracooke parents: diff changeset	582 * Validation: Indicates the validation level of the protein group.
a5f9b959d5d1 Uploaded iracooke parents: diff changeset	583
a5f9b959d5d1 Uploaded iracooke parents: diff changeset	584
a5f9b959d5d1 Uploaded iracooke parents: diff changeset	585 ------
a5f9b959d5d1 Uploaded iracooke parents: diff changeset	586
a5f9b959d5d1 Uploaded iracooke parents: diff changeset	587 Citation
a5f9b959d5d1 Uploaded iracooke parents: diff changeset	588
30 ad60446b1e93 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit bdb5ee12705a3494eee96d1963f16f68bbe41d5c galaxyp parents: 29 diff changeset	589 To cite the underlying tools (PeptideShaker and SearchGUI) please refer to the list of papers at http://compomics.github.io
18 a5f9b959d5d1 Uploaded iracooke parents: diff changeset	590
30 ad60446b1e93 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit bdb5ee12705a3494eee96d1963f16f68bbe41d5c galaxyp parents: 29 diff changeset	591 If you use this tool in Galaxy, please cite Chilton J, Ira Cooke, Bjoern Gruening et al.
18 a5f9b959d5d1 Uploaded iracooke parents: diff changeset	592 </help>
20 2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b iracooke parents: 18 diff changeset	593 <expand macro="citations" />
18 a5f9b959d5d1 Uploaded iracooke parents: diff changeset	594 </tool>

Mercurial > repos > galaxyp > peptideshaker

annotate peptide_shaker.xml @ 45:5fa8b409599e draft