peptideshaker: peptide_shaker.xml annotate

annotate peptide_shaker.xml @ 53:d67a3c1bfd09 draft

planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 1327a0e10d66e5ed6a8b63b211672a724fcac424

author	galaxyp
date	Wed, 08 May 2019 14:06:07 -0400
parents	864bd76db767
children	7fdd9119cc4f

rev	line source
53 d67a3c1bfd09 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 1327a0e10d66e5ed6a8b63b211672a724fcac424 galaxyp parents: 52 diff changeset	1 <tool id="peptide_shaker" name="Peptide Shaker" version="@PEPTIDESHAKER_VERSION@.3">
18 a5f9b959d5d1 Uploaded iracooke parents: diff changeset	2 <description>
20 2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b iracooke parents: 18 diff changeset	3 Perform protein identification using various search engines based on results from SearchGUI
18 a5f9b959d5d1 Uploaded iracooke parents: diff changeset	4 </description>
20 2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b iracooke parents: 18 diff changeset	5 <macros>
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b iracooke parents: 18 diff changeset	6 <import>macros.xml</import>
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b iracooke parents: 18 diff changeset	7 </macros>
21 dfaea053e32f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 327a3944f2f56668d607c3d6cb08ae7d588e208c iracooke parents: 20 diff changeset	8 <requirements>
49 58a3e6cb2598 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6e846f7195a9e939047ac975c6523e8cf99da6b4 galaxyp parents: 46 diff changeset	9 <requirement type="package" version="@PEPTIDESHAKER_VERSION@">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" />
49 58a3e6cb2598 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6e846f7195a9e939047ac975c6523e8cf99da6b4 galaxyp parents: 46 diff changeset	12
58a3e6cb2598 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6e846f7195a9e939047ac975c6523e8cf99da6b4 galaxyp parents: 46 diff changeset	13 <command><![CDATA[
58a3e6cb2598 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6e846f7195a9e939047ac975c6523e8cf99da6b4 galaxyp parents: 46 diff changeset	14 ## When supporting more advanced Galaxy versions: command use_shared_home="false"
18 a5f9b959d5d1 Uploaded iracooke parents: diff changeset	15 #from datetime import datetime
a5f9b959d5d1 Uploaded iracooke parents: diff changeset	16 #set $exp_str = "Galaxy_Experiment_%s" % datetime.now().strftime("%Y%m%d%H%M%s")
a5f9b959d5d1 Uploaded iracooke parents: diff changeset	17 #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	18 #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	19 #set $bin_dir = "bin"
18 a5f9b959d5d1 Uploaded iracooke parents: diff changeset	20
22 e3be595c0bf5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 5ca27ef280bee8b65fd3d0d2cd5ff280a2cebb3d iracooke parents: 21 diff changeset	21
49 58a3e6cb2598 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6e846f7195a9e939047ac975c6523e8cf99da6b4 galaxyp parents: 46 diff changeset	22 mkdir output_reports &&
58a3e6cb2598 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6e846f7195a9e939047ac975c6523e8cf99da6b4 galaxyp parents: 46 diff changeset	23 cwd=`pwd` &&
58a3e6cb2598 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6e846f7195a9e939047ac975c6523e8cf99da6b4 galaxyp parents: 46 diff changeset	24 export HOME=\$cwd &&
58a3e6cb2598 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6e846f7195a9e939047ac975c6523e8cf99da6b4 galaxyp parents: 46 diff changeset	25
58a3e6cb2598 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6e846f7195a9e939047ac975c6523e8cf99da6b4 galaxyp parents: 46 diff changeset	26 echo "" > $temp_stderr &&
18 a5f9b959d5d1 Uploaded iracooke parents: diff changeset	27
20 2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b iracooke parents: 18 diff changeset	28 ln -s '$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	29 jar xvf searchgui_input.zip SEARCHGUI_IdentificationParameters.par &&
49 58a3e6cb2598 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6e846f7195a9e939047ac975c6523e8cf99da6b4 galaxyp parents: 46 diff changeset	30
58a3e6cb2598 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6e846f7195a9e939047ac975c6523e8cf99da6b4 galaxyp parents: 46 diff changeset	31
58a3e6cb2598 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6e846f7195a9e939047ac975c6523e8cf99da6b4 galaxyp parents: 46 diff changeset	32 peptide-shaker eu.isas.peptideshaker.cmd.PathSettingsCLI
58a3e6cb2598 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6e846f7195a9e939047ac975c6523e8cf99da6b4 galaxyp parents: 46 diff changeset	33 --exec_dir="\$cwd/${bin_dir}"
58a3e6cb2598 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6e846f7195a9e939047ac975c6523e8cf99da6b4 galaxyp parents: 46 diff changeset	34 -temp_folder \$cwd/PathSettingsCLI
58a3e6cb2598 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6e846f7195a9e939047ac975c6523e8cf99da6b4 galaxyp parents: 46 diff changeset	35 -log \$cwd/peptideshaker.log &&
58a3e6cb2598 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6e846f7195a9e939047ac975c6523e8cf99da6b4 galaxyp parents: 46 diff changeset	36
58a3e6cb2598 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6e846f7195a9e939047ac975c6523e8cf99da6b4 galaxyp parents: 46 diff changeset	37 #if str($exporting_options.output_reports) != "None"
58a3e6cb2598 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6e846f7195a9e939047ac975c6523e8cf99da6b4 galaxyp parents: 46 diff changeset	38 #set $output_reports_list = set(str($exporting_options.output_reports).split(','))
58a3e6cb2598 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6e846f7195a9e939047ac975c6523e8cf99da6b4 galaxyp parents: 46 diff changeset	39 #else
58a3e6cb2598 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6e846f7195a9e939047ac975c6523e8cf99da6b4 galaxyp parents: 46 diff changeset	40 #set $output_reports_list = set()
58a3e6cb2598 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6e846f7195a9e939047ac975c6523e8cf99da6b4 galaxyp parents: 46 diff changeset	41 #end if
58a3e6cb2598 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6e846f7195a9e939047ac975c6523e8cf99da6b4 galaxyp parents: 46 diff changeset	42
18 a5f9b959d5d1 Uploaded iracooke parents: diff changeset	43 ######################
a5f9b959d5d1 Uploaded iracooke parents: diff changeset	44 ## PeptideShakerCLI ##
a5f9b959d5d1 Uploaded iracooke parents: diff changeset	45 ######################
49 58a3e6cb2598 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6e846f7195a9e939047ac975c6523e8cf99da6b4 galaxyp parents: 46 diff changeset	46 (peptide-shaker -Djava.awt.headless=true eu.isas.peptideshaker.cmd.PeptideShakerCLI
30 ad60446b1e93 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit bdb5ee12705a3494eee96d1963f16f68bbe41d5c galaxyp parents: 29 diff changeset	47 --exec_dir="\$cwd/${bin_dir}"
49 58a3e6cb2598 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6e846f7195a9e939047ac975c6523e8cf99da6b4 galaxyp parents: 46 diff changeset	48 -gui 0
20 2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b iracooke parents: 18 diff changeset	49 -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	50 -experiment '$exp_str'
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b iracooke parents: 18 diff changeset	51 -sample '$samp_str'
18 a5f9b959d5d1 Uploaded iracooke parents: diff changeset	52 -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	53 -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	54 -id_params \$cwd/SEARCHGUI_IdentificationParameters.par
24 815f93bb3e1b Uploaded galaxyp parents: 22 diff changeset	55 -out \$cwd/peptideshaker_output.cpsx
49 58a3e6cb2598 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6e846f7195a9e939047ac975c6523e8cf99da6b4 galaxyp parents: 46 diff changeset	56 #if $exporting_options.zip_conditional.zip_output_boolean == 'zip':
20 2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b iracooke parents: 18 diff changeset	57 -zip \$cwd/peptideshaker_output.zip
49 58a3e6cb2598 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6e846f7195a9e939047ac975c6523e8cf99da6b4 galaxyp parents: 46 diff changeset	58 #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	59 -threads "\${GALAXY_SLOTS:-12}"
18 a5f9b959d5d1 Uploaded iracooke parents: diff changeset	60
49 58a3e6cb2598 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6e846f7195a9e939047ac975c6523e8cf99da6b4 galaxyp parents: 46 diff changeset	61 ##Optional processing parameters:
58a3e6cb2598 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6e846f7195a9e939047ac975c6523e8cf99da6b4 galaxyp parents: 46 diff changeset	62 #if $processing_options.processing_options_selector == "yes"
58a3e6cb2598 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6e846f7195a9e939047ac975c6523e8cf99da6b4 galaxyp parents: 46 diff changeset	63 -protein_fdr "${processing_options.protein_fdr}"
58a3e6cb2598 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6e846f7195a9e939047ac975c6523e8cf99da6b4 galaxyp parents: 46 diff changeset	64 -peptide_fdr "${processing_options.peptide_fdr}"
58a3e6cb2598 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6e846f7195a9e939047ac975c6523e8cf99da6b4 galaxyp parents: 46 diff changeset	65 -psm_fdr "${processing_options.psm_fdr}"
58a3e6cb2598 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6e846f7195a9e939047ac975c6523e8cf99da6b4 galaxyp parents: 46 diff changeset	66 -ptm_score "${processing_options.ptm_score.ptm_score_selector}"
58a3e6cb2598 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6e846f7195a9e939047ac975c6523e8cf99da6b4 galaxyp parents: 46 diff changeset	67 #if $processing_options.ptm_score.ptm_score_selector == 1
58a3e6cb2598 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6e846f7195a9e939047ac975c6523e8cf99da6b4 galaxyp parents: 46 diff changeset	68 -score_neutral_losses "${processing_options.ptm_score.neutral_losses}"
58a3e6cb2598 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6e846f7195a9e939047ac975c6523e8cf99da6b4 galaxyp parents: 46 diff changeset	69 #if str($processing_options.ptm_score.ptm_threshold) != ''
58a3e6cb2598 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6e846f7195a9e939047ac975c6523e8cf99da6b4 galaxyp parents: 46 diff changeset	70 -ptm_threshold "${processing_options.ptm_score.ptm_threshold}"
18 a5f9b959d5d1 Uploaded iracooke parents: diff changeset	71 #end if
a5f9b959d5d1 Uploaded iracooke parents: diff changeset	72 #end if
49 58a3e6cb2598 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6e846f7195a9e939047ac975c6523e8cf99da6b4 galaxyp parents: 46 diff changeset	73 -ptm_alignment "${processing_options.ptm_alignment}"
58a3e6cb2598 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6e846f7195a9e939047ac975c6523e8cf99da6b4 galaxyp parents: 46 diff changeset	74 -ptm_sequence_matching_type "${processing_options.ptm_sequence_matching_type}"
58a3e6cb2598 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6e846f7195a9e939047ac975c6523e8cf99da6b4 galaxyp parents: 46 diff changeset	75 -protein_fraction_mw_confidence "${processing_options.protein_fraction_mw_confidence}"
58a3e6cb2598 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6e846f7195a9e939047ac975c6523e8cf99da6b4 galaxyp parents: 46 diff changeset	76 #end if
58a3e6cb2598 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6e846f7195a9e939047ac975c6523e8cf99da6b4 galaxyp parents: 46 diff changeset	77
58a3e6cb2598 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6e846f7195a9e939047ac975c6523e8cf99da6b4 galaxyp parents: 46 diff changeset	78 ##Optional filtering parameters:
58a3e6cb2598 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6e846f7195a9e939047ac975c6523e8cf99da6b4 galaxyp parents: 46 diff changeset	79 #if $filtering_options.filtering_options_selector == "yes":
58a3e6cb2598 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6e846f7195a9e939047ac975c6523e8cf99da6b4 galaxyp parents: 46 diff changeset	80 -import_peptide_length_min "${filtering_options.min_peptide_length}"
58a3e6cb2598 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6e846f7195a9e939047ac975c6523e8cf99da6b4 galaxyp parents: 46 diff changeset	81 -import_peptide_length_max "${filtering_options.max_peptide_length}"
58a3e6cb2598 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6e846f7195a9e939047ac975c6523e8cf99da6b4 galaxyp parents: 46 diff changeset	82 -import_precurosor_mz "${filtering_options.max_precursor_error}"
58a3e6cb2598 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6e846f7195a9e939047ac975c6523e8cf99da6b4 galaxyp parents: 46 diff changeset	83 -import_precurosor_mz_ppm "${filtering_options.max_precursor_error_type}"
58a3e6cb2598 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6e846f7195a9e939047ac975c6523e8cf99da6b4 galaxyp parents: 46 diff changeset	84 ##-max_xtandem_e "${filtering_options.max_xtandem_e}"
58a3e6cb2598 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6e846f7195a9e939047ac975c6523e8cf99da6b4 galaxyp parents: 46 diff changeset	85 ##-max_omssa_e "${filtering_options.max_omssa_e}"
58a3e6cb2598 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6e846f7195a9e939047ac975c6523e8cf99da6b4 galaxyp parents: 46 diff changeset	86 ##-max_mascot_e "${filtering_options.max_mascot_e}"
58a3e6cb2598 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6e846f7195a9e939047ac975c6523e8cf99da6b4 galaxyp parents: 46 diff changeset	87 -exclude_unknown_ptms "${filtering_options.exclude_unknown_ptms}"
58a3e6cb2598 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6e846f7195a9e939047ac975c6523e8cf99da6b4 galaxyp parents: 46 diff changeset	88 #end if
18 a5f9b959d5d1 Uploaded iracooke parents: diff changeset	89
49 58a3e6cb2598 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6e846f7195a9e939047ac975c6523e8cf99da6b4 galaxyp parents: 46 diff changeset	90 ##################################
58a3e6cb2598 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6e846f7195a9e939047ac975c6523e8cf99da6b4 galaxyp parents: 46 diff changeset	91 ## mzidCLI options ##
58a3e6cb2598 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6e846f7195a9e939047ac975c6523e8cf99da6b4 galaxyp parents: 46 diff changeset	92 ##################################
58a3e6cb2598 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6e846f7195a9e939047ac975c6523e8cf99da6b4 galaxyp parents: 46 diff changeset	93
58a3e6cb2598 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6e846f7195a9e939047ac975c6523e8cf99da6b4 galaxyp parents: 46 diff changeset	94 #if $exporting_options.mzidentml_conditional.mzidentml_creation == 1:
58a3e6cb2598 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6e846f7195a9e939047ac975c6523e8cf99da6b4 galaxyp parents: 46 diff changeset	95 -output_file \$cwd/output.mzid
58a3e6cb2598 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6e846f7195a9e939047ac975c6523e8cf99da6b4 galaxyp parents: 46 diff changeset	96 -include_sequences ${exporting_options.mzidentml_conditional.include_sequences}
58a3e6cb2598 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6e846f7195a9e939047ac975c6523e8cf99da6b4 galaxyp parents: 46 diff changeset	97 #if $contact_options.contact_options_selector == "yes":
58a3e6cb2598 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6e846f7195a9e939047ac975c6523e8cf99da6b4 galaxyp parents: 46 diff changeset	98 -contact_first_name "$contact_options.contact_first_name"
58a3e6cb2598 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6e846f7195a9e939047ac975c6523e8cf99da6b4 galaxyp parents: 46 diff changeset	99 -contact_last_name "$contact_options.contact_last_name"
58a3e6cb2598 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6e846f7195a9e939047ac975c6523e8cf99da6b4 galaxyp parents: 46 diff changeset	100 -contact_email "$contact_options.contact_email"
58a3e6cb2598 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6e846f7195a9e939047ac975c6523e8cf99da6b4 galaxyp parents: 46 diff changeset	101 -contact_address "$contact_options.contact_address"
58a3e6cb2598 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6e846f7195a9e939047ac975c6523e8cf99da6b4 galaxyp parents: 46 diff changeset	102 #if str($contact_options.contact_url).strip() != '':
58a3e6cb2598 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6e846f7195a9e939047ac975c6523e8cf99da6b4 galaxyp parents: 46 diff changeset	103 -contact_url = "$contact_options.contact_url"
58a3e6cb2598 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6e846f7195a9e939047ac975c6523e8cf99da6b4 galaxyp parents: 46 diff changeset	104 #end if
58a3e6cb2598 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6e846f7195a9e939047ac975c6523e8cf99da6b4 galaxyp parents: 46 diff changeset	105 -organization_name "$contact_options.organization_name"
58a3e6cb2598 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6e846f7195a9e939047ac975c6523e8cf99da6b4 galaxyp parents: 46 diff changeset	106 -organization_email "$contact_options.organization_email"
58a3e6cb2598 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6e846f7195a9e939047ac975c6523e8cf99da6b4 galaxyp parents: 46 diff changeset	107 -organization_address "$contact_options.organization_address"
58a3e6cb2598 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6e846f7195a9e939047ac975c6523e8cf99da6b4 galaxyp parents: 46 diff changeset	108 #if str($contact_options.organization_url).strip() != '':
58a3e6cb2598 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6e846f7195a9e939047ac975c6523e8cf99da6b4 galaxyp parents: 46 diff changeset	109 -organization_url = "$contact_options.organization_url"
58a3e6cb2598 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6e846f7195a9e939047ac975c6523e8cf99da6b4 galaxyp parents: 46 diff changeset	110 #end if
58a3e6cb2598 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6e846f7195a9e939047ac975c6523e8cf99da6b4 galaxyp parents: 46 diff changeset	111 #else:
58a3e6cb2598 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6e846f7195a9e939047ac975c6523e8cf99da6b4 galaxyp parents: 46 diff changeset	112 -contact_first_name "Proteomics"
58a3e6cb2598 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6e846f7195a9e939047ac975c6523e8cf99da6b4 galaxyp parents: 46 diff changeset	113 -contact_last_name "Galaxy"
58a3e6cb2598 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6e846f7195a9e939047ac975c6523e8cf99da6b4 galaxyp parents: 46 diff changeset	114 -contact_email "galaxyp@umn.edu"
58a3e6cb2598 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6e846f7195a9e939047ac975c6523e8cf99da6b4 galaxyp parents: 46 diff changeset	115 -contact_address "galaxyp@umn.edu"
58a3e6cb2598 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6e846f7195a9e939047ac975c6523e8cf99da6b4 galaxyp parents: 46 diff changeset	116 -organization_name "University of Minnesota"
58a3e6cb2598 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6e846f7195a9e939047ac975c6523e8cf99da6b4 galaxyp parents: 46 diff changeset	117 -organization_email "galaxyp@umn.edu"
58a3e6cb2598 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6e846f7195a9e939047ac975c6523e8cf99da6b4 galaxyp parents: 46 diff changeset	118 -organization_address "Minneapolis, MN 55455, Vereinigte Staaten"
18 a5f9b959d5d1 Uploaded iracooke parents: diff changeset	119 #end if
49 58a3e6cb2598 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6e846f7195a9e939047ac975c6523e8cf99da6b4 galaxyp parents: 46 diff changeset	120 #end if
18 a5f9b959d5d1 Uploaded iracooke parents: diff changeset	121
a5f9b959d5d1 Uploaded iracooke parents: diff changeset	122 ##################################
a5f9b959d5d1 Uploaded iracooke parents: diff changeset	123 ## PeptideShaker Report options ##
a5f9b959d5d1 Uploaded iracooke parents: diff changeset	124 ##################################
49 58a3e6cb2598 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6e846f7195a9e939047ac975c6523e8cf99da6b4 galaxyp parents: 46 diff changeset	125 ## Generate Reports if the user has selected one of the 11 additional reports
58a3e6cb2598 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6e846f7195a9e939047ac975c6523e8cf99da6b4 galaxyp parents: 46 diff changeset	126 #if len($output_reports_list) > 0
58a3e6cb2598 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6e846f7195a9e939047ac975c6523e8cf99da6b4 galaxyp parents: 46 diff changeset	127 -out_reports \$cwd/output_reports
58a3e6cb2598 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6e846f7195a9e939047ac975c6523e8cf99da6b4 galaxyp parents: 46 diff changeset	128 -reports #echo ','.join($output_reports_list)#
18 a5f9b959d5d1 Uploaded iracooke parents: diff changeset	129 #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	130
49 58a3e6cb2598 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6e846f7195a9e939047ac975c6523e8cf99da6b4 galaxyp parents: 46 diff changeset	131 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	132
53 d67a3c1bfd09 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 1327a0e10d66e5ed6a8b63b211672a724fcac424 galaxyp parents: 52 diff changeset	133 ## If the user chose to zip the results but also export reports out of the zip, we have to unzip them
d67a3c1bfd09 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 1327a0e10d66e5ed6a8b63b211672a724fcac424 galaxyp parents: 52 diff changeset	134 #if $exporting_options.zip_conditional.zip_output_boolean == 'zip' and $exporting_options.zip_conditional.export_reports_when_zip:
d67a3c1bfd09 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 1327a0e10d66e5ed6a8b63b211672a724fcac424 galaxyp parents: 52 diff changeset	135 && unzip \$cwd/peptideshaker_output.zip 'reports/*' -d \$cwd/output_reports
d67a3c1bfd09 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 1327a0e10d66e5ed6a8b63b211672a724fcac424 galaxyp parents: 52 diff changeset	136 #end if
d67a3c1bfd09 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 1327a0e10d66e5ed6a8b63b211672a724fcac424 galaxyp parents: 52 diff changeset	137
49 58a3e6cb2598 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6e846f7195a9e939047ac975c6523e8cf99da6b4 galaxyp parents: 46 diff changeset	138 #if len(output_reports_list)>0:
58a3e6cb2598 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6e846f7195a9e939047ac975c6523e8cf99da6b4 galaxyp parents: 46 diff changeset	139 #if '0' in $output_reports_list:
58a3e6cb2598 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6e846f7195a9e939047ac975c6523e8cf99da6b4 galaxyp parents: 46 diff changeset	140 && find \$cwd/output_reports -name '*Certificate_of_Analysis.txt' -exec bash -c 'mv "$0" "certificate.txt"' {} \;
58a3e6cb2598 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6e846f7195a9e939047ac975c6523e8cf99da6b4 galaxyp parents: 46 diff changeset	141 #end if
58a3e6cb2598 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6e846f7195a9e939047ac975c6523e8cf99da6b4 galaxyp parents: 46 diff changeset	142 #if '1' in $output_reports_list:
58a3e6cb2598 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6e846f7195a9e939047ac975c6523e8cf99da6b4 galaxyp parents: 46 diff changeset	143 && find \$cwd/output_reports -name '*Default_Hierarchical_Report.txt' -exec bash -c 'mv "$0" "hierarchical.txt"' {} \;
58a3e6cb2598 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6e846f7195a9e939047ac975c6523e8cf99da6b4 galaxyp parents: 46 diff changeset	144 #end if
58a3e6cb2598 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6e846f7195a9e939047ac975c6523e8cf99da6b4 galaxyp parents: 46 diff changeset	145 #if '2' in $output_reports_list:
58a3e6cb2598 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6e846f7195a9e939047ac975c6523e8cf99da6b4 galaxyp parents: 46 diff changeset	146 && find \$cwd/output_reports -name '*Default_PSM_Phosphorylation_Report.txt' -exec bash -c 'mv "$0" "psm_phospho.txt"' {} \;
58a3e6cb2598 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6e846f7195a9e939047ac975c6523e8cf99da6b4 galaxyp parents: 46 diff changeset	147 #end if`
58a3e6cb2598 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6e846f7195a9e939047ac975c6523e8cf99da6b4 galaxyp parents: 46 diff changeset	148 #if '3' in $output_reports_list:
58a3e6cb2598 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6e846f7195a9e939047ac975c6523e8cf99da6b4 galaxyp parents: 46 diff changeset	149 && find \$cwd/output_reports -name '*Default_PSM_Report.txt' -exec bash -c 'mv "$0" "psm.txt"' {} \;
58a3e6cb2598 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6e846f7195a9e939047ac975c6523e8cf99da6b4 galaxyp parents: 46 diff changeset	150 #end if
58a3e6cb2598 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6e846f7195a9e939047ac975c6523e8cf99da6b4 galaxyp parents: 46 diff changeset	151 #if '4' in $output_reports_list:
58a3e6cb2598 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6e846f7195a9e939047ac975c6523e8cf99da6b4 galaxyp parents: 46 diff changeset	152 && find \$cwd/output_reports -name '*Default_PSM_Report_with_non-validated_matches.txt' -exec bash -c 'mv "$0" "psm_nonvalidated.txt"' {} \;
58a3e6cb2598 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6e846f7195a9e939047ac975c6523e8cf99da6b4 galaxyp parents: 46 diff changeset	153 #end if
58a3e6cb2598 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6e846f7195a9e939047ac975c6523e8cf99da6b4 galaxyp parents: 46 diff changeset	154 #if '5' in $output_reports_list:
58a3e6cb2598 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6e846f7195a9e939047ac975c6523e8cf99da6b4 galaxyp parents: 46 diff changeset	155 && find \$cwd/output_reports -name '*Default_Peptide_Phosphorylation_Report.txt' -exec bash -c 'mv "$0" "peptides_phospho.txt"' {} \;
58a3e6cb2598 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6e846f7195a9e939047ac975c6523e8cf99da6b4 galaxyp parents: 46 diff changeset	156 #end if
58a3e6cb2598 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6e846f7195a9e939047ac975c6523e8cf99da6b4 galaxyp parents: 46 diff changeset	157 #if '6' in $output_reports_list:
58a3e6cb2598 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6e846f7195a9e939047ac975c6523e8cf99da6b4 galaxyp parents: 46 diff changeset	158 && find \$cwd/output_reports -name '*Default_Peptide_Report.txt' -exec bash -c 'mv "$0" "peptides.txt"' {} \;
58a3e6cb2598 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6e846f7195a9e939047ac975c6523e8cf99da6b4 galaxyp parents: 46 diff changeset	159 #end if
58a3e6cb2598 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6e846f7195a9e939047ac975c6523e8cf99da6b4 galaxyp parents: 46 diff changeset	160 #if '7' in $output_reports_list:
58a3e6cb2598 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6e846f7195a9e939047ac975c6523e8cf99da6b4 galaxyp parents: 46 diff changeset	161 && find \$cwd/output_reports -name '*Default_Peptide_Report_with_non-validated_matches.txt' -exec bash -c 'mv "$0" "peptides_nonvalidated.txt"' {} \;
58a3e6cb2598 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6e846f7195a9e939047ac975c6523e8cf99da6b4 galaxyp parents: 46 diff changeset	162 #end if
58a3e6cb2598 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6e846f7195a9e939047ac975c6523e8cf99da6b4 galaxyp parents: 46 diff changeset	163 #if '8' in $output_reports_list:
58a3e6cb2598 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6e846f7195a9e939047ac975c6523e8cf99da6b4 galaxyp parents: 46 diff changeset	164 && find \$cwd/output_reports -name '*Default_Protein_Phosphorylation_Report.txt' -exec bash -c 'mv "$0" "proteins_phospho.txt"' {} \;
58a3e6cb2598 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6e846f7195a9e939047ac975c6523e8cf99da6b4 galaxyp parents: 46 diff changeset	165 #end if
58a3e6cb2598 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6e846f7195a9e939047ac975c6523e8cf99da6b4 galaxyp parents: 46 diff changeset	166 #if '9' in $output_reports_list:
58a3e6cb2598 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6e846f7195a9e939047ac975c6523e8cf99da6b4 galaxyp parents: 46 diff changeset	167 && find \$cwd/output_reports -name '*Default_Protein_Report.txt' -exec bash -c 'mv "$0" "proteins.txt"' {} \;
58a3e6cb2598 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6e846f7195a9e939047ac975c6523e8cf99da6b4 galaxyp parents: 46 diff changeset	168 #end if
58a3e6cb2598 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6e846f7195a9e939047ac975c6523e8cf99da6b4 galaxyp parents: 46 diff changeset	169 #if '10' in $output_reports_list:
58a3e6cb2598 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6e846f7195a9e939047ac975c6523e8cf99da6b4 galaxyp parents: 46 diff changeset	170 && find \$cwd/output_reports -name '*Default_Protein_Report_with_non-validated_matches.txt' -exec bash -c 'mv "$0" "proteins_nonvalidated.txt"' {} \;
58a3e6cb2598 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6e846f7195a9e939047ac975c6523e8cf99da6b4 galaxyp parents: 46 diff changeset	171 #end if
58a3e6cb2598 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6e846f7195a9e939047ac975c6523e8cf99da6b4 galaxyp parents: 46 diff changeset	172 #if '11' in $output_reports_list:
58a3e6cb2598 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6e846f7195a9e939047ac975c6523e8cf99da6b4 galaxyp parents: 46 diff changeset	173 && find \$cwd/output_reports -name '*Extended_PSM_Report.txt' -exec bash -c 'mv "$0" "psmx.txt"' {} \;
58a3e6cb2598 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6e846f7195a9e939047ac975c6523e8cf99da6b4 galaxyp parents: 46 diff changeset	174 #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	175 #end if
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b iracooke parents: 18 diff changeset	176
49 58a3e6cb2598 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6e846f7195a9e939047ac975c6523e8cf99da6b4 galaxyp parents: 46 diff changeset	177 && cat $temp_stderr 2>&1;
20 2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b iracooke parents: 18 diff changeset	178 ]]>
18 a5f9b959d5d1 Uploaded iracooke parents: diff changeset	179 </command>
a5f9b959d5d1 Uploaded iracooke parents: diff changeset	180 <inputs>
21 dfaea053e32f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 327a3944f2f56668d607c3d6cb08ae7d588e208c iracooke parents: 20 diff changeset	181 <param name="searchgui_input" format="searchgui_archive" type="data" label="Compressed SearchGUI results"
24 815f93bb3e1b Uploaded galaxyp parents: 22 diff changeset	182 help="SearchGUI Results from History">
815f93bb3e1b Uploaded galaxyp parents: 22 diff changeset	183 <options options_filter_attribute="metadata.searchgui_major_version" >
815f93bb3e1b Uploaded galaxyp parents: 22 diff changeset	184 <filter type="add_value" value="@SEARCHGUI_MAJOR_VERSION@" />
815f93bb3e1b Uploaded galaxyp parents: 22 diff changeset	185 </options>
815f93bb3e1b Uploaded galaxyp parents: 22 diff changeset	186 </param>
18 a5f9b959d5d1 Uploaded iracooke parents: diff changeset	187 <conditional name="processing_options">
a5f9b959d5d1 Uploaded iracooke parents: diff changeset	188 <param name="processing_options_selector" type="select" label="Specify Advanced PeptideShaker Processing Options">
a5f9b959d5d1 Uploaded iracooke parents: diff changeset	189 <option value="no" selected="True">Default Processing Options</option>
a5f9b959d5d1 Uploaded iracooke parents: diff changeset	190 <option value="yes">Advanced Processing Options</option>
a5f9b959d5d1 Uploaded iracooke parents: diff changeset	191 </param>
a5f9b959d5d1 Uploaded iracooke parents: diff changeset	192 <when value="no" />
a5f9b959d5d1 Uploaded iracooke parents: diff changeset	193 <when value="yes">
a5f9b959d5d1 Uploaded iracooke parents: diff changeset	194 <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	195 <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	196 <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	197 <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	198 help="default 95%: '95.0'" />
a5f9b959d5d1 Uploaded iracooke parents: diff changeset	199 <conditional name="ptm_score">
a5f9b959d5d1 Uploaded iracooke parents: diff changeset	200 <param name="ptm_score_selector" type="select" label="The PTM probabilistic score to use for PTM localization">
52 864bd76db767 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 9dc7c9c3ebd64f14c0ce95a0dc190361a90fa4fb galaxyp parents: 50 diff changeset	201 <option value="0">A-score</option>
864bd76db767 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 9dc7c9c3ebd64f14c0ce95a0dc190361a90fa4fb galaxyp parents: 50 diff changeset	202 <option value="1" selected="True">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	203 <option value="2">None</option>
18 a5f9b959d5d1 Uploaded iracooke parents: diff changeset	204 </param>
a5f9b959d5d1 Uploaded iracooke parents: diff changeset	205 <when value="0" />
a5f9b959d5d1 Uploaded iracooke parents: diff changeset	206 <when value="1">
a5f9b959d5d1 Uploaded iracooke parents: diff changeset	207 <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	208 <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	209 help="Automatic mode will be used if not set" />
a5f9b959d5d1 Uploaded iracooke parents: diff changeset	210 </when>
38 79e37eff006d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 48984afa5f3d1b80ecbbff2847645c15acd81fe6 galaxyp parents: 37 diff changeset	211 <when value="2" />
18 a5f9b959d5d1 Uploaded iracooke parents: diff changeset	212 </conditional>
38 79e37eff006d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 48984afa5f3d1b80ecbbff2847645c15acd81fe6 galaxyp parents: 37 diff changeset	213 <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	214 <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	215 <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	216 <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	217 </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	218 <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	219 <!-- SKIPPING -protein_fraction_mw_confidence ${processing_options.protein_fraction_mw_confidence} -->
a5f9b959d5d1 Uploaded iracooke parents: diff changeset	220 </when>
a5f9b959d5d1 Uploaded iracooke parents: diff changeset	221 </conditional>
a5f9b959d5d1 Uploaded iracooke parents: diff changeset	222 <conditional name="filtering_options">
a5f9b959d5d1 Uploaded iracooke parents: diff changeset	223 <param name="filtering_options_selector" type="select" label="Specify Advanced Filtering Options"
a5f9b959d5d1 Uploaded iracooke parents: diff changeset	224 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	225 <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	226 <option value="yes">Advanced Filtering Options</option>
18 a5f9b959d5d1 Uploaded iracooke parents: diff changeset	227 </param>
a5f9b959d5d1 Uploaded iracooke parents: diff changeset	228 <when value="no" />
a5f9b959d5d1 Uploaded iracooke parents: diff changeset	229 <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	230 <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	231 <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	232 <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	233 help="Next option specifies units (Da or ppm)" />
18 a5f9b959d5d1 Uploaded iracooke parents: diff changeset	234 <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	235 <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	236 <option value="0">Daltons</option>
18 a5f9b959d5d1 Uploaded iracooke parents: diff changeset	237 </param>
20 2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b iracooke parents: 18 diff changeset	238 <!--param name="max_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	239 <!--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	240 <!--param name="max_mascot_e" label="Maximum Mascot e-value filter" value="100" type="float" help="" /-->
18 a5f9b959d5d1 Uploaded iracooke parents: diff changeset	241 <param name="exclude_unknown_ptms" label="Exclude Unknown PTMs" type="boolean" truevalue="1" falsevalue="0" checked="true" />
a5f9b959d5d1 Uploaded iracooke parents: diff changeset	242 </when>
a5f9b959d5d1 Uploaded iracooke parents: diff changeset	243 </conditional>
30 ad60446b1e93 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit bdb5ee12705a3494eee96d1963f16f68bbe41d5c galaxyp parents: 29 diff changeset	244 <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	245 <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	246 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	247 <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	248 <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	249 </param>
ad60446b1e93 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit bdb5ee12705a3494eee96d1963f16f68bbe41d5c galaxyp parents: 29 diff changeset	250 <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	251 <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	252 <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	253 <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	254 </param>
ad60446b1e93 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit bdb5ee12705a3494eee96d1963f16f68bbe41d5c galaxyp parents: 29 diff changeset	255 <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	256 <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	257 </param>
ad60446b1e93 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit bdb5ee12705a3494eee96d1963f16f68bbe41d5c galaxyp parents: 29 diff changeset	258 <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	259 <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	260 </param>
ad60446b1e93 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit bdb5ee12705a3494eee96d1963f16f68bbe41d5c galaxyp parents: 29 diff changeset	261 <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	262 <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	263 </param>
ad60446b1e93 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit bdb5ee12705a3494eee96d1963f16f68bbe41d5c galaxyp parents: 29 diff changeset	264 <param name="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	265 </param>
ad60446b1e93 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit bdb5ee12705a3494eee96d1963f16f68bbe41d5c galaxyp parents: 29 diff changeset	266 <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	267 <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	268 </param>
ad60446b1e93 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit bdb5ee12705a3494eee96d1963f16f68bbe41d5c galaxyp parents: 29 diff changeset	269 <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	270 <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	271 </param>
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="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	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="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	276 </param>
ad60446b1e93 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit bdb5ee12705a3494eee96d1963f16f68bbe41d5c galaxyp parents: 29 diff changeset	277 </when>
ad60446b1e93 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit bdb5ee12705a3494eee96d1963f16f68bbe41d5c galaxyp parents: 29 diff changeset	278 </conditional>
ad60446b1e93 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit bdb5ee12705a3494eee96d1963f16f68bbe41d5c galaxyp parents: 29 diff changeset	279
49 58a3e6cb2598 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6e846f7195a9e939047ac975c6523e8cf99da6b4 galaxyp parents: 46 diff changeset	280 <section name="exporting_options" expanded="true" title="Exporting options">
58a3e6cb2598 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6e846f7195a9e939047ac975c6523e8cf99da6b4 galaxyp parents: 46 diff changeset	281
58a3e6cb2598 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6e846f7195a9e939047ac975c6523e8cf99da6b4 galaxyp parents: 46 diff changeset	282 <conditional name="mzidentml_conditional">
58a3e6cb2598 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6e846f7195a9e939047ac975c6523e8cf99da6b4 galaxyp parents: 46 diff changeset	283 <param name="mzidentml_creation" type="boolean" truevalue="1" falsevalue="0" checked="true" label="Creates a mzIdentML file" />
58a3e6cb2598 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6e846f7195a9e939047ac975c6523e8cf99da6b4 galaxyp parents: 46 diff changeset	284 <when value="1">
58a3e6cb2598 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6e846f7195a9e939047ac975c6523e8cf99da6b4 galaxyp parents: 46 diff changeset	285 <param name="include_sequences" type="boolean" truevalue="1" falsevalue="0" checked="false" label="Include the protein sequences in the mzIdentML file" />
58a3e6cb2598 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6e846f7195a9e939047ac975c6523e8cf99da6b4 galaxyp parents: 46 diff changeset	286 </when>
58a3e6cb2598 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6e846f7195a9e939047ac975c6523e8cf99da6b4 galaxyp parents: 46 diff changeset	287 <when value="0" />
58a3e6cb2598 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6e846f7195a9e939047ac975c6523e8cf99da6b4 galaxyp parents: 46 diff changeset	288 </conditional>
58a3e6cb2598 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6e846f7195a9e939047ac975c6523e8cf99da6b4 galaxyp parents: 46 diff changeset	289
58a3e6cb2598 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6e846f7195a9e939047ac975c6523e8cf99da6b4 galaxyp parents: 46 diff changeset	290 <conditional name="zip_conditional">
58a3e6cb2598 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6e846f7195a9e939047ac975c6523e8cf99da6b4 galaxyp parents: 46 diff changeset	291 <param name="zip_output_boolean" type="boolean" truevalue="zip" falsevalue="separate" checked="false" label="Compress results into a single zip file" />
58a3e6cb2598 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6e846f7195a9e939047ac975c6523e8cf99da6b4 galaxyp parents: 46 diff changeset	292 <when value="separate">
58a3e6cb2598 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6e846f7195a9e939047ac975c6523e8cf99da6b4 galaxyp parents: 46 diff changeset	293 <param name="export_cps" type="boolean" truevalue="1" falsevalue="0" checked="false" label="Exports the CPS file" />
58a3e6cb2598 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6e846f7195a9e939047ac975c6523e8cf99da6b4 galaxyp parents: 46 diff changeset	294 </when>
53 d67a3c1bfd09 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 1327a0e10d66e5ed6a8b63b211672a724fcac424 galaxyp parents: 52 diff changeset	295 <when value="zip">
d67a3c1bfd09 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 1327a0e10d66e5ed6a8b63b211672a724fcac424 galaxyp parents: 52 diff changeset	296 <param name="export_reports_when_zip" type="boolean" truevalue="1" falsevalue="0" checked="false" label="Also export reports out of the zip" />
d67a3c1bfd09 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 1327a0e10d66e5ed6a8b63b211672a724fcac424 galaxyp parents: 52 diff changeset	297 </when>
49 58a3e6cb2598 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6e846f7195a9e939047ac975c6523e8cf99da6b4 galaxyp parents: 46 diff changeset	298 </conditional>
58a3e6cb2598 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6e846f7195a9e939047ac975c6523e8cf99da6b4 galaxyp parents: 46 diff changeset	299
58a3e6cb2598 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6e846f7195a9e939047ac975c6523e8cf99da6b4 galaxyp parents: 46 diff changeset	300 <param name="output_reports" type="select" display="checkboxes" multiple="True" optional="true" label="Reports to be generated">
58a3e6cb2598 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6e846f7195a9e939047ac975c6523e8cf99da6b4 galaxyp parents: 46 diff changeset	301 <option value="3">PSM Report</option>
58a3e6cb2598 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6e846f7195a9e939047ac975c6523e8cf99da6b4 galaxyp parents: 46 diff changeset	302 <option value="4">PSM Report with non-validated matches</option>
58a3e6cb2598 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6e846f7195a9e939047ac975c6523e8cf99da6b4 galaxyp parents: 46 diff changeset	303 <option value="2">PSM Phosphorylation Report</option>
58a3e6cb2598 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6e846f7195a9e939047ac975c6523e8cf99da6b4 galaxyp parents: 46 diff changeset	304 <option value="11">Extended PSM Report</option>
58a3e6cb2598 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6e846f7195a9e939047ac975c6523e8cf99da6b4 galaxyp parents: 46 diff changeset	305 <option value="6">Peptide Report</option>
58a3e6cb2598 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6e846f7195a9e939047ac975c6523e8cf99da6b4 galaxyp parents: 46 diff changeset	306 <option value="7">Peptide Report with non-validated matches</option>
58a3e6cb2598 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6e846f7195a9e939047ac975c6523e8cf99da6b4 galaxyp parents: 46 diff changeset	307 <option value="5">Peptide Phosphorylation Report</option>
58a3e6cb2598 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6e846f7195a9e939047ac975c6523e8cf99da6b4 galaxyp parents: 46 diff changeset	308 <option value="9">Protein Report</option>
58a3e6cb2598 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6e846f7195a9e939047ac975c6523e8cf99da6b4 galaxyp parents: 46 diff changeset	309 <option value="10">Protein Report with non-validated matches</option>
58a3e6cb2598 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6e846f7195a9e939047ac975c6523e8cf99da6b4 galaxyp parents: 46 diff changeset	310 <option value="8">Protein Phosphorylation Report</option>
58a3e6cb2598 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6e846f7195a9e939047ac975c6523e8cf99da6b4 galaxyp parents: 46 diff changeset	311 <option value="0">Certificate of Analysis</option>
58a3e6cb2598 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6e846f7195a9e939047ac975c6523e8cf99da6b4 galaxyp parents: 46 diff changeset	312 <option value="1">Hierarchical Report</option>
58a3e6cb2598 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6e846f7195a9e939047ac975c6523e8cf99da6b4 galaxyp parents: 46 diff changeset	313 </param>
58a3e6cb2598 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6e846f7195a9e939047ac975c6523e8cf99da6b4 galaxyp parents: 46 diff changeset	314
58a3e6cb2598 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6e846f7195a9e939047ac975c6523e8cf99da6b4 galaxyp parents: 46 diff changeset	315 </section>
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 ${on_string}: mzidentML file">
53 d67a3c1bfd09 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 1327a0e10d66e5ed6a8b63b211672a724fcac424 galaxyp parents: 52 diff changeset	320 <filter>exporting_options['zip_conditional']['zip_output_boolean'] is False and exporting_options['mzidentml_conditional']['mzidentml_creation'] is True</filter>
18 a5f9b959d5d1 Uploaded iracooke parents: diff changeset	321 </data>
44 f35bb9d0c93e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 981be1bde91d6d565693cd691553f77465e653bb galaxyp parents: 38 diff changeset	322 <data format="peptideshaker_archive" name="output_cps" from_work_dir="peptideshaker_output.cpsx" label="${tool.name} on ${on_string}: CPS file">
49 58a3e6cb2598 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6e846f7195a9e939047ac975c6523e8cf99da6b4 galaxyp parents: 46 diff changeset	323 <filter>exporting_options['zip_conditional']['zip_output_boolean'] is False and exporting_options['zip_conditional']['export_cps'] is True</filter>
18 a5f9b959d5d1 Uploaded iracooke parents: diff changeset	324 </data>
20 2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b iracooke parents: 18 diff changeset	325 <data format="zip" name="output_zip" from_work_dir="peptideshaker_output.zip" label="${tool.name} on ${on_string}: Archive">
49 58a3e6cb2598 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6e846f7195a9e939047ac975c6523e8cf99da6b4 galaxyp parents: 46 diff changeset	326 <filter>exporting_options['zip_conditional']['zip_output_boolean'] is True</filter>
20 2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b iracooke parents: 18 diff changeset	327 </data>
49 58a3e6cb2598 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6e846f7195a9e939047ac975c6523e8cf99da6b4 galaxyp parents: 46 diff changeset	328 <!--
58a3e6cb2598 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6e846f7195a9e939047ac975c6523e8cf99da6b4 galaxyp parents: 46 diff changeset	329 <data format="tabular" name="reports">
58a3e6cb2598 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6e846f7195a9e939047ac975c6523e8cf99da6b4 galaxyp parents: 46 diff changeset	330 <discover_datasets pattern="(?P<designation>.+)\.txt" format="tabular" directory="output_reports" visible="true" assign_primary_output="true" />
58a3e6cb2598 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6e846f7195a9e939047ac975c6523e8cf99da6b4 galaxyp parents: 46 diff changeset	331 </data>
58a3e6cb2598 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6e846f7195a9e939047ac975c6523e8cf99da6b4 galaxyp parents: 46 diff changeset	332 -->
58a3e6cb2598 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6e846f7195a9e939047ac975c6523e8cf99da6b4 galaxyp parents: 46 diff changeset	333 <data format="txt" name="output_certificate" from_work_dir="certificate.txt" label="${tool.name} on ${on_string}: Parameters">
53 d67a3c1bfd09 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 1327a0e10d66e5ed6a8b63b211672a724fcac424 galaxyp parents: 52 diff changeset	334 <filter>(exporting_options['zip_conditional']['zip_output_boolean'] is False or (exporting_options['zip_conditional']['zip_output_boolean'] is True and exporting_options['zip_conditional']['export_reports_when_zip'] is True) ) and str(exporting_options['output_reports']) != 'None' and '0' in exporting_options['output_reports']</filter>
18 a5f9b959d5d1 Uploaded iracooke parents: diff changeset	335 </data>
20 2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b iracooke parents: 18 diff changeset	336 <data format="tabular" name="output_hierarchical" from_work_dir="hierarchical.txt" label="${tool.name} on ${on_string}: Hierarchical Report">
53 d67a3c1bfd09 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 1327a0e10d66e5ed6a8b63b211672a724fcac424 galaxyp parents: 52 diff changeset	337 <filter>(exporting_options['zip_conditional']['zip_output_boolean'] is False or (exporting_options['zip_conditional']['zip_output_boolean'] is True and exporting_options['zip_conditional']['export_reports_when_zip'] is True) ) and str(exporting_options['output_reports']) != 'None' and '1' in exporting_options['output_reports']</filter>
20 2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b iracooke parents: 18 diff changeset	338 </data>
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b iracooke parents: 18 diff changeset	339 <data format="tabular" name="output_psm_phosphorylation" from_work_dir="psm_phospho.txt" label="${tool.name} on ${on_string}: PSM Phosphorylation Report">
53 d67a3c1bfd09 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 1327a0e10d66e5ed6a8b63b211672a724fcac424 galaxyp parents: 52 diff changeset	340 <filter>(exporting_options['zip_conditional']['zip_output_boolean'] is False or (exporting_options['zip_conditional']['zip_output_boolean'] is True and exporting_options['zip_conditional']['export_reports_when_zip'] is True) ) and str(exporting_options['output_reports']) != 'None' and '2' in exporting_options['output_reports']</filter>
18 a5f9b959d5d1 Uploaded iracooke parents: diff changeset	341 </data>
20 2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b iracooke parents: 18 diff changeset	342 <data format="tabular" name="output_psm" from_work_dir="psm.txt" label="${tool.name} on ${on_string}: PSM Report">
53 d67a3c1bfd09 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 1327a0e10d66e5ed6a8b63b211672a724fcac424 galaxyp parents: 52 diff changeset	343 <filter>(exporting_options['zip_conditional']['zip_output_boolean'] is False or (exporting_options['zip_conditional']['zip_output_boolean'] is True and exporting_options['zip_conditional']['export_reports_when_zip'] is True) ) and str(exporting_options['output_reports']) != 'None' and '3' in exporting_options['output_reports']</filter>
49 58a3e6cb2598 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6e846f7195a9e939047ac975c6523e8cf99da6b4 galaxyp parents: 46 diff changeset	344 </data>
58a3e6cb2598 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6e846f7195a9e939047ac975c6523e8cf99da6b4 galaxyp parents: 46 diff changeset	345 <data format="tabular" name="output_psm_nonvalidated" from_work_dir="psm_nonvalidated.txt" label="${tool.name} on ${on_string}: PSM Report with non-validated matches">
53 d67a3c1bfd09 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 1327a0e10d66e5ed6a8b63b211672a724fcac424 galaxyp parents: 52 diff changeset	346 <filter>(exporting_options['zip_conditional']['zip_output_boolean'] is False or (exporting_options['zip_conditional']['zip_output_boolean'] is True and exporting_options['zip_conditional']['export_reports_when_zip'] is True) ) and str(exporting_options['output_reports']) != 'None' and '4' in exporting_options['output_reports']</filter>
18 a5f9b959d5d1 Uploaded iracooke parents: diff changeset	347 </data>
30 ad60446b1e93 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit bdb5ee12705a3494eee96d1963f16f68bbe41d5c galaxyp parents: 29 diff changeset	348 <data format="tabular" name="output_extended_psm" from_work_dir="psmx.txt" label="${tool.name} on ${on_string}: Extended PSM Report">
53 d67a3c1bfd09 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 1327a0e10d66e5ed6a8b63b211672a724fcac424 galaxyp parents: 52 diff changeset	349 <filter>(exporting_options['zip_conditional']['zip_output_boolean'] is False or (exporting_options['zip_conditional']['zip_output_boolean'] is True and exporting_options['zip_conditional']['export_reports_when_zip'] is True) ) and str(exporting_options['output_reports']) != 'None' and '11' in exporting_options['output_reports']</filter>
30 ad60446b1e93 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit bdb5ee12705a3494eee96d1963f16f68bbe41d5c galaxyp parents: 29 diff changeset	350 </data>
20 2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b iracooke parents: 18 diff changeset	351 <data format="tabular" name="output_peptides_phosphorylation" from_work_dir="peptides_phospho.txt" label="${tool.name} on ${on_string}: Peptide Phosphorylation Report">
53 d67a3c1bfd09 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 1327a0e10d66e5ed6a8b63b211672a724fcac424 galaxyp parents: 52 diff changeset	352 <filter>(exporting_options['zip_conditional']['zip_output_boolean'] is False or (exporting_options['zip_conditional']['zip_output_boolean'] is True and exporting_options['zip_conditional']['export_reports_when_zip'] is True) ) and str(exporting_options['output_reports']) != 'None' and '5' in exporting_options['output_reports']</filter>
18 a5f9b959d5d1 Uploaded iracooke parents: diff changeset	353 </data>
20 2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b iracooke parents: 18 diff changeset	354 <data format="tabular" name="output_peptides" from_work_dir="peptides.txt" label="${tool.name} on ${on_string}: Peptide Report">
53 d67a3c1bfd09 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 1327a0e10d66e5ed6a8b63b211672a724fcac424 galaxyp parents: 52 diff changeset	355 <filter>(exporting_options['zip_conditional']['zip_output_boolean'] is False or (exporting_options['zip_conditional']['zip_output_boolean'] is True and exporting_options['zip_conditional']['export_reports_when_zip'] is True) ) and str(exporting_options['output_reports']) != 'None' and '6' in exporting_options['output_reports']</filter>
49 58a3e6cb2598 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6e846f7195a9e939047ac975c6523e8cf99da6b4 galaxyp parents: 46 diff changeset	356 </data>
58a3e6cb2598 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6e846f7195a9e939047ac975c6523e8cf99da6b4 galaxyp parents: 46 diff changeset	357 <data format="tabular" name="output_peptides_nonvalidated" from_work_dir="peptides_nonvalidated.txt" label="${tool.name} on ${on_string}: Peptide Report with non-validated matches">
53 d67a3c1bfd09 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 1327a0e10d66e5ed6a8b63b211672a724fcac424 galaxyp parents: 52 diff changeset	358 <filter>(exporting_options['zip_conditional']['zip_output_boolean'] is False or (exporting_options['zip_conditional']['zip_output_boolean'] is True and exporting_options['zip_conditional']['export_reports_when_zip'] is True) ) and str(exporting_options['output_reports']) != 'None' and '7' in exporting_options['output_reports']</filter>
20 2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b iracooke parents: 18 diff changeset	359 </data>
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b iracooke parents: 18 diff changeset	360 <data format="tabular" name="output_proteins_phosphorylation" from_work_dir="proteins_phospho.txt" label="${tool.name} on ${on_string}: Protein Phosphorylation Report">
53 d67a3c1bfd09 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 1327a0e10d66e5ed6a8b63b211672a724fcac424 galaxyp parents: 52 diff changeset	361 <filter>(exporting_options['zip_conditional']['zip_output_boolean'] is False or (exporting_options['zip_conditional']['zip_output_boolean'] is True and exporting_options['zip_conditional']['export_reports_when_zip'] is True) ) and str(exporting_options['output_reports']) != 'None' and '8' in exporting_options['output_reports']</filter>
20 2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b iracooke parents: 18 diff changeset	362 </data>
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b iracooke parents: 18 diff changeset	363 <data format="tabular" name="output_proteins" from_work_dir="proteins.txt" label="${tool.name} on ${on_string}: Protein Report">
53 d67a3c1bfd09 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 1327a0e10d66e5ed6a8b63b211672a724fcac424 galaxyp parents: 52 diff changeset	364 <filter>(exporting_options['zip_conditional']['zip_output_boolean'] is False or (exporting_options['zip_conditional']['zip_output_boolean'] is True and exporting_options['zip_conditional']['export_reports_when_zip'] is True) ) and str(exporting_options['output_reports']) != 'None' and '9' in exporting_options['output_reports']</filter>
49 58a3e6cb2598 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6e846f7195a9e939047ac975c6523e8cf99da6b4 galaxyp parents: 46 diff changeset	365 </data>
58a3e6cb2598 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6e846f7195a9e939047ac975c6523e8cf99da6b4 galaxyp parents: 46 diff changeset	366 <data format="tabular" name="output_proteins_nonvalidated" from_work_dir="proteins_nonvalidated.txt" label="${tool.name} on ${on_string}: Protein Repor with non-validated matches">
53 d67a3c1bfd09 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 1327a0e10d66e5ed6a8b63b211672a724fcac424 galaxyp parents: 52 diff changeset	367 <filter>(exporting_options['zip_conditional']['zip_output_boolean'] is False or (exporting_options['zip_conditional']['zip_output_boolean'] is True and exporting_options['zip_conditional']['export_reports_when_zip'] is True) ) and str(exporting_options['output_reports']) != 'None' and '10' in exporting_options['output_reports']</filter>
18 a5f9b959d5d1 Uploaded iracooke parents: diff changeset	368 </data>
a5f9b959d5d1 Uploaded iracooke parents: diff changeset	369 </outputs>
a5f9b959d5d1 Uploaded iracooke parents: diff changeset	370 <tests>
53 d67a3c1bfd09 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 1327a0e10d66e5ed6a8b63b211672a724fcac424 galaxyp parents: 52 diff changeset	371 <test expect_num_outputs="1">
46 baeced706dbc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 57426db0c017009ac7ab0498f8580efc453398c8 galaxyp parents: 45 diff changeset	372 <param name="searchgui_input" value="tiny_searchgui_modifications_result1.zip" ftype="searchgui_archive"/>
18 a5f9b959d5d1 Uploaded iracooke parents: diff changeset	373 <param name="processing_options_selector" value="no"/>
a5f9b959d5d1 Uploaded iracooke parents: diff changeset	374 <param name="filtering_options_selector" value="no"/>
49 58a3e6cb2598 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6e846f7195a9e939047ac975c6523e8cf99da6b4 galaxyp parents: 46 diff changeset	375 <param name="mzidentml_creation" value="0"/>
58a3e6cb2598 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6e846f7195a9e939047ac975c6523e8cf99da6b4 galaxyp parents: 46 diff changeset	376 <param name="zip_output_boolean" value="zip"/>
58a3e6cb2598 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6e846f7195a9e939047ac975c6523e8cf99da6b4 galaxyp parents: 46 diff changeset	377 <param name="export_cps" value="1"/>
46 baeced706dbc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 57426db0c017009ac7ab0498f8580efc453398c8 galaxyp parents: 45 diff changeset	378 <output name="output_zip" file="peptide_shaker_modifications_result1.zip" ftype="zip" compare="sim_size" delta="3000" />
20 2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b iracooke parents: 18 diff changeset	379 </test>
53 d67a3c1bfd09 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 1327a0e10d66e5ed6a8b63b211672a724fcac424 galaxyp parents: 52 diff changeset	380 <test expect_num_outputs="12">
46 baeced706dbc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 57426db0c017009ac7ab0498f8580efc453398c8 galaxyp parents: 45 diff changeset	381 <param name="searchgui_input" value="tiny_searchgui_modifications_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	382 <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	383 <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	384 <param name="min_peptide_length" value="1"/>
49 58a3e6cb2598 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6e846f7195a9e939047ac975c6523e8cf99da6b4 galaxyp parents: 46 diff changeset	385 <param name="mzidentml_creation" value="0"/>
58a3e6cb2598 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6e846f7195a9e939047ac975c6523e8cf99da6b4 galaxyp parents: 46 diff changeset	386 <param name="zip_output_boolean" value="separate"/>
58a3e6cb2598 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6e846f7195a9e939047ac975c6523e8cf99da6b4 galaxyp parents: 46 diff changeset	387 <param name="output_reports" value="0,1,2,3,4,5,6,7,8,9,10,11"/>
50 5814883aa217 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f420e6a9af6569a7fe61702c7d273030a36e84dd galaxyp parents: 49 diff changeset	388 <output name="output_certificate" file="peptide_shaker_modifications_result1.output_certificate" ftype="txt" lines_diff="8"/>
49 58a3e6cb2598 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6e846f7195a9e939047ac975c6523e8cf99da6b4 galaxyp parents: 46 diff changeset	389 <output name="output_hierarchical" file="peptide_shaker_modifications_result1.output_hierarchical" ftype="tabular"/>
58a3e6cb2598 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6e846f7195a9e939047ac975c6523e8cf99da6b4 galaxyp parents: 46 diff changeset	390 <output name="output_extended_psm" file="peptide_shaker_modifications_result1.output_extended_psm" ftype="tabular"/>
58a3e6cb2598 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6e846f7195a9e939047ac975c6523e8cf99da6b4 galaxyp parents: 46 diff changeset	391 <output name="output_psm" file="peptide_shaker_modifications_result1.output_psm" ftype="tabular"/>
58a3e6cb2598 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6e846f7195a9e939047ac975c6523e8cf99da6b4 galaxyp parents: 46 diff changeset	392 <output name="output_psm_phosphorylation" file="peptide_shaker_modifications_result1.output_psm_phosphorylation" ftype="tabular"/>
58a3e6cb2598 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6e846f7195a9e939047ac975c6523e8cf99da6b4 galaxyp parents: 46 diff changeset	393 <output name="output_psm_nonvalidated" file="peptide_shaker_modifications_result1.output_psm_nonvalidated" ftype="tabular"/>
58a3e6cb2598 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6e846f7195a9e939047ac975c6523e8cf99da6b4 galaxyp parents: 46 diff changeset	394 <output name="output_peptides" file="peptide_shaker_modifications_result1.output_peptides" ftype="tabular"/>
58a3e6cb2598 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6e846f7195a9e939047ac975c6523e8cf99da6b4 galaxyp parents: 46 diff changeset	395 <output name="output_peptides_phosphorylation" file="peptide_shaker_modifications_result1.output_peptides_phosphorylation" ftype="tabular"/>
58a3e6cb2598 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6e846f7195a9e939047ac975c6523e8cf99da6b4 galaxyp parents: 46 diff changeset	396 <output name="output_peptides_nonvalidated" file="peptide_shaker_modifications_result1.output_peptides_nonvalidated" ftype="tabular"/>
58a3e6cb2598 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6e846f7195a9e939047ac975c6523e8cf99da6b4 galaxyp parents: 46 diff changeset	397 <output name="output_proteins" file="peptide_shaker_modifications_result1.output_proteins" ftype="tabular"/>
58a3e6cb2598 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6e846f7195a9e939047ac975c6523e8cf99da6b4 galaxyp parents: 46 diff changeset	398 <output name="output_proteins_phosphorylation" file="peptide_shaker_modifications_result1.output_proteins_phosphorylation" ftype="tabular"/>
58a3e6cb2598 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6e846f7195a9e939047ac975c6523e8cf99da6b4 galaxyp parents: 46 diff changeset	399 <output name="output_proteins_nonvalidated" file="peptide_shaker_modifications_result1.output_proteins_nonvalidated" ftype="tabular"/>
20 2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b iracooke parents: 18 diff changeset	400 </test>
53 d67a3c1bfd09 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 1327a0e10d66e5ed6a8b63b211672a724fcac424 galaxyp parents: 52 diff changeset	401 <test expect_num_outputs="2">
46 baeced706dbc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 57426db0c017009ac7ab0498f8580efc453398c8 galaxyp parents: 45 diff changeset	402 <param name="searchgui_input" value="tiny_searchgui_modifications_result1.zip" ftype="searchgui_archive"/>
44 f35bb9d0c93e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 981be1bde91d6d565693cd691553f77465e653bb galaxyp parents: 38 diff changeset	403 <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	404 <param name="filtering_options_selector" value="no"/>
49 58a3e6cb2598 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6e846f7195a9e939047ac975c6523e8cf99da6b4 galaxyp parents: 46 diff changeset	405 <param name="mzidentml_creation" value="0"/>
58a3e6cb2598 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6e846f7195a9e939047ac975c6523e8cf99da6b4 galaxyp parents: 46 diff changeset	406 <param name="zip_output_boolean" value="separate"/>
58a3e6cb2598 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6e846f7195a9e939047ac975c6523e8cf99da6b4 galaxyp parents: 46 diff changeset	407 <param name="export_cps" value="1"/>
58a3e6cb2598 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6e846f7195a9e939047ac975c6523e8cf99da6b4 galaxyp parents: 46 diff changeset	408 <param name="output_reports" value="3"/>
46 baeced706dbc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 57426db0c017009ac7ab0498f8580efc453398c8 galaxyp parents: 45 diff changeset	409 <output name="output_cps" file="peptide_shaker_modifications_result1.cpsx" ftype="peptideshaker_archive" compare="sim_size" delta="3000"/>
49 58a3e6cb2598 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6e846f7195a9e939047ac975c6523e8cf99da6b4 galaxyp parents: 46 diff changeset	410 <output name="output_psm" file="peptide_shaker_modifications_result1.output_psm" ftype="tabular"/>
44 f35bb9d0c93e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 981be1bde91d6d565693cd691553f77465e653bb galaxyp parents: 38 diff changeset	411 </test>
18 a5f9b959d5d1 Uploaded iracooke parents: diff changeset	412 </tests>
a5f9b959d5d1 Uploaded iracooke parents: diff changeset	413 <help>
a5f9b959d5d1 Uploaded iracooke parents: diff changeset	414 What it does
a5f9b959d5d1 Uploaded iracooke parents: diff changeset	415
49 58a3e6cb2598 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6e846f7195a9e939047ac975c6523e8cf99da6b4 galaxyp parents: 46 diff changeset	416 PeptideShaker is a search engine for interpretation of proteomics identification results from multiple search engines, currently supporting X!Tandem, MS-GF+, MS Amanda, OMSSA, MyriMatch, Comet, Tide, Mascot, Andromeda and mzIdentML.
18 a5f9b959d5d1 Uploaded iracooke parents: diff changeset	417
30 ad60446b1e93 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit bdb5ee12705a3494eee96d1963f16f68bbe41d5c galaxyp parents: 29 diff changeset	418 http://compomics.github.io/projects/peptide-shaker.html
18 a5f9b959d5d1 Uploaded iracooke parents: diff changeset	419
a5f9b959d5d1 Uploaded iracooke parents: diff changeset	420 ----
a5f9b959d5d1 Uploaded iracooke parents: diff changeset	421
a5f9b959d5d1 Uploaded iracooke parents: diff changeset	422 Reports
a5f9b959d5d1 Uploaded iracooke parents: diff changeset	423 =======
a5f9b959d5d1 Uploaded iracooke parents: diff changeset	424
a5f9b959d5d1 Uploaded iracooke parents: diff changeset	425
a5f9b959d5d1 Uploaded iracooke parents: diff changeset	426 PSM Report
a5f9b959d5d1 Uploaded iracooke parents: diff changeset	427 ----------
a5f9b959d5d1 Uploaded iracooke parents: diff changeset	428
a5f9b959d5d1 Uploaded iracooke parents: diff changeset	429 * 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	430 * 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	431 * Variable Modifications: The variable modifications
18 a5f9b959d5d1 Uploaded iracooke parents: diff changeset	432 * D-score: D-score for variable PTM localization
a5f9b959d5d1 Uploaded iracooke parents: diff changeset	433 * probabilistic PTM score: The probabilistic score (e.g. A-score or PhosphoRS) used for variable PTM localization.
a5f9b959d5d1 Uploaded iracooke parents: diff changeset	434 * Localization Confidence: The confidence in variable PTM localization.
a5f9b959d5d1 Uploaded iracooke parents: diff changeset	435 * Fixed Modifications: The fixed modifications.
a5f9b959d5d1 Uploaded iracooke parents: diff changeset	436 * Spectrum File: The spectrum file.
a5f9b959d5d1 Uploaded iracooke parents: diff changeset	437 * Spectrum Title: The title of the spectrum.
a5f9b959d5d1 Uploaded iracooke parents: diff changeset	438 * Spectrum Scan Number: The spectrum scan number.
a5f9b959d5d1 Uploaded iracooke parents: diff changeset	439 * RT: Retention time
a5f9b959d5d1 Uploaded iracooke parents: diff changeset	440 * m/z: Measured m/z
a5f9b959d5d1 Uploaded iracooke parents: diff changeset	441 * Measured Charge: The charge as given in the spectrum file.
a5f9b959d5d1 Uploaded iracooke parents: diff changeset	442 * Identification Charge: The charge as inferred by the search engine.
a5f9b959d5d1 Uploaded iracooke parents: diff changeset	443 * Theoretical Mass: The theoretical mass of the peptide.
a5f9b959d5d1 Uploaded iracooke parents: diff changeset	444 * Isotope Number: The isotope number targetted by the instrument.
a5f9b959d5d1 Uploaded iracooke parents: diff changeset	445 * Precursor m/z Error: The precursor m/z matching error.
a5f9b959d5d1 Uploaded iracooke parents: diff changeset	446 * Score: Score of the retained peptide as a combination of the algorithm scores (used to rank PSMs).
a5f9b959d5d1 Uploaded iracooke parents: diff changeset	447 * Confidence: Confidence in percent associated to the retained PSM.
a5f9b959d5d1 Uploaded iracooke parents: diff changeset	448 * Decoy: Indicates whether the peptide is a decoy (1: yes, 0: no).
a5f9b959d5d1 Uploaded iracooke parents: diff changeset	449 * Validation: Indicates the validation level of the protein group.
a5f9b959d5d1 Uploaded iracooke parents: diff changeset	450
a5f9b959d5d1 Uploaded iracooke parents: diff changeset	451
a5f9b959d5d1 Uploaded iracooke parents: diff changeset	452 Protein Report
a5f9b959d5d1 Uploaded iracooke parents: diff changeset	453 --------------
a5f9b959d5d1 Uploaded iracooke parents: diff changeset	454
a5f9b959d5d1 Uploaded iracooke parents: diff changeset	455 * Main Accession: Main accession of the protein group.
a5f9b959d5d1 Uploaded iracooke parents: diff changeset	456 * Description: Description of the protein designed by the main accession.
a5f9b959d5d1 Uploaded iracooke parents: diff changeset	457 * Gene Name: The gene names of the Ensembl gene ID associated to the main accession.
a5f9b959d5d1 Uploaded iracooke parents: diff changeset	458 * Chromosome: The chromosome of the Ensembl gene ID associated to the main accession.
a5f9b959d5d1 Uploaded iracooke parents: diff changeset	459 * PI: Protein Inference status of the protein group.
a5f9b959d5d1 Uploaded iracooke parents: diff changeset	460 * Secondary Accessions: Other accessions in the protein group (alphabetical order).
a5f9b959d5d1 Uploaded iracooke parents: diff changeset	461 * Protein Group: The complete protein group (alphabetical order).
a5f9b959d5d1 Uploaded iracooke parents: diff changeset	462 * #Peptides: Total number of peptides.
a5f9b959d5d1 Uploaded iracooke parents: diff changeset	463 * #Validated Peptides: Number of validated peptides.
a5f9b959d5d1 Uploaded iracooke parents: diff changeset	464 * #Unique: Total number of peptides unique to this protein group.
a5f9b959d5d1 Uploaded iracooke parents: diff changeset	465 * #PSMs: Number of PSMs
a5f9b959d5d1 Uploaded iracooke parents: diff changeset	466 * #Validated PSMs: Number of validated PSMs
a5f9b959d5d1 Uploaded iracooke parents: diff changeset	467 * Coverage (%): Sequence coverage in percent of the protein designed by the main accession.
a5f9b959d5d1 Uploaded iracooke parents: diff changeset	468 * 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	469 * MW (kDa): Molecular Weight.
a5f9b959d5d1 Uploaded iracooke parents: diff changeset	470 * Spectrum Counting NSAF: Normalized Spectrum Abundance Factor (NSAF)
a5f9b959d5d1 Uploaded iracooke parents: diff changeset	471 * Spectrum Counting emPAI: exponentially modified Protein Abundance Index (emPAI)
a5f9b959d5d1 Uploaded iracooke parents: diff changeset	472 * 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	473 * 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	474 * Score: Score of the protein group.
a5f9b959d5d1 Uploaded iracooke parents: diff changeset	475 * Confidence: Confidence in percent associated to the protein group.
a5f9b959d5d1 Uploaded iracooke parents: diff changeset	476 * Decoy: Indicates whether the protein group is a decoy (1: yes, 0: no).
a5f9b959d5d1 Uploaded iracooke parents: diff changeset	477 * Validation: Indicates the validation level of the protein group.
a5f9b959d5d1 Uploaded iracooke parents: diff changeset	478
a5f9b959d5d1 Uploaded iracooke parents: diff changeset	479
a5f9b959d5d1 Uploaded iracooke parents: diff changeset	480 Peptide Report
a5f9b959d5d1 Uploaded iracooke parents: diff changeset	481 --------------
a5f9b959d5d1 Uploaded iracooke parents: diff changeset	482
a5f9b959d5d1 Uploaded iracooke parents: diff changeset	483
a5f9b959d5d1 Uploaded iracooke parents: diff changeset	484 * Protein(s): Protein(s) to which this peptide can be attached.
a5f9b959d5d1 Uploaded iracooke parents: diff changeset	485 * AAs Before: The amino-acids before the sequence.
a5f9b959d5d1 Uploaded iracooke parents: diff changeset	486 * Sequence: Sequence of the peptide.
a5f9b959d5d1 Uploaded iracooke parents: diff changeset	487 * AAs After: The amino-acids after the sequence.
a5f9b959d5d1 Uploaded iracooke parents: diff changeset	488 * Modified Sequence: The peptide sequence annotated with variable modifications.
a5f9b959d5d1 Uploaded iracooke parents: diff changeset	489 * Variable Modifications: The variable modifications.
a5f9b959d5d1 Uploaded iracooke parents: diff changeset	490 * Localization Confidence: The confidence in PTMs localization.
a5f9b959d5d1 Uploaded iracooke parents: diff changeset	491 * Fixed Modifications: The fixed modifications.
a5f9b959d5d1 Uploaded iracooke parents: diff changeset	492 * #Validated PSMs: Number of validated PSMs.
a5f9b959d5d1 Uploaded iracooke parents: diff changeset	493 * #PSMs: Number of PSMs.
a5f9b959d5d1 Uploaded iracooke parents: diff changeset	494 * Score: Score of the peptide.
a5f9b959d5d1 Uploaded iracooke parents: diff changeset	495 * Confidence: Confidence in percent associated to the peptide.
a5f9b959d5d1 Uploaded iracooke parents: diff changeset	496 * Decoy: Indicates whether the peptide is a decoy (1: yes, 0: no).
a5f9b959d5d1 Uploaded iracooke parents: diff changeset	497 * Validation: Indicates the validation level of the protein group.
a5f9b959d5d1 Uploaded iracooke parents: diff changeset	498
a5f9b959d5d1 Uploaded iracooke parents: diff changeset	499
a5f9b959d5d1 Uploaded iracooke parents: diff changeset	500 Hierachical Report
a5f9b959d5d1 Uploaded iracooke parents: diff changeset	501 ------------------
a5f9b959d5d1 Uploaded iracooke parents: diff changeset	502
a5f9b959d5d1 Uploaded iracooke parents: diff changeset	503 * Main Accession: Main accession of the protein group.
a5f9b959d5d1 Uploaded iracooke parents: diff changeset	504 * Description: Description of the protein designed by the main accession.
a5f9b959d5d1 Uploaded iracooke parents: diff changeset	505 * PI: Protein Inference status of the protein group.
a5f9b959d5d1 Uploaded iracooke parents: diff changeset	506 * Secondary Accessions: Other accessions in the protein group (alphabetical order).
a5f9b959d5d1 Uploaded iracooke parents: diff changeset	507 * Protein Group: The complete protein group (alphabetical order).
a5f9b959d5d1 Uploaded iracooke parents: diff changeset	508 * #Peptides: Total number of peptides.
a5f9b959d5d1 Uploaded iracooke parents: diff changeset	509 * #Validated Peptides: Number of validated peptides.
a5f9b959d5d1 Uploaded iracooke parents: diff changeset	510 * #Unique: Total number of peptides unique to this protein group.
a5f9b959d5d1 Uploaded iracooke parents: diff changeset	511 * #PSMs: Number of PSMs
a5f9b959d5d1 Uploaded iracooke parents: diff changeset	512 * #Validated PSMs: Number of validated PSMs
a5f9b959d5d1 Uploaded iracooke parents: diff changeset	513 * Coverage (%): Sequence coverage in percent of the protein designed by the main accession.
a5f9b959d5d1 Uploaded iracooke parents: diff changeset	514 * 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	515 * MW (kDa): Molecular Weight.
a5f9b959d5d1 Uploaded iracooke parents: diff changeset	516 * Spectrum Counting NSAF: Normalized Spectrum Abundance Factor (NSAF)
a5f9b959d5d1 Uploaded iracooke parents: diff changeset	517 * Spectrum Counting emPAI: exponentially modified Protein Abundance Index (emPAI)
a5f9b959d5d1 Uploaded iracooke parents: diff changeset	518 * Confident Modification Sites: # Confident Modification Sites List of the sites where a variable modification was confidently localized.
a5f9b959d5d1 Uploaded iracooke parents: diff changeset	519 * Other Modification Sites: # Other Modification Sites List of the non-confident sites where a variable modification was localized.
a5f9b959d5d1 Uploaded iracooke parents: diff changeset	520 * Score: Score of the protein group.
a5f9b959d5d1 Uploaded iracooke parents: diff changeset	521 * Confidence: Confidence in percent associated to the protein group.
a5f9b959d5d1 Uploaded iracooke parents: diff changeset	522 * Decoy: Indicates whether the protein group is a decoy (1: yes, 0: no).
a5f9b959d5d1 Uploaded iracooke parents: diff changeset	523 * Validation: Indicates the validation level of the protein group.
a5f9b959d5d1 Uploaded iracooke parents: diff changeset	524 * Protein(s): Protein(s) to which this peptide can be attached.
a5f9b959d5d1 Uploaded iracooke parents: diff changeset	525 * AAs Before: The amino-acids before the sequence.
a5f9b959d5d1 Uploaded iracooke parents: diff changeset	526 * Sequence: Sequence of the peptide.
a5f9b959d5d1 Uploaded iracooke parents: diff changeset	527 * AAs After: The amino-acids after the sequence.
a5f9b959d5d1 Uploaded iracooke parents: diff changeset	528 * Variable Modifications: The variable modifications.
a5f9b959d5d1 Uploaded iracooke parents: diff changeset	529 * Localization Confidence: The confidence in PTMs localization.
a5f9b959d5d1 Uploaded iracooke parents: diff changeset	530 * Fixed Modifications: The fixed modifications.
a5f9b959d5d1 Uploaded iracooke parents: diff changeset	531 * #Validated PSMs: Number of validated PSMs.
a5f9b959d5d1 Uploaded iracooke parents: diff changeset	532 * #PSMs: Number of PSMs.
a5f9b959d5d1 Uploaded iracooke parents: diff changeset	533 * Score: Score of the peptide.
a5f9b959d5d1 Uploaded iracooke parents: diff changeset	534 * Confidence: Confidence in percent associated to the peptide.
a5f9b959d5d1 Uploaded iracooke parents: diff changeset	535 * Decoy: Indicates whether the peptide is a decoy (1: yes, 0: no).
a5f9b959d5d1 Uploaded iracooke parents: diff changeset	536 * Validation: Indicates the validation level of the protein group.
a5f9b959d5d1 Uploaded iracooke parents: diff changeset	537 * Protein(s): Protein(s) to which the peptide can be attached.
a5f9b959d5d1 Uploaded iracooke parents: diff changeset	538 * Sequence: Sequence of the peptide.
a5f9b959d5d1 Uploaded iracooke parents: diff changeset	539 * Modified Sequence: The peptide sequence annotated with variable modifications.
a5f9b959d5d1 Uploaded iracooke parents: diff changeset	540 * Variable Modifications: The variable modifications.
a5f9b959d5d1 Uploaded iracooke parents: diff changeset	541 * D-score: D-score for variable PTM localization.
a5f9b959d5d1 Uploaded iracooke parents: diff changeset	542 * probabilistic PTM score: The probabilistic score (e.g. A-score or PhosphoRS) used for variable PTM localization.
a5f9b959d5d1 Uploaded iracooke parents: diff changeset	543 * Localization Confidence: The confidence in variable PTM localization.
a5f9b959d5d1 Uploaded iracooke parents: diff changeset	544 * Fixed Modifications: The fixed modifications.
a5f9b959d5d1 Uploaded iracooke parents: diff changeset	545 * Spectrum File: The spectrum file.
a5f9b959d5d1 Uploaded iracooke parents: diff changeset	546 * Spectrum Title: The title of the spectrum.
a5f9b959d5d1 Uploaded iracooke parents: diff changeset	547 * Spectrum Scan Number: The spectrum scan number.
a5f9b959d5d1 Uploaded iracooke parents: diff changeset	548 * RT: Retention time
a5f9b959d5d1 Uploaded iracooke parents: diff changeset	549 * m/z: Measured m/z
a5f9b959d5d1 Uploaded iracooke parents: diff changeset	550 * Measured Charge: The charge as given in the spectrum file.
a5f9b959d5d1 Uploaded iracooke parents: diff changeset	551 * Identification Charge: The charge as inferred by the search engine.
a5f9b959d5d1 Uploaded iracooke parents: diff changeset	552 * Theoretical Mass: The theoretical mass of the peptide.
a5f9b959d5d1 Uploaded iracooke parents: diff changeset	553 * Isotope Number: The isotope number targetted by the instrument.
a5f9b959d5d1 Uploaded iracooke parents: diff changeset	554 * Precursor m/z Error: The precursor m/z matching error.
a5f9b959d5d1 Uploaded iracooke parents: diff changeset	555 * Score: Score of the retained peptide as a combination of the algorithm scores (used to rank PSMs).
a5f9b959d5d1 Uploaded iracooke parents: diff changeset	556 * Confidence: Confidence in percent associated to the retained PSM.
a5f9b959d5d1 Uploaded iracooke parents: diff changeset	557 * Decoy: Indicates whether the peptide is a decoy (1: yes, 0: no).
a5f9b959d5d1 Uploaded iracooke parents: diff changeset	558 * Validation: Indicates the validation level of the protein group.
a5f9b959d5d1 Uploaded iracooke parents: diff changeset	559
a5f9b959d5d1 Uploaded iracooke parents: diff changeset	560
a5f9b959d5d1 Uploaded iracooke parents: diff changeset	561 ------
a5f9b959d5d1 Uploaded iracooke parents: diff changeset	562
a5f9b959d5d1 Uploaded iracooke parents: diff changeset	563 Citation
a5f9b959d5d1 Uploaded iracooke parents: diff changeset	564
30 ad60446b1e93 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit bdb5ee12705a3494eee96d1963f16f68bbe41d5c galaxyp parents: 29 diff changeset	565 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	566
30 ad60446b1e93 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit bdb5ee12705a3494eee96d1963f16f68bbe41d5c galaxyp parents: 29 diff changeset	567 If you use this tool in Galaxy, please cite Chilton J, Ira Cooke, Bjoern Gruening et al.
18 a5f9b959d5d1 Uploaded iracooke parents: diff changeset	568 </help>
20 2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b iracooke parents: 18 diff changeset	569 <expand macro="citations" />
18 a5f9b959d5d1 Uploaded iracooke parents: diff changeset	570 </tool>

Mercurial > repos > galaxyp > peptideshaker

annotate peptide_shaker.xml @ 53:d67a3c1bfd09 draft