peptideshaker: peptide_shaker.xml annotate

annotate peptide_shaker.xml @ 58:07ff622ec007 draft

"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0f6ab8b5647a33b2b051d7aa808ef42546436b23"

author	galaxyp
date	Sat, 10 Apr 2021 15:57:17 +0000
parents	da885ca16cb2
children	943a34df6047

rev	line source
57 da885ca16cb2 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 44a20633e04b2396fad4b568904a257769b2bbc1" galaxyp parents: 55 diff changeset	1 <tool id="peptide_shaker"
da885ca16cb2 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 44a20633e04b2396fad4b568904a257769b2bbc1" galaxyp parents: 55 diff changeset	2 name="Peptide Shaker"
da885ca16cb2 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 44a20633e04b2396fad4b568904a257769b2bbc1" galaxyp parents: 55 diff changeset	3 version="@PEPTIDESHAKER_VERSION@+galaxy@PEPTIDESHAKER_VERSION_SUFFIX@"
da885ca16cb2 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 44a20633e04b2396fad4b568904a257769b2bbc1" galaxyp parents: 55 diff changeset	4 profile="20.01"
da885ca16cb2 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 44a20633e04b2396fad4b568904a257769b2bbc1" galaxyp parents: 55 diff changeset	5 >
da885ca16cb2 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 44a20633e04b2396fad4b568904a257769b2bbc1" galaxyp parents: 55 diff changeset	6
18 a5f9b959d5d1 Uploaded iracooke parents: diff changeset	7 <description>
20 2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b iracooke parents: 18 diff changeset	8 Perform protein identification using various search engines based on results from SearchGUI
18 a5f9b959d5d1 Uploaded iracooke parents: diff changeset	9 </description>
20 2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b iracooke parents: 18 diff changeset	10 <macros>
55 bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	11 <import>macros_basic.xml</import>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	12 <import>macros_modifications.xml</import>
20 2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b iracooke parents: 18 diff changeset	13 </macros>
21 dfaea053e32f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 327a3944f2f56668d607c3d6cb08ae7d588e208c iracooke parents: 20 diff changeset	14 <requirements>
49 58a3e6cb2598 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6e846f7195a9e939047ac975c6523e8cf99da6b4 galaxyp parents: 46 diff changeset	15 <requirement type="package" version="@PEPTIDESHAKER_VERSION@">peptide-shaker</requirement>
55 bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	16 <requirement type="package">unzip</requirement>
21 dfaea053e32f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 327a3944f2f56668d607c3d6cb08ae7d588e208c iracooke parents: 20 diff changeset	17 </requirements>
20 2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b iracooke parents: 18 diff changeset	18 <expand macro="stdio" />
57 da885ca16cb2 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 44a20633e04b2396fad4b568904a257769b2bbc1" galaxyp parents: 55 diff changeset	19 <!-- TODO: check trap comment.
da885ca16cb2 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 44a20633e04b2396fad4b568904a257769b2bbc1" galaxyp parents: 55 diff changeset	20 <command use_shared_home="false">
da885ca16cb2 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 44a20633e04b2396fad4b568904a257769b2bbc1" galaxyp parents: 55 diff changeset	21 -->
da885ca16cb2 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 44a20633e04b2396fad4b568904a257769b2bbc1" galaxyp parents: 55 diff changeset	22 <command>
da885ca16cb2 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 44a20633e04b2396fad4b568904a257769b2bbc1" galaxyp parents: 55 diff changeset	23 <![CDATA[
18 a5f9b959d5d1 Uploaded iracooke parents: diff changeset	24 #from datetime import datetime
a5f9b959d5d1 Uploaded iracooke parents: diff changeset	25 #set $exp_str = "Galaxy_Experiment_%s" % datetime.now().strftime("%Y%m%d%H%M%s")
a5f9b959d5d1 Uploaded iracooke parents: diff changeset	26 #set $samp_str = "Sample_%s" % datetime.now().strftime("%Y%m%d%H%M%s")
30 ad60446b1e93 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit bdb5ee12705a3494eee96d1963f16f68bbe41d5c galaxyp parents: 29 diff changeset	27 #set $bin_dir = "bin"
55 bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	28 #set $exporting_followup_boolean = False
57 da885ca16cb2 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 44a20633e04b2396fad4b568904a257769b2bbc1" galaxyp parents: 55 diff changeset	29 ## TODO: Re-enable again when solving writing paths.txt to user-related folders and non-existing exportFactory.json file.
da885ca16cb2 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 44a20633e04b2396fad4b568904a257769b2bbc1" galaxyp parents: 55 diff changeset	30 ## trap ">&2 cat resources/*.log" EXIT;
22 e3be595c0bf5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 5ca27ef280bee8b65fd3d0d2cd5ff280a2cebb3d iracooke parents: 21 diff changeset	31
49 58a3e6cb2598 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6e846f7195a9e939047ac975c6523e8cf99da6b4 galaxyp parents: 46 diff changeset	32 mkdir output_reports &&
58a3e6cb2598 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6e846f7195a9e939047ac975c6523e8cf99da6b4 galaxyp parents: 46 diff changeset	33 cwd=`pwd` &&
58a3e6cb2598 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6e846f7195a9e939047ac975c6523e8cf99da6b4 galaxyp parents: 46 diff changeset	34 export HOME=\$cwd &&
58a3e6cb2598 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6e846f7195a9e939047ac975c6523e8cf99da6b4 galaxyp parents: 46 diff changeset	35
20 2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b iracooke parents: 18 diff changeset	36 ln -s '$searchgui_input' searchgui_input.zip &&
49 58a3e6cb2598 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6e846f7195a9e939047ac975c6523e8cf99da6b4 galaxyp parents: 46 diff changeset	37
55 bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	38 ## OPTIONAL MAIN PARAMETERS
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	39 ## If we have a specific Identification Parameters file to use, we will use it instead of the one provided in the search_gui file
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	40 #if $optional_main_parameters.input_optional_identification_parameters:
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	41 cp '${optional_main_parameters.input_optional_identification_parameters}' SEARCHGUI_IdentificationParameters.par &&
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	42 #else:
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	43 jar xvf searchgui_input.zip SEARCHGUI_IdentificationParameters.par &&
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	44 #end if
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	45 ## Optional Fasta file
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	46 #if $optional_main_parameters.input_fasta_file:
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	47 ## copy the input .fasta file to the working folder
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	48 cp '${optional_main_parameters.input_fasta_file}' './input_fasta_file.fasta' &&
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	49 #end if
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	50 ## Optional Spectrum files: if the user specified input spectra files, we use them
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	51 ## NOTE: != None DOES NOT SEEM TO WORK ANYMORE ON MODERN GALAXIES
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	52 #if str($optional_main_parameters.input_optional_spectrum_files) != 'None' and str($optional_main_parameters.input_optional_spectrum_files) != '':
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	53 mkdir peaklist_input_files &&
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	54 #for $peak_list_file in $optional_main_parameters.input_optional_spectrum_files:
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	55 #if $peak_list_file.is_of_type("mgf"):
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	56 #set $input_name = $peak_list_file.element_identifier.split('/')[-1].replace(".mgf", "") + ".mgf"
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	57 #else if $peak_list_file.is_of_type("mzml"):
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	58 #set $input_name = $peak_list_file.element_identifier.split('/')[-1].replace(".mzml", "") + ".mzml"
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	59 #end if
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	60 ln -s -f '${peak_list_file}' 'peaklist_input_files/${input_name}' &&
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	61 #end for
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	62 #end if
49 58a3e6cb2598 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6e846f7195a9e939047ac975c6523e8cf99da6b4 galaxyp parents: 46 diff changeset	63
55 bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	64 #if str($exporting_options.output_reports) != "None" and str($exporting_options.output_reports) != ""
49 58a3e6cb2598 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6e846f7195a9e939047ac975c6523e8cf99da6b4 galaxyp parents: 46 diff changeset	65 #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	66 #else
58a3e6cb2598 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6e846f7195a9e939047ac975c6523e8cf99da6b4 galaxyp parents: 46 diff changeset	67 #set $output_reports_list = set()
55 bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	68 #end if
49 58a3e6cb2598 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6e846f7195a9e939047ac975c6523e8cf99da6b4 galaxyp parents: 46 diff changeset	69
18 a5f9b959d5d1 Uploaded iracooke parents: diff changeset	70 ######################
a5f9b959d5d1 Uploaded iracooke parents: diff changeset	71 ## PeptideShakerCLI ##
a5f9b959d5d1 Uploaded iracooke parents: diff changeset	72 ######################
57 da885ca16cb2 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 44a20633e04b2396fad4b568904a257769b2bbc1" galaxyp parents: 55 diff changeset	73 peptide-shaker -Djava.awt.headless=true eu.isas.peptideshaker.cmd.PeptideShakerCLI
49 58a3e6cb2598 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6e846f7195a9e939047ac975c6523e8cf99da6b4 galaxyp parents: 46 diff changeset	74 -gui 0
20 2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b iracooke parents: 18 diff changeset	75 -temp_folder \$cwd/PeptideShakerCLI
55 bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	76 -log \$cwd/resources
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	77 -reference '$exp_str'
20 2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b iracooke parents: 18 diff changeset	78 -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	79 -id_params \$cwd/SEARCHGUI_IdentificationParameters.par
55 bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	80 #if $optional_main_parameters.input_fasta_file:
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	81 -fasta_file './input_fasta_file.fasta'
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	82 #end if
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	83 #if str($optional_main_parameters.input_optional_spectrum_files) != 'None' and str($optional_main_parameters.input_optional_spectrum_files) != '':
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	84 -spectrum_files \$cwd/peaklist_input_files
49 58a3e6cb2598 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6e846f7195a9e939047ac975c6523e8cf99da6b4 galaxyp parents: 46 diff changeset	85 #end if
58a3e6cb2598 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6e846f7195a9e939047ac975c6523e8cf99da6b4 galaxyp parents: 46 diff changeset	86
55 bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	87 #if $exporting_options.zip_conditional.zip_output_boolean == 'zip':
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	88 -zip \$cwd/peptideshaker_output.zip
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	89 -out \$cwd/peptideshaker_output.psdb
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	90 #if $exporting_options.zip_conditional.export_mgf_when_zip:
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	91 -output_mgf 1
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	92 #end if
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	93 #else:
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	94 #if $exporting_options.zip_conditional.export_psdb:
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	95 -out \$cwd/peptideshaker_output.psdb
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	96 #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	97 #end if
18 a5f9b959d5d1 Uploaded iracooke parents: diff changeset	98
55 bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	99 -threads "\${GALAXY_SLOTS:-12}"
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	100
49 58a3e6cb2598 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6e846f7195a9e939047ac975c6523e8cf99da6b4 galaxyp parents: 46 diff changeset	101 ##################################
58a3e6cb2598 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6e846f7195a9e939047ac975c6523e8cf99da6b4 galaxyp parents: 46 diff changeset	102 ## mzidCLI options ##
58a3e6cb2598 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6e846f7195a9e939047ac975c6523e8cf99da6b4 galaxyp parents: 46 diff changeset	103 ##################################
58a3e6cb2598 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6e846f7195a9e939047ac975c6523e8cf99da6b4 galaxyp parents: 46 diff changeset	104
58a3e6cb2598 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6e846f7195a9e939047ac975c6523e8cf99da6b4 galaxyp parents: 46 diff changeset	105 #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	106 -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	107 -include_sequences ${exporting_options.mzidentml_conditional.include_sequences}
55 bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	108 #if $exporting_options.mzidentml_conditional.contact_options.contact_options_selector == "yes":
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	109 -contact_first_name "$exporting_options.mzidentml_conditional.contact_options.contact_first_name"
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	110 -contact_last_name "$exporting_options.mzidentml_conditional.contact_options.contact_last_name"
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	111 -contact_email "$exporting_options.mzidentml_conditional.contact_options.contact_email"
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	112 -contact_address "$exporting_options.mzidentml_conditional.contact_options.contact_address"
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	113 #if str($exporting_options.mzidentml_conditional.contact_options.contact_url).strip() != '':
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	114 -contact_url = "$exporting_options.mzidentml_conditional.contact_options.contact_url"
49 58a3e6cb2598 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6e846f7195a9e939047ac975c6523e8cf99da6b4 galaxyp parents: 46 diff changeset	115 #end if
55 bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	116 -organization_name "$exporting_options.mzidentml_conditional.contact_options.organization_name"
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	117 -organization_email "$exporting_options.mzidentml_conditional.contact_options.organization_email"
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	118 -organization_address "$exporting_options.mzidentml_conditional.contact_options.organization_address"
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	119 #if str($exporting_options.mzidentml_conditional.contact_options.organization_url).strip() != '':
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	120 -organization_url = "$exporting_options.mzidentml_conditional.contact_options.organization_url"
49 58a3e6cb2598 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6e846f7195a9e939047ac975c6523e8cf99da6b4 galaxyp parents: 46 diff changeset	121 #end if
58a3e6cb2598 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6e846f7195a9e939047ac975c6523e8cf99da6b4 galaxyp parents: 46 diff changeset	122 #else:
58a3e6cb2598 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6e846f7195a9e939047ac975c6523e8cf99da6b4 galaxyp parents: 46 diff changeset	123 -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	124 -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	125 -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	126 -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	127 -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	128 -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	129 -organization_address "Minneapolis, MN 55455, Vereinigte Staaten"
18 a5f9b959d5d1 Uploaded iracooke parents: diff changeset	130 #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	131 #end if
18 a5f9b959d5d1 Uploaded iracooke parents: diff changeset	132
55 bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	133 ####################################################################
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	134 ## PeptideShaker Identification Features Reports options ##
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	135 ####################################################################
49 58a3e6cb2598 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6e846f7195a9e939047ac975c6523e8cf99da6b4 galaxyp parents: 46 diff changeset	136 ## 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	137 #if len($output_reports_list) > 0
58a3e6cb2598 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6e846f7195a9e939047ac975c6523e8cf99da6b4 galaxyp parents: 46 diff changeset	138 -out_reports \$cwd/output_reports
58a3e6cb2598 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6e846f7195a9e939047ac975c6523e8cf99da6b4 galaxyp parents: 46 diff changeset	139 -reports #echo ','.join($output_reports_list)#
18 a5f9b959d5d1 Uploaded iracooke parents: diff changeset	140 #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	141
55 bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	142 ####################################################
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	143 ## PeptideShaker Follow-Up Analysis options ##
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	144 ####################################################
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	145 ## TODO: When done in the app, export graph databases, TPP export, recalibrate espectra
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	146
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	147 #if $exporting_options.followup_conditional.followup_conditional_selector == "yes"
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	148 #if $exporting_options.followup_conditional.followup_export_spectra != "off"
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	149 #set $exporting_followup_boolean = True
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	150 -spectrum_folder \$cwd/output_reports -psm_type $exporting_options.followup_conditional.followup_export_spectra
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	151 #end if
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	152 #if $exporting_options.followup_conditional.followup_export_accession_numbers != "off"
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	153 #set $exporting_followup_boolean = True
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	154 -accessions_file \$cwd/output_reports/proteins_accession_numbers.txt -accessions_type $exporting_options.followup_conditional.followup_export_accession_numbers
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	155 #end if
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	156 #if $exporting_options.followup_conditional.followup_export_sequences != "off"
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	157 #set $exporting_followup_boolean = True
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	158 -sequences_file \$cwd/output_reports/proteins_sequences.fasta -sequences_type $exporting_options.followup_conditional.followup_export_sequences
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	159 #end if
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	160 #if $exporting_options.followup_conditional.followup_export_proteoforms != "off"
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	161 #set $exporting_followup_boolean = True
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	162 -proteoforms_file \$cwd/output_reports/proteins_proteoforms.txt
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	163 #end if
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	164 #if $exporting_options.followup_conditional.followup_export_progenesis_conditional.followup_export_progenesis_selector != "off"
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	165 #set $exporting_followup_boolean = True
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	166 -progenesis_file \$cwd/output_reports/progenesis.txt -progenesis_type $exporting_options.followup_conditional.followup_export_progenesis_conditional.followup_export_progenesis_selector
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	167 #if $exporting_options.followup_conditional.followup_export_progenesis_conditional.followup_export_progenesis_selector == "3"
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	168 #set $progenesis_ptms = $exporting_options.followup_conditional.followup_export_progenesis_conditional.followup_export_progenesis_ptms or ''
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	169 #if $progenesis_ptms
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	170 -progenesis_ptms "$progenesis_ptms"
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	171 #end if
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	172 #end if
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	173 #end if
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	174 #if $exporting_options.followup_conditional.followup_export_inclusion_list_conditional.followup_export_inclusion_list_selector != "off"
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	175 #set $exporting_followup_boolean = True
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	176 -inclusion_list_file \$cwd/output_reports/inclusion_list.txt -inclusion_list_format $exporting_options.followup_conditional.followup_export_inclusion_list_conditional.followup_export_inclusion_list_selector
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	177 #set $peptide_filters = $exporting_options.followup_conditional.followup_export_inclusion_list_conditional.followup_export_inclusion_list_peptide_filters or ''
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	178 #if $peptide_filters
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	179 -inclusion_list_peptide_filters "$peptide_filters"
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	180 #end if
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	181 #set $protein_filters = $exporting_options.followup_conditional.followup_export_inclusion_list_conditional.followup_export_inclusion_list_protein_filters or ''
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	182 #if $protein_filters
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	183 -inclusion_list_protein_filters "$protein_filters"
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	184 #end if
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	185 #if $exporting_options.followup_conditional.followup_export_inclusion_list_conditional.followup_export_inclusion_list_rt_window
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	186 -inclusion_list_rt_window $exporting_options.followup_conditional.followup_export_inclusion_list_conditional.followup_export_inclusion_list_rt_window
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	187 #end if
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	188 #end if
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	189 #end if
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	190
53 d67a3c1bfd09 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 1327a0e10d66e5ed6a8b63b211672a724fcac424 galaxyp parents: 52 diff changeset	191 ## If the user chose to zip the results but also export reports out of the zip, we have to unzip them
55 bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	192 #if $exporting_options.zip_conditional.zip_output_boolean == 'zip' and $exporting_options.zip_conditional.export_reports_when_zip and (len(output_reports_list)>0 or $exporting_followup_boolean):
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	193 ## This unzipping command creates a reports folder into the current folder!
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	194 && unzip \$cwd/peptideshaker_output.zip "reports/*" -d \$cwd
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	195 && mv reports/* output_reports
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	196 && rm -r reports
53 d67a3c1bfd09 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 1327a0e10d66e5ed6a8b63b211672a724fcac424 galaxyp parents: 52 diff changeset	197 #end if
d67a3c1bfd09 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 1327a0e10d66e5ed6a8b63b211672a724fcac424 galaxyp parents: 52 diff changeset	198
55 bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	199 ## If the user chose to export mgf file/s out of the zip file
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	200 #if $exporting_options.zip_conditional.zip_output_boolean == 'zip' and $exporting_options.zip_conditional.export_mgf_when_zip:
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	201 && mkdir output_mgf
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	202 && mkdir output_cui
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	203 && mv \$cwd/*.mgf output_mgf
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	204 && mv \$cwd/*.cui output_cui
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	205 #end if
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	206
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	207 ## Renaming identification features reports to findable names and moving them to the root folder
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	208 #if len(output_reports_list)>0:
49 58a3e6cb2598 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6e846f7195a9e939047ac975c6523e8cf99da6b4 galaxyp parents: 46 diff changeset	209 #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	210 && 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	211 #end if
58a3e6cb2598 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6e846f7195a9e939047ac975c6523e8cf99da6b4 galaxyp parents: 46 diff changeset	212 #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	213 && 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	214 #end if
58a3e6cb2598 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6e846f7195a9e939047ac975c6523e8cf99da6b4 galaxyp parents: 46 diff changeset	215 #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	216 && find \$cwd/output_reports -name '*Default_PSM_Phosphorylation_Report.txt' -exec bash -c 'mv "$0" "psm_phospho.txt"' {} \;
54 7fdd9119cc4f "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit e17bb5a0e4a22c7376b2e7a70cf690262a44a0c6" galaxyp parents: 53 diff changeset	217 #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	218 #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	219 && 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	220 #end if
58a3e6cb2598 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6e846f7195a9e939047ac975c6523e8cf99da6b4 galaxyp parents: 46 diff changeset	221 #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	222 && 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	223 #end if
58a3e6cb2598 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6e846f7195a9e939047ac975c6523e8cf99da6b4 galaxyp parents: 46 diff changeset	224 #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	225 && 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	226 #end if
58a3e6cb2598 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6e846f7195a9e939047ac975c6523e8cf99da6b4 galaxyp parents: 46 diff changeset	227 #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	228 && 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	229 #end if
58a3e6cb2598 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6e846f7195a9e939047ac975c6523e8cf99da6b4 galaxyp parents: 46 diff changeset	230 #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	231 && 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	232 #end if
58a3e6cb2598 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6e846f7195a9e939047ac975c6523e8cf99da6b4 galaxyp parents: 46 diff changeset	233 #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	234 && 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	235 #end if
58a3e6cb2598 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6e846f7195a9e939047ac975c6523e8cf99da6b4 galaxyp parents: 46 diff changeset	236 #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	237 && 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	238 #end if
58a3e6cb2598 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6e846f7195a9e939047ac975c6523e8cf99da6b4 galaxyp parents: 46 diff changeset	239 #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	240 && 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	241 #end if
58a3e6cb2598 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6e846f7195a9e939047ac975c6523e8cf99da6b4 galaxyp parents: 46 diff changeset	242 #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	243 && 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	244 #end if
57 da885ca16cb2 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 44a20633e04b2396fad4b568904a257769b2bbc1" galaxyp parents: 55 diff changeset	245 ## the last ; is removed from the generated command line
da885ca16cb2 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 44a20633e04b2396fad4b568904a257769b2bbc1" galaxyp parents: 55 diff changeset	246 ## thus we need to make sure that the above `find ... -exec ... \;`
da885ca16cb2 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 44a20633e04b2396fad4b568904a257769b2bbc1" galaxyp parents: 55 diff changeset	247 ## is not the last command
da885ca16cb2 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 44a20633e04b2396fad4b568904a257769b2bbc1" galaxyp parents: 55 diff changeset	248 && true
20 2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b iracooke parents: 18 diff changeset	249 #end if
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b iracooke parents: 18 diff changeset	250
55 bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	251 ## Moving followup analysis to the root folder (it is necessary if zip option was not chosen, or it was chosen but also exporting out of the zip)
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	252 #if $exporting_options.followup_conditional.followup_conditional_selector == "yes" and ($exporting_options.zip_conditional.zip_output_boolean != 'zip' or ($exporting_options.zip_conditional.zip_output_boolean == 'zip' and $exporting_options.zip_conditional.export_reports_when_zip)):
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	253 ## Spectrum analysis are already expected to be into the output_reports folder itself
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	254 #if $exporting_options.followup_conditional.followup_export_accession_numbers != "off"
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	255 && mv \$cwd/output_reports/proteins_accession_numbers.txt \$cwd/proteins_accession_numbers.txt
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	256 #end if
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	257 #if $exporting_options.followup_conditional.followup_export_sequences != "off"
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	258 && mv \$cwd/output_reports/proteins_sequences.fasta \$cwd/proteins_sequences.fasta
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	259 #end if
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	260 #if $exporting_options.followup_conditional.followup_export_proteoforms != "off"
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	261 && mv \$cwd/output_reports/proteins_proteoforms.txt \$cwd/proteins_proteoforms.txt
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	262 #end if
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	263 #if $exporting_options.followup_conditional.followup_export_progenesis_conditional.followup_export_progenesis_selector != "off"
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	264 && mv \$cwd/output_reports/progenesis.txt \$cwd/progenesis.txt
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	265 #end if
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	266 #if $exporting_options.followup_conditional.followup_export_inclusion_list_conditional.followup_export_inclusion_list_selector != "off"
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	267 && mv \$cwd/output_reports/inclusion_list.txt \$cwd/inclusion_list.txt
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	268 #end if
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	269 #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	270 ]]>
18 a5f9b959d5d1 Uploaded iracooke parents: diff changeset	271 </command>
a5f9b959d5d1 Uploaded iracooke parents: diff changeset	272 <inputs>
21 dfaea053e32f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 327a3944f2f56668d607c3d6cb08ae7d588e208c iracooke parents: 20 diff changeset	273 <param name="searchgui_input" format="searchgui_archive" type="data" label="Compressed SearchGUI results"
24 815f93bb3e1b Uploaded galaxyp parents: 22 diff changeset	274 help="SearchGUI Results from History">
815f93bb3e1b Uploaded galaxyp parents: 22 diff changeset	275 <options options_filter_attribute="metadata.searchgui_major_version" >
815f93bb3e1b Uploaded galaxyp parents: 22 diff changeset	276 <filter type="add_value" value="@SEARCHGUI_MAJOR_VERSION@" />
815f93bb3e1b Uploaded galaxyp parents: 22 diff changeset	277 </options>
815f93bb3e1b Uploaded galaxyp parents: 22 diff changeset	278 </param>
55 bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	279
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	280 <section name="optional_main_parameters" expanded="false" title="Optional main parameters">
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	281 <param format="json" name="input_optional_identification_parameters" type="data" label="Identification parameters" optional="true" help="This optional parameter file will be used instead of the default one"/>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	282 <param format="fasta" name="input_fasta_file" type="data" label="Fasta file" optional="true" help="This optional fasta file will be used instead of the one included in the SearchGUI file (if it exists). If the SearchGUI file does not include the fasta file, this parameter is must be considered as mandatory."/>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	283 <param format="mgf,mzml" name="input_optional_spectrum_files" type="data" label="Spectrum files" optional="true" multiple="true" help="Optional spectrum files will be used together with spectra included in the SearchGUI output"/>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	284 </section>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	285
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	286 <section name="exporting_options" expanded="true" title="Exporting options" help="All different outputs PeptideShaker may produce">
30 ad60446b1e93 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit bdb5ee12705a3494eee96d1963f16f68bbe41d5c galaxyp parents: 29 diff changeset	287
55 bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	288 <conditional name="zip_conditional">
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	289 <param name="zip_output_boolean" type="boolean" truevalue="zip" falsevalue="separate" checked="false" label="Compress results into a single zip file" />
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	290 <when value="separate">
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	291 <param name="export_psdb" type="boolean" truevalue="1" falsevalue="0" checked="false" label="Exports PeptideShakers‘ .psdb file" />
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	292 </when>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	293 <when value="zip">
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	294 <param name="export_reports_when_zip" type="boolean" truevalue="1" falsevalue="0" checked="false" label="Also export reports out of the zip" />
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	295 <param name="export_mgf_when_zip" type="boolean" truevalue="1" falsevalue="0" checked="false" label="Also export mgf file/s out of the zip" help=".cui index files are exported as a different collection too" />
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	296 </when>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	297 </conditional>
49 58a3e6cb2598 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6e846f7195a9e939047ac975c6523e8cf99da6b4 galaxyp parents: 46 diff changeset	298
58a3e6cb2598 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6e846f7195a9e939047ac975c6523e8cf99da6b4 galaxyp parents: 46 diff changeset	299 <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	300 <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	301 <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	302 <param name="include_sequences" type="boolean" truevalue="1" falsevalue="0" checked="false" label="Include the protein sequences in the mzIdentML file" />
55 bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	303
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	304 <conditional name="contact_options">
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	305 <param name="contact_options_selector" type="select" label="Contact Information"
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	306 help="Create a Galaxy workflow to save these values">
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	307 <option value="no" selected="True">GalaxyP Project contact (Not suitable for PRIDE submission)</option>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	308 <option value="yes">Specify Contact Information</option>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	309 </param>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	310 <when value="no" />
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	311 <when value="yes">
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	312 <param name="contact_first_name" type="text" value="" label="Contact first name.">
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	313 <validator type="regex" message="">\S+.*</validator>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	314 </param>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	315 <param name="contact_last_name" type="text" value="" label="Contact last name.">
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	316 <validator type="regex" message="">\S+.*</validator>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	317 </param>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	318 <param name="contact_email" type="text" value="" label="Contact e-mail.">
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	319 <validator type="regex" message="">\S+@\S+</validator>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	320 </param>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	321 <param name="contact_address" type="text" value="" label="Contact address.">
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	322 <validator type="regex" message="">\S+.*</validator>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	323 </param>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	324 <param name="contact_url" type="text" value="" optional="true" label="Contact URL.">
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	325 </param>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	326 <param name="organization_name" type="text" value="" label="Organization name.">
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	327 <validator type="regex" message="">\S+.*</validator>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	328 </param>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	329 <param name="organization_email" type="text" value="" label="Organization e-mail.">
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	330 <validator type="regex" message="">\S+@\S+</validator>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	331 </param>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	332 <param name="organization_address" type="text" value="" label="Organization address.">
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	333 <validator type="regex" message="">\S+.*</validator>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	334 </param>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	335 <param name="organization_url" type="text" value="" optional="true" label="Organization URL.">
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	336 </param>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	337 </when>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	338 </conditional>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	339
49 58a3e6cb2598 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6e846f7195a9e939047ac975c6523e8cf99da6b4 galaxyp parents: 46 diff changeset	340 </when>
58a3e6cb2598 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6e846f7195a9e939047ac975c6523e8cf99da6b4 galaxyp parents: 46 diff changeset	341 <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	342 </conditional>
58a3e6cb2598 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6e846f7195a9e939047ac975c6523e8cf99da6b4 galaxyp parents: 46 diff changeset	343
55 bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	344 <!-- FOLLOW-UP REPORTS -->
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	345 <conditional name="followup_conditional">
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	346 <param name="followup_conditional_selector" type="select" label="Follow-up analysis export options">
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	347 <option value="yes">Export follow-up analysis</option>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	348 <option value="no" selected="True">Do not export</option>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	349 </param>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	350 <when value="no" />
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	351 <when value="yes">
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	352 <param name="followup_export_spectra" label="Spectra: Export spectrum files as MGF" type="select" help="Commonly: spectra of Non-Validated PSMs">
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	353 <option value="0" >Spectra of Non-Validated PSMs</option>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	354 <option value="1" >Spectra of Non-Validated Peptides</option>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	355 <option value="2" >Spectra of Non-Validated Proteins</option>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	356 <option value="3" >Spectra of Validated PSMs</option>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	357 <option value="4" >Spectra of Validated PSMs of Validated Peptides</option>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	358 <option value="5" >Spectra of validated PSMs of Validated Peptides of Validated Proteins</option>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	359 <option value="off" selected="True">Do not export</option>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	360 </param>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	361 <param name="followup_export_accession_numbers" label="Proteins: Export accession numbers as TXT" type="select" help="Commonly: Main Accession of Validated Protein Groups">
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	362 <option value="0" >Main Accession of Validated Protein Groups</option>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	363 <option value="1" >All Accessions of Validated Protein Groups</option>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	364 <option value="2" >Non-Validated Accessions</option>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	365 <option value="off" selected="True">Do not export</option>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	366 </param>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	367 <param name="followup_export_sequences" label="Proteins: Export protein details/sequences in fasta format" type="select" help="Commonly: Main Accession of Validated Protein Groups">
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	368 <option value="0" >Main Accession of Validated Protein Groups</option>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	369 <option value="1" >All Accessions of Validated Protein Groups</option>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	370 <option value="2" >Non-Validated Accessions</option>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	371 <option value="off" selected="True">Do not export</option>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	372 </param>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	373 <param name="followup_export_proteoforms" label="Proteins: Export proteoforms as TXT" type="select">
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	374 <option value="on">Export</option>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	375 <option value="off" selected="True">Do not export</option>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	376 </param>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	377 <conditional name="followup_export_progenesis_conditional">
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	378 <param name="followup_export_progenesis_selector" label="Label free quantification: Exports identification results in Progenesis LC-MS compatible format as TXT" type="select" help="Commonly: Validated PSMs of Validated Peptides of Validated Proteins">
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	379 <option value="0">Validated PSMs of Validated Peptides of Validated Proteins</option>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	380 <option value="1">Validated PSMs of Validated Peptides</option>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	381 <option value="2">Validated PSMs</option>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	382 <option value="3">Confidently localized PTMs of Validated PSMs of Validated Peptides of Validated Proteins</option>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	383 <option value="off" selected="True">Do not export</option>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	384 </param>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	385 <when value="0"/>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	386 <when value="1"/>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	387 <when value="2"/>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	388 <when value="3">
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	389 <param name="followup_export_progenesis_ptms" type="select" label="Targeted PTMs" multiple="true"
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	390 help="">
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	391 <expand macro="modifications"/>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	392 </param>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	393 </when>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	394 <when value="off"/>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	395 </conditional>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	396 <conditional name="followup_export_inclusion_list_conditional">
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	397 <param name="followup_export_inclusion_list_selector" label="Inclusion/Exclusion list: Exports a file for an inclusion list of validated hits" type="select" help="Commonly: Thermo">
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	398 <option value="0" >Thermo</option>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	399 <option value="1" >ABI</option>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	400 <option value="2" >Bruker</option>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	401 <option value="3" >MassLynx</option>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	402 <option value="off" selected="True">Do not export</option>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	403 </param>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	404 <when value="0">
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	405 <param name="followup_export_inclusion_list_peptide_filters" type="select" label="Peptide Filters" multiple="true" optional="true" display="checkboxes"
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	406 help="">
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	407 <option value="0">Miscleaved Peptides</option>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	408 <option value="1">Reactive Peptides</option>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	409 <option value="2">Degenerated Peptides</option>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	410 </param>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	411 <param name="followup_export_inclusion_list_protein_filters" type="select" label="Protein Filters" multiple="true" optional="true" display="checkboxes"
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	412 help="">
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	413 <option value="1">Related Proteins</option>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	414 <option value="2">Related and Unrelated Proteins</option>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	415 <option value="3">Unrelated Proteins</option>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	416 </param>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	417 <param name="followup_export_inclusion_list_rt_window" type="integer" value="20" label="Retention time window for the inclusion list export (in seconds)"
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	418 help=""/>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	419 </when>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	420 <when value="1">
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	421 <param name="followup_export_inclusion_list_peptide_filters" type="select" label="Peptide Filters" multiple="true" optional="true" display="checkboxes"
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	422 help="">
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	423 <option value="0">Miscleaved Peptides</option>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	424 <option value="1">Reactive Peptides</option>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	425 <option value="2">Degenerated Peptides</option>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	426 </param>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	427 <param name="followup_export_inclusion_list_protein_filters" type="select" label="Protein Filters" multiple="true" optional="true" display="checkboxes"
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	428 help="">
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	429 <option value="1">Related Proteins</option>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	430 <option value="2">Related and Unrelated Proteins</option>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	431 <option value="3">Unrelated Proteins</option>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	432 </param>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	433 <param name="followup_export_inclusion_list_rt_window" type="integer" value="20" label="Retention time window for the inclusion list export (in seconds)"
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	434 help=""/>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	435 </when>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	436 <when value="2">
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	437 <param name="followup_export_inclusion_list_peptide_filters" type="select" label="Peptide Filters" multiple="true" optional="true" display="checkboxes"
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	438 help="">
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	439 <option value="0">Miscleaved Peptides</option>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	440 <option value="1">Reactive Peptides</option>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	441 <option value="2">Degenerated Peptides</option>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	442 </param>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	443 <param name="followup_export_inclusion_list_protein_filters" type="select" label="Protein Filters" multiple="true" optional="true" display="checkboxes"
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	444 help="">
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	445 <option value="1">Related Proteins</option>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	446 <option value="2">Related and Unrelated Proteins</option>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	447 <option value="3">Unrelated Proteins</option>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	448 </param>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	449 <param name="followup_export_inclusion_list_rt_window" type="integer" value="20" label="Retention time window for the inclusion list export (in seconds)"
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	450 help=""/>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	451 </when>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	452 <when value="3">
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	453 <param name="followup_export_inclusion_list_peptide_filters" type="select" label="Peptide Filters" multiple="true" optional="true" display="checkboxes"
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	454 help="">
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	455 <option value="0">Miscleaved Peptides</option>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	456 <option value="1">Reactive Peptides</option>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	457 <option value="2">Degenerated Peptides</option>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	458 </param>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	459 <param name="followup_export_inclusion_list_protein_filters" type="select" label="Protein Filters" multiple="true" optional="true" display="checkboxes"
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	460 help="">
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	461 <option value="1">Related Proteins</option>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	462 <option value="2">Related and Unrelated Proteins</option>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	463 <option value="3">Unrelated Proteins</option>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	464 </param>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	465 <param name="followup_export_inclusion_list_rt_window" type="integer" value="20" label="Retention time window for the inclusion list export (in seconds)"
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	466 help=""/>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	467 </when>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	468 <when value="off"/>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	469 </conditional>
53 d67a3c1bfd09 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 1327a0e10d66e5ed6a8b63b211672a724fcac424 galaxyp parents: 52 diff changeset	470 </when>
49 58a3e6cb2598 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6e846f7195a9e939047ac975c6523e8cf99da6b4 galaxyp parents: 46 diff changeset	471 </conditional>
58a3e6cb2598 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6e846f7195a9e939047ac975c6523e8cf99da6b4 galaxyp parents: 46 diff changeset	472
55 bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	473 <!-- IDENTIFICATION FEATURES REPORTS -->
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	474 <param name="output_reports" type="select" display="checkboxes" multiple="True" optional="true" label="Identification features reports to be generated">
49 58a3e6cb2598 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6e846f7195a9e939047ac975c6523e8cf99da6b4 galaxyp parents: 46 diff changeset	475 <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	476 <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	477 <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	478 <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	479 <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	480 <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	481 <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	482 <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	483 <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	484 <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	485 <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	486 <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	487 </param>
58a3e6cb2598 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6e846f7195a9e939047ac975c6523e8cf99da6b4 galaxyp parents: 46 diff changeset	488
58a3e6cb2598 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6e846f7195a9e939047ac975c6523e8cf99da6b4 galaxyp parents: 46 diff changeset	489 </section>
20 2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b iracooke parents: 18 diff changeset	490
18 a5f9b959d5d1 Uploaded iracooke parents: diff changeset	491 </inputs>
a5f9b959d5d1 Uploaded iracooke parents: diff changeset	492 <outputs>
20 2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b iracooke parents: 18 diff changeset	493 <data format="zip" name="output_zip" from_work_dir="peptideshaker_output.zip" label="${tool.name} on ${on_string}: Archive">
49 58a3e6cb2598 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6e846f7195a9e939047ac975c6523e8cf99da6b4 galaxyp parents: 46 diff changeset	494 <filter>exporting_options['zip_conditional']['zip_output_boolean'] is True</filter>
20 2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b iracooke parents: 18 diff changeset	495 </data>
55 bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	496 <data format="mzid" name="mzidentML" from_work_dir="output.mzid" label="${tool.name} on ${on_string}: mzidentML file">
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	497 <filter>exporting_options['zip_conditional']['zip_output_boolean'] is False and exporting_options['mzidentml_conditional']['mzidentml_creation'] is True</filter>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	498 </data>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	499 <data format="peptideshaker_archive" name="output_psdb" from_work_dir="peptideshaker_output.psdb" label="${tool.name} on ${on_string}: PSDB file">
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	500 <filter>exporting_options['zip_conditional']['zip_output_boolean'] is False and exporting_options['zip_conditional']['export_psdb'] is True</filter>
49 58a3e6cb2598 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6e846f7195a9e939047ac975c6523e8cf99da6b4 galaxyp parents: 46 diff changeset	501 </data>
55 bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	502 <collection name="output_mgf" type="list" label="${tool.name} on ${on_string}: Mgf" >
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	503 <filter>exporting_options['zip_conditional']['zip_output_boolean'] is True and exporting_options['zip_conditional']['export_mgf_when_zip'] is True</filter>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	504 <discover_datasets pattern="__name_and_ext__" directory="output_mgf" ext="mgf"/>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	505 </collection>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	506 <collection name="output_cui" type="list" label="${tool.name} on ${on_string}: Cui" >
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	507 <filter>exporting_options['zip_conditional']['zip_output_boolean'] is True and exporting_options['zip_conditional']['export_mgf_when_zip'] is True</filter>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	508 <discover_datasets pattern="__name_and_ext__" directory="output_cui" ext="cui"/>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	509 </collection>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	510
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	511 <!-- Follow-up analysis -->
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	512 <collection name="output_spectra" type="list" label="${tool.name} on ${on_string}: Spectra" >
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	513 <filter>(exporting_options['zip_conditional']['zip_output_boolean'] is False or exporting_options['zip_conditional']['export_reports_when_zip'] is True) and exporting_options['followup_conditional']['followup_conditional_selector'] == 'yes' and exporting_options['followup_conditional']['followup_export_spectra'] != 'off' </filter>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	514 <discover_datasets pattern="__name_and_ext__" directory="output_reports" ext="mgf"/>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	515 </collection>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	516 <data format="txt" name="output_proteins_accessions" from_work_dir="proteins_accession_numbers.txt" label="${tool.name} on ${on_string}: Proteins Accession Numbers">
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	517 <filter>(exporting_options['zip_conditional']['zip_output_boolean'] is False or exporting_options['zip_conditional']['export_reports_when_zip'] is True) and exporting_options['followup_conditional']['followup_conditional_selector'] == 'yes' and exporting_options['followup_conditional']['followup_export_accession_numbers'] != 'off' </filter>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	518 </data>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	519 <data format="fasta" name="output_proteins_sequences" from_work_dir="proteins_sequences.fasta" label="${tool.name} on ${on_string}: Proteins Sequences">
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	520 <filter>(exporting_options['zip_conditional']['zip_output_boolean'] is False or exporting_options['zip_conditional']['export_reports_when_zip'] is True) and exporting_options['followup_conditional']['followup_conditional_selector'] == 'yes' and exporting_options['followup_conditional']['followup_export_sequences'] != 'off' </filter>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	521 </data>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	522 <data format="txt" name="output_proteoforms" from_work_dir="proteins_proteoforms.txt" label="${tool.name} on ${on_string}: Proteins Proteoforms">
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	523 <filter>(exporting_options['zip_conditional']['zip_output_boolean'] is False or exporting_options['zip_conditional']['export_reports_when_zip'] is True) and exporting_options['followup_conditional']['followup_conditional_selector'] == 'yes' and exporting_options['followup_conditional']['followup_export_proteoforms'] != 'off' </filter>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	524 </data>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	525 <data format="txt" name="output_progenesis" from_work_dir="progenesis.txt" label="${tool.name} on ${on_string}: Progenesis">
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	526 <filter>(exporting_options['zip_conditional']['zip_output_boolean'] is False or exporting_options['zip_conditional']['export_reports_when_zip'] is True) and exporting_options['followup_conditional']['followup_conditional_selector'] == 'yes' and exporting_options['followup_conditional']['followup_export_progenesis_conditional']['followup_export_progenesis_selector'] != 'off' </filter>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	527 </data>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	528 <data format="txt" name="output_inclusion_list" from_work_dir="inclusion_list.txt" label="${tool.name} on ${on_string}: Inclusion/Exclusion List">
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	529 <filter>(exporting_options['zip_conditional']['zip_output_boolean'] is False or exporting_options['zip_conditional']['export_reports_when_zip'] is True) and exporting_options['followup_conditional']['followup_conditional_selector'] == 'yes' and exporting_options['followup_conditional']['followup_export_inclusion_list_conditional']['followup_export_inclusion_list_selector'] != 'off' </filter>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	530 </data>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	531
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	532 <!-- Identification Features outputs -->
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	533 <data format="txt" name="output_certificate" from_work_dir="certificate.txt" label="${tool.name} on ${on_string}: Certificate of Analysis">
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	534 <filter>(exporting_options['zip_conditional']['zip_output_boolean'] is False or exporting_options['zip_conditional']['export_reports_when_zip'] is True) and str(exporting_options['output_reports']) != 'None' and str(exporting_options['output_reports']) != '' and '0' in exporting_options['output_reports']</filter>
18 a5f9b959d5d1 Uploaded iracooke parents: diff changeset	535 </data>
20 2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b iracooke parents: 18 diff changeset	536 <data format="tabular" name="output_hierarchical" from_work_dir="hierarchical.txt" label="${tool.name} on ${on_string}: Hierarchical Report">
55 bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	537 <filter>(exporting_options['zip_conditional']['zip_output_boolean'] is False or exporting_options['zip_conditional']['export_reports_when_zip'] is True) and str(exporting_options['output_reports']) != 'None' and str(exporting_options['output_reports']) != '' and '1' in exporting_options['output_reports']</filter>
20 2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b iracooke parents: 18 diff changeset	538 </data>
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b iracooke parents: 18 diff changeset	539 <data format="tabular" name="output_psm_phosphorylation" from_work_dir="psm_phospho.txt" label="${tool.name} on ${on_string}: PSM Phosphorylation Report">
55 bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	540 <filter>(exporting_options['zip_conditional']['zip_output_boolean'] is False or exporting_options['zip_conditional']['export_reports_when_zip'] is True) and str(exporting_options['output_reports']) != 'None' and str(exporting_options['output_reports']) != '' and '2' in exporting_options['output_reports']</filter>
18 a5f9b959d5d1 Uploaded iracooke parents: diff changeset	541 </data>
20 2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b iracooke parents: 18 diff changeset	542 <data format="tabular" name="output_psm" from_work_dir="psm.txt" label="${tool.name} on ${on_string}: PSM Report">
55 bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	543 <filter>(exporting_options['zip_conditional']['zip_output_boolean'] is False or exporting_options['zip_conditional']['export_reports_when_zip'] is True) and str(exporting_options['output_reports']) != 'None' and str(exporting_options['output_reports']) != '' and '3' in exporting_options['output_reports']</filter>
49 58a3e6cb2598 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6e846f7195a9e939047ac975c6523e8cf99da6b4 galaxyp parents: 46 diff changeset	544 </data>
58a3e6cb2598 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6e846f7195a9e939047ac975c6523e8cf99da6b4 galaxyp parents: 46 diff changeset	545 <data format="tabular" name="output_psm_nonvalidated" from_work_dir="psm_nonvalidated.txt" label="${tool.name} on ${on_string}: PSM Report with non-validated matches">
55 bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	546 <filter>(exporting_options['zip_conditional']['zip_output_boolean'] is False or exporting_options['zip_conditional']['export_reports_when_zip'] is True) and str(exporting_options['output_reports']) != 'None' and str(exporting_options['output_reports']) != '' and '4' in exporting_options['output_reports']</filter>
18 a5f9b959d5d1 Uploaded iracooke parents: diff changeset	547 </data>
30 ad60446b1e93 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit bdb5ee12705a3494eee96d1963f16f68bbe41d5c galaxyp parents: 29 diff changeset	548 <data format="tabular" name="output_extended_psm" from_work_dir="psmx.txt" label="${tool.name} on ${on_string}: Extended PSM Report">
55 bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	549 <filter>(exporting_options['zip_conditional']['zip_output_boolean'] is False or exporting_options['zip_conditional']['export_reports_when_zip'] is True) and str(exporting_options['output_reports']) != 'None' and str(exporting_options['output_reports']) != '' and '11' in exporting_options['output_reports']</filter>
30 ad60446b1e93 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit bdb5ee12705a3494eee96d1963f16f68bbe41d5c galaxyp parents: 29 diff changeset	550 </data>
20 2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b iracooke parents: 18 diff changeset	551 <data format="tabular" name="output_peptides_phosphorylation" from_work_dir="peptides_phospho.txt" label="${tool.name} on ${on_string}: Peptide Phosphorylation Report">
55 bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	552 <filter>(exporting_options['zip_conditional']['zip_output_boolean'] is False or exporting_options['zip_conditional']['export_reports_when_zip'] is True) and str(exporting_options['output_reports']) != 'None' and str(exporting_options['output_reports']) != '' and '5' in exporting_options['output_reports']</filter>
18 a5f9b959d5d1 Uploaded iracooke parents: diff changeset	553 </data>
20 2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b iracooke parents: 18 diff changeset	554 <data format="tabular" name="output_peptides" from_work_dir="peptides.txt" label="${tool.name} on ${on_string}: Peptide Report">
55 bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	555 <filter>(exporting_options['zip_conditional']['zip_output_boolean'] is False or exporting_options['zip_conditional']['export_reports_when_zip'] is True) and str(exporting_options['output_reports']) != 'None' and str(exporting_options['output_reports']) != '' and '6' in exporting_options['output_reports']</filter>
49 58a3e6cb2598 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6e846f7195a9e939047ac975c6523e8cf99da6b4 galaxyp parents: 46 diff changeset	556 </data>
58a3e6cb2598 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6e846f7195a9e939047ac975c6523e8cf99da6b4 galaxyp parents: 46 diff changeset	557 <data format="tabular" name="output_peptides_nonvalidated" from_work_dir="peptides_nonvalidated.txt" label="${tool.name} on ${on_string}: Peptide Report with non-validated matches">
55 bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	558 <filter>(exporting_options['zip_conditional']['zip_output_boolean'] is False or exporting_options['zip_conditional']['export_reports_when_zip'] is True) and str(exporting_options['output_reports']) != 'None' and str(exporting_options['output_reports']) != '' and '7' in exporting_options['output_reports']</filter>
20 2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b iracooke parents: 18 diff changeset	559 </data>
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b iracooke parents: 18 diff changeset	560 <data format="tabular" name="output_proteins_phosphorylation" from_work_dir="proteins_phospho.txt" label="${tool.name} on ${on_string}: Protein Phosphorylation Report">
55 bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	561 <filter>(exporting_options['zip_conditional']['zip_output_boolean'] is False or exporting_options['zip_conditional']['export_reports_when_zip'] is True) and str(exporting_options['output_reports']) != 'None' and str(exporting_options['output_reports']) != '' and '8' in exporting_options['output_reports']</filter>
20 2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b iracooke parents: 18 diff changeset	562 </data>
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b iracooke parents: 18 diff changeset	563 <data format="tabular" name="output_proteins" from_work_dir="proteins.txt" label="${tool.name} on ${on_string}: Protein Report">
55 bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	564 <filter>(exporting_options['zip_conditional']['zip_output_boolean'] is False or exporting_options['zip_conditional']['export_reports_when_zip'] is True) and str(exporting_options['output_reports']) != 'None' and str(exporting_options['output_reports']) != '' and '9' in exporting_options['output_reports']</filter>
49 58a3e6cb2598 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6e846f7195a9e939047ac975c6523e8cf99da6b4 galaxyp parents: 46 diff changeset	565 </data>
55 bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	566 <data format="tabular" name="output_proteins_nonvalidated" from_work_dir="proteins_nonvalidated.txt" label="${tool.name} on ${on_string}: Protein Report with non-validated matches">
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	567 <filter>(exporting_options['zip_conditional']['zip_output_boolean'] is False or exporting_options['zip_conditional']['export_reports_when_zip'] is True) and str(exporting_options['output_reports']) != 'None' and str(exporting_options['output_reports']) != '' and '10' in exporting_options['output_reports']</filter>
18 a5f9b959d5d1 Uploaded iracooke parents: diff changeset	568 </data>
a5f9b959d5d1 Uploaded iracooke parents: diff changeset	569 </outputs>
55 bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	570
18 a5f9b959d5d1 Uploaded iracooke parents: diff changeset	571 <tests>
55 bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	572 <!-- Basic test: default identification parameters, searchgui_tinydb1.fasta, 4 search engines xx-->
58 07ff622ec007 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0f6ab8b5647a33b2b051d7aa808ef42546436b23" galaxyp parents: 57 diff changeset	573 <test expect_num_outputs="2">
55 bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	574 <param name="searchgui_input" value="searchgui_tiny_result_default_4engines.zip" ftype="searchgui_archive"/>
58 07ff622ec007 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0f6ab8b5647a33b2b051d7aa808ef42546436b23" galaxyp parents: 57 diff changeset	575 <param name="mzidentml_creation" value="1"/>
55 bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	576 <param name="export_psdb" value="1"/>
58 07ff622ec007 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0f6ab8b5647a33b2b051d7aa808ef42546436b23" galaxyp parents: 57 diff changeset	577 <output name="mzidentML" ftype="mzid">
07ff622ec007 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0f6ab8b5647a33b2b051d7aa808ef42546436b23" galaxyp parents: 57 diff changeset	578 <assert_contents>
07ff622ec007 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0f6ab8b5647a33b2b051d7aa808ef42546436b23" galaxyp parents: 57 diff changeset	579 <has_text text="MzIdentML"/>
07ff622ec007 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0f6ab8b5647a33b2b051d7aa808ef42546436b23" galaxyp parents: 57 diff changeset	580 </assert_contents>
07ff622ec007 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0f6ab8b5647a33b2b051d7aa808ef42546436b23" galaxyp parents: 57 diff changeset	581 </output>
55 bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	582 <output name="output_psdb" ftype="peptideshaker_archive">
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	583 <assert_contents>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	584 <has_size value="122880" delta="3000"/>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	585 </assert_contents>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	586 </output>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	587 </test>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	588
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	589 <!-- Modifications test: default identification parameters with modifications, searchgui_tinydb1.fasta, 4 search engines -->
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	590 <test expect_num_outputs="1">
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	591 <param name="searchgui_input" value="searchgui_tiny_result_default_4engines_modifications.zip" ftype="searchgui_archive"/>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	592 <param name="mzidentml_creation" value="0"/>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	593 <param name="export_psdb" value="1"/>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	594 <output name="output_zip" ftype="peptideshaker_archive">
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	595 <assert_contents>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	596 <has_size value="126976" delta="3000"/>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	597 </assert_contents>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	598 </output>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	599 </test>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	600
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	601 <!-- Reports tests: default identification parameters, small spectra, some search engines (XTandem,MSGF+, OMSSA), all identification reports -->
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	602 <test expect_num_outputs="12">
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	603 <param name="searchgui_input" value="searchgui_smallsearch_default_somesearchengines_modifications.zip" ftype="searchgui_archive"/>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	604 <param name="mzidentml_creation" value="0"/>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	605 <param name="zip_output_boolean" value="separate"/>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	606 <param name="export_psdb" value="0"/>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	607 <param name="output_reports" value="0,1,2,3,4,5,6,7,8,9,10,11"/>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	608 <output name="output_certificate" file="peptideshaker_reports_output_certificate.txt" ftype="txt" lines_diff="8"/>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	609 <output name="output_hierarchical" file="peptideshaker_reports_output_hierarchical.tabular" ftype="tabular"/>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	610 <output name="output_extended_psm" file="peptideshaker_reports_output_extendedpsm.tabular" ftype="tabular"/>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	611 <output name="output_psm" file="peptideshaker_reports_output_psm.tabular" ftype="tabular"/>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	612 <output name="output_psm_phosphorylation" file="peptideshaker_reports_output_psmphosphorylation.tabular" ftype="tabular"/>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	613 <output name="output_psm_nonvalidated" file="peptideshaker_reports_output_psmnonvalidated.tabular" ftype="tabular"/>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	614 <output name="output_peptides" file="peptideshaker_reports_output_peptides.tabular" ftype="tabular"/>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	615 <output name="output_peptides_phosphorylation" file="peptideshaker_reports_output_peptidesphosphorylation.tabular" ftype="tabular"/>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	616 <output name="output_peptides_nonvalidated" file="peptideshaker_reports_output_peptidesnonvalidated.tabular" ftype="tabular"/>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	617 <output name="output_proteins" file="peptideshaker_reports_output_proteins.tabular" ftype="tabular"/>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	618 <output name="output_proteins_phosphorylation" file="peptideshaker_reports_output_proteinsphosphorylation.tabular" ftype="tabular"/>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	619 <output name="output_proteins_nonvalidated" file="peptideshaker_reports_output_proteinsnonvalidated.tabular" ftype="tabular"/>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	620 </test>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	621
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	622 <!-- followup analysis tests: default identification parameters, small spectra, some search engines (XTandem,MSGF+, OMSSA), all followup analysis -->
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	623 <test expect_num_outputs="5">
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	624 <param name="searchgui_input" value="searchgui_smallsearch_default_somesearchengines_modifications.zip" ftype="searchgui_archive"/>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	625 <param name="mzidentml_creation" value="0"/>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	626 <param name="zip_output_boolean" value="separate"/>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	627 <param name="export_psdb" value="0"/>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	628 <param name="followup_conditional_selector" value="yes"/>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	629 <param name="followup_export_spectra" value="0"/>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	630 <param name="followup_export_accession_numbers" value="0"/>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	631 <param name="followup_export_sequences" value="0"/>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	632 <param name="followup_export_proteoforms" value="on"/>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	633 <param name="followup_export_progenesis_selector" value="0"/>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	634 <output_collection name="output_spectra" type="list">
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	635 <element name="searchgui_smallspectra_non_validated_PSMs" ftype="mgf">
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	636 <assert_contents>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	637 <has_line_matching expression="236.0470428 11.674492836"/>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	638 <has_line_matching expression="520.9862671 4666.4399414063"/>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	639 <has_line_matching expression="267.4349976 50.7710571289"/>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	640 <has_line_matching expression="665.7418213 3.8165459633"/>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	641 <has_line_matching expression="634.7792969 2367.6374511719"/>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	642 </assert_contents>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	643 </element>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	644 </output_collection>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	645 <output name="output_proteins_accessions" ftype="txt">
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	646 <assert_contents>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	647 <has_line_matching expression="cds.comp41779_c0_seq1"/>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	648 <has_line_matching expression="cds.comp41890_c0_seq1"/>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	649 <has_line_matching expression="cds.comp41890_c0_seq1_REVERSED"/>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	650 <has_line_matching expression="cds.comp8310_c0_seq2"/>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	651 </assert_contents>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	652 </output>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	653 <output name="output_proteins_sequences" ftype="fasta">
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	654 <assert_contents>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	655 <has_line_matching expression=">generic\|cds.comp41779_c0_seq1\|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-6"/>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	656 <has_line_matching expression="METTKERKEKSTVVTKRQSMGATAHVQPKFIQVNRRSHVVGAGLGGGSMGSMNQSMSLHGGRASLGMAAGVAGGIATKDMGTMKVKREGEKKDMQNLNDRFAGYIAKVRSLQAENEQLRLKLSKKRREFDVEPLKEAYQAEIDEAKNLLLDANKENGELKISITTYEEEIEDLHATARINEDRIDELQDKVNKLIDENSHREAECSMLHKKLDELEKQVAHWRAKYNEVNTQLQATRADLKDETQQRIFLQQKVGNLEEELEFLRSVTDAEIKEYKAMLSKEDDTGTNVSAAWNNEMSNCMKELREEYDQRLADISDEMSARYESQLSQIRQSAHAEPVAAVHTKSEKSTGMVSVQKDMRIKELESQLERMKMEIITITNQLQRSNEDLENEKDLRTTEVNKLHVEMESMIEELQMLMDAKLSLELEIAAYRKLLEGEENRISTGYITENIGGFRSEAGDNLANILEFGSGGGGGGGGGGSGSGSGSGLAGDSASTSTLTGRLTIQRSSKSVISIGEVESEGQYVTLENTSSGRSKTSVNMKGWKLDRLISATSISPEHKIDFLFKDPVVLEGEQSIKIWAKNYQKMAKKGDIIATVDEWGPVNRNSVFSLYDEKDALKANLSTKVVT"/>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	657 <has_line_matching expression="generic\|cds.comp41890_c0_seq1_REVERSED\|m.9546 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 38.58 EValue:4.0e-20-REVERSED"/>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	658 <has_line_matching expression="LNYTTELNYTAKEDGRTNLLVTNVKAGVGLRSKNHWVLDGSNPDGMGNAWVKAFGGPKLVLNEIEYESIDINDSNQMIKWGSLDVTHSNSTNELLIFSGDRDTESIAVPGKNNKRYTSHEQLEGKVLAPTPSQY"/>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	659 </assert_contents>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	660 </output>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	661 <output name="output_proteoforms" ftype="txt">
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	662 <assert_contents>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	663 <has_line_matching expression="cds.comp8310_c0_seq2"/>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	664 <has_line_matching expression="cds.comp41890_c0_seq1_REVERSED"/>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	665 <has_line_matching expression="cds.comp41779_c0_seq1"/>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	666 <has_line_matching expression="cds.comp41779_c0_seq2"/>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	667 <has_line_matching expression="cds.comp41779_c0_seq3"/>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	668 </assert_contents>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	669 </output>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	670 <output name="output_progenesis" ftype="txt">
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	671 <assert_contents>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	672 <has_text_matching expression="NLVAEESMNMLKNK\t:::::::::::::::\t100.0\tcds.comp8310_c0_seq2\tm.1138 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 22.01 EValue:2.0e-16\tsmall.17.17."/>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	673 <has_text_matching expression="LDRLISATSISPEHKIDFLFK\t::::::::::::::::::::::\t100.0\tcds.comp41779_c0_seq1\tm.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67\tsmall.3.3."/>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	674 <has_n_columns n="8" />
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	675 </assert_contents>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	676 </output>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	677
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	678 </test>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	679
18 a5f9b959d5d1 Uploaded iracooke parents: diff changeset	680 </tests>
a5f9b959d5d1 Uploaded iracooke parents: diff changeset	681 <help>
a5f9b959d5d1 Uploaded iracooke parents: diff changeset	682 What it does
a5f9b959d5d1 Uploaded iracooke parents: diff changeset	683
49 58a3e6cb2598 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6e846f7195a9e939047ac975c6523e8cf99da6b4 galaxyp parents: 46 diff changeset	684 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	685
30 ad60446b1e93 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit bdb5ee12705a3494eee96d1963f16f68bbe41d5c galaxyp parents: 29 diff changeset	686 http://compomics.github.io/projects/peptide-shaker.html
18 a5f9b959d5d1 Uploaded iracooke parents: diff changeset	687
a5f9b959d5d1 Uploaded iracooke parents: diff changeset	688 ----
a5f9b959d5d1 Uploaded iracooke parents: diff changeset	689
55 bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	690 Outputs
18 a5f9b959d5d1 Uploaded iracooke parents: diff changeset	691 =======
a5f9b959d5d1 Uploaded iracooke parents: diff changeset	692
55 bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	693 zip
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	694 ------
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	695
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	696 When choosing zip option, all other outputs are compressed and included into the zip file and, by default, no other file is shown in the Galaxy history. This last behaviour may be changed in order to have all other outputs also available in the history.
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	697
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	698 psdb
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	699 ------
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	700
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	701 psdb is the native format used by PeptideShaker. It contains all the information required by PeptideShaker to run.
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	702
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	703 mzIdentML
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	704 -----------
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	705
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	706 PeptideShaker can load results from virtually any identification algorithm in the mzIdentML format as long as the minimal peptide to spectrum match information is present in the file.
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	707
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	708 The following is required:
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	709
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	710 • Spectrum file format has to be mgf.
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	711 • Each PSM has a score or e-value as a PSM score CV term.
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	712
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	713
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	714 Follow-up analysis
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	715 --------------------
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	716
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	717 Spectra
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	718 '''''''
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	719
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	720 Exports the spectra according to the category of the PSMs:
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	721
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	722 • Spectra of Non-Validated PSMs
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	723 • Spectra of Non-Validated Peptides
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	724 • Spectra of Non-Validated Proteins
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	725 • Spectra of Validated PSMs
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	726 • Spectra of Validated PSMs of Validated Peptides
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	727 • Spectra of validated PSMs of Validated Peptides of Validated Proteins.
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	728
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	729 Exported results are in mgf format.
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	730
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	731 Proteins: Accession numbers
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	732 '''''''''''''''''''''''''''
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	733
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	734 Export the protein accessions according to the category of the proteins:
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	735
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	736 • Main Accession of Validated Protein Groups
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	737 • All Accessions of Validated Protein Groups
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	738 • Non-Validated Accessions
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	739
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	740 Exported protein accessions are text format as TXT.
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	741
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	742
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	743 Proteins: Sequences
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	744 '''''''''''''''''''
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	745
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	746 Exports the protein details according to a category of proteins:
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	747
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	748 • Main Accession of Validated Protein Groups
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	749 • All Accessions of Validated Protein Groups
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	750 • Non-Validated Accessions.
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	751
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	752 Exported protein details are in fasta format.
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	753
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	754
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	755 Proteins: Proteoforms
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	756 '''''''''''''''''''''
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	757
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	758 Exports all possible proteoforms of the validated proteins.
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	759
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	760 Exported results are in text format as TXT.
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	761 Results file can be easily imported and used by PathwayMatcher_ tool.
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	762
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	763 .. _PathwayMatcher: https://toolshed.g2.bx.psu.edu/repository?repository_id=6d75f02b86acc421
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	764
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	765
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	766 Label free quantification
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	767 '''''''''''''''''''''''''
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	768
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	769 Exports the spectra from different categories of PSMs according to the export type:
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	770
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	771 • Validated PSMs of Validated Peptides of Validated Proteins
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	772 • Validated PSMs of Validated Peptides
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	773 • Validated PSMs
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	774 • Confidently localized PTMs of Validated PSMs of Validated Peptides of Validated Proteins
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	775
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	776 Exported identification results are in Progenesis LC-MS compatible format as TXT.
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	777
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	778
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	779 Inclusion/Exclusion list
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	780 ''''''''''''''''''''''''
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	781
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	782 Exports an inclusion list of validated hits.
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	783
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	784 Inclusion list may be filtered according to peptide types:
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	785
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	786 • Miscleaved Peptides
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	787 • Reactive Peptides
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	788 • Degenerated Peptides.
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	789
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	790 and also according to protein inferences:
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	791
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	792 • Related Proteins
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	793 • Related and Unrelated Proteins
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	794 • Unrelated Proteins.
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	795
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	796 Finally, a retention time window may be established as a final filter.
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	797
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	798 Exported results can be in Thermo, ABI, Bruker or MassLynx formats.
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	799
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	800
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	801
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	802 Identification Features Reports
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	803 ---------------------------------
18 a5f9b959d5d1 Uploaded iracooke parents: diff changeset	804
a5f9b959d5d1 Uploaded iracooke parents: diff changeset	805 PSM Report
55 bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	806 ''''''''''
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	807 ============================= ========================================
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	808 Column Description
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	809 ============================= ========================================
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	810 Protein(s) Protein(s) to which the peptide can be attached
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	811 Sequence Sequence of the peptide
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	812 AAs Before The amino acids before the sequence
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	813 AAs After The amino acids after the sequence
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	814 Position Position of the peptide in the protein sequence(s).
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	815 Modified Sequence The amino acids sequence annotated with variable modifications.
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	816 Variable Modifications The variable modifications
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	817 Fixed Modifications The fixed modifications.
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	818 Spectrum File The spectrum file.
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	819 Spectrum Title The title of the spectrum.
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	820 Spectrum Scan Number The spectrum scan number.
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	821 RT Retention time
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	822 m/z Measured m/z
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	823 Measured Charge The charge as given in the spectrum file.
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	824 Identification Charge The charge as inferred by the search engine.
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	825 Theoretical Mass The theoretical mass of the peptide.
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	826 Isotope Number The isotope number targetted by the instrument.
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	827 Precursor m/z Error [ppm] The precursor m/z matching error.
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	828 Localization Confidence The confidence in variable PTM localization.
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	829 probabilistic PTM score The probabilistic score (e.g. A-score or PhosphoRS) used for variable PTM localization.
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	830 D-score D-score for variable PTM localization
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	831 Confidence Confidence in percent associated to the retained PSM.
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	832 Validation Indicates the validation level of the protein group.
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	833 ============================= ========================================
18 a5f9b959d5d1 Uploaded iracooke parents: diff changeset	834
55 bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	835
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	836 PSM Report with non-validated matches
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	837 '''''''''''''''''''''''''''''''''''''
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	838
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	839 Same columns as the original PSM report but also includes non-validated matches.
18 a5f9b959d5d1 Uploaded iracooke parents: diff changeset	840
a5f9b959d5d1 Uploaded iracooke parents: diff changeset	841
55 bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	842 PSM Phosphorylation Report
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	843 ''''''''''''''''''''''''''
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	844 ============================= =========================================================
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	845 Column Description
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	846 ============================= =========================================================
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	847 Protein(s) Protein(s) to which the peptide can be attached
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	848 Sequence Sequence of the peptide
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	849 Variable Modifications The variable modifications
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	850 Fixed Modifications The fixed modifications.
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	851 Spectrum File The spectrum file.
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	852 Spectrum Title The title of the spectrum.
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	853 Spectrum Scan Number The spectrum scan number.
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	854 RT Retention time
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	855 m/z Measured m/z
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	856 Measured Charge The charge as given in the spectrum file.
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	857 Identification Charge The charge as inferred by the search engine.
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	858 Theoretical Mass The theoretical mass of the peptide.
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	859 Isotope Number The isotope number targetted by the instrument.
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	860 Precursor m/z Error [ppm] The precursor m/z matching error.
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	861 Localization Confidence The confidence in variable PTM localization.
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	862 probabilistic PTM score The probabilistic score (e.g. A-score or PhosphoRS) used for variable PTM localization.
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	863 D-score D-score for variable PTM localization
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	864 Confident Phosphosites List of the sites where a phosphorylation was confidently localized.
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	865 #Confident Phosphosites Number of confidently localized phosphorylations.
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	866 Ambiguous Phosphosites List of the sites where a phosphorylation was ambiguously localized.
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	867 #Ambiguous Phosphosites Number of ambiguously localized phosphorylations.
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	868 Confidence [%] Confidence in percent associated to the retained PSM.
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	869 Validation Indicates the validation level of the protein group.
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	870 ============================= =========================================================
18 a5f9b959d5d1 Uploaded iracooke parents: diff changeset	871
55 bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	872
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	873 Extended PSM Report
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	874 '''''''''''''''''''
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	875
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	876 Same as the ordinary PSM report but adds a ``Decoy`` column and lacks the ``Confidence`` column.
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	877
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	878 ============================= =========================================================
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	879 Extra column Description
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	880 ============================= =========================================================
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	881 Decoy Indicates whether the peptide is a decoy (1: yes, 0: no).
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	882
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	883 ============================= =========================================================
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	884
18 a5f9b959d5d1 Uploaded iracooke parents: diff changeset	885
a5f9b959d5d1 Uploaded iracooke parents: diff changeset	886
a5f9b959d5d1 Uploaded iracooke parents: diff changeset	887 Peptide Report
55 bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	888 ''''''''''''''
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	889
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	890 ========================================== =====================================================
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	891 Column Description
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	892 ========================================== =====================================================
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	893 Protein(s): Protein(s) to which this peptide can be attached.
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	894 Protein Group(s) List of identified protein groups this peptide can map to with associated validation level.
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	895 #Validated Protein Group(s) Indicates the number of protein groups this peptide maps to.
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	896 Unique Group Indicates whether the peptide maps to a unique protein group.
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	897 Sequence Sequence of the peptide.
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	898 Modified Sequence The peptide sequence annotated with variable modifications.
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	899 Position Position of the peptide in the protein sequence(s).
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	900 AAs Before The amino acids before the sequence.
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	901 AAs After The amino acids after the sequence.
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	902 Variable Modifications The variable modifications.
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	903 Fixed Modifications The fixed modifications.
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	904 Localization Confidence The confidence in PTMs localization.
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	905 #Validated PSMs Number of validated PSMs.
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	906 #PSMs Number of PSMs.
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	907 Confidence [%] Confidence in percent associated to the peptide.
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	908 Validation Indicates the validation level of the peptide.
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	909 ========================================== =====================================================
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	910
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	911
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	912 Peptide Report with non-validated matches
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	913 '''''''''''''''''''''''''''''''''''''''''
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	914
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	915 Same columns as the original Peptide report but also includes non-validated matches.
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	916
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	917
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	918 Peptide Phosphorylation Report
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	919 ''''''''''''''''''''''''''''''
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	920
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	921 ========================================== =====================================================
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	922 Column Description
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	923 ========================================== =====================================================
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	924 Protein(s): Protein(s) to which this peptide can be attached.
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	925 Protein Group(s) List of identified protein groups this peptide can map to with associated validation level.
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	926 #Validated Protein Group(s) Indicates the number of protein groups this peptide maps to.
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	927 Unique Group Indicates whether the peptide maps to a unique protein group.
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	928 Sequence Sequence of the peptide.
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	929 Modified Sequence The peptide sequence annotated with variable modifications.
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	930 AAs Before The amino acids before the sequence.
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	931 AAs After The amino acids after the sequence.
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	932 Variable Modifications The variable modifications.
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	933 Fixed Modifications The fixed modifications.
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	934 Localization Confidence The confidence in PTMs localization.
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	935 Confident Phosphosites List of the sites where a phosphorylation was confidently localized.
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	936 #Confident Phosphosites Number of confidently localized phosphorylations.
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	937 Ambiguous Phosphosites List of the sites where a phosphorylation was ambiguously localized.
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	938 #Ambiguous Phosphosites Number of ambiguously localized phosphorylations.
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	939 #Validated PSMs Number of validated PSMs.
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	940 #PSMs Number of PSMs.
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	941 Confidence [%] Confidence in percent associated to the peptide.
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	942 Validation Indicates the validation level of the peptide.
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	943 ========================================== =====================================================
18 a5f9b959d5d1 Uploaded iracooke parents: diff changeset	944
a5f9b959d5d1 Uploaded iracooke parents: diff changeset	945
55 bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	946 Protein Report
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	947 ''''''''''''''
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	948
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	949 ========================================== =====================================================
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	950 Column Description
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	951 ========================================== =====================================================
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	952 Main Accession Main accession of the protein group.
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	953 Description Description of the protein designed by the main accession.
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	954 Gene Name The gene names of the Ensembl gene ID associated to the main accession.
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	955 Chromosome The chromosome of the Ensembl gene ID associated to the main accession.
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	956 MW (kDa) Molecular Weight.
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	957 Possible Coverage (%) Possible sequence coverage in percent of the protein designed by the main accession according to the search settings.
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	958 Coverage (%) Sequence coverage in percent of the protein designed by the main accession.
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	959 Spectrum Counting The selected spectrum counting metric.
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	960 Confidently Localized Modification Sites List of the sites where a variable modification was confidently localized.
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	961 # Confidently Localized Modification Sites Number of sites where a variable modification was confidently localized.
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	962 Ambiguously Localized Modification Sites List of the sites where ambiguously localized variable modification could possibly be located.
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	963 #Ambiguously Localized Modification Sites Number of ambiguously localized modifications.
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	964 Protein Inference Protein Inference status of the protein group.
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	965 Secondary Accessions Other accessions in the protein group (alphabetical order).
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	966 Protein Group The complete protein group (alphabetical order).
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	967 #Validated Peptides Number of validated peptides.
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	968 #Peptides Total number of peptides.
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	969 #Unique Total number of peptides unique to this protein group.
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	970 #Validated Unique Total number of peptides unique to this protein group.
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	971 #Validated PSMs Number of validated PSMs.
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	972 #PSMs Number of PSMs.
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	973 Confidence [%] Confidence in percent associated to the protein group.
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	974 Validation Indicates the validation level of the protein group.
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	975 ========================================== =====================================================
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	976
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	977
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	978 Protein Report with non-validated matches
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	979 '''''''''''''''''''''''''''''''''''''''''
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	980
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	981 Same columns as the original Protein report but also includes non-validated matches.
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	982
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	983
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	984 Protein Phosphorylation Report
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	985 ''''''''''''''''''''''''''''''
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	986
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	987 ========================================== =====================================================
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	988 Column Description
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	989 ========================================== =====================================================
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	990 Main Accession Main accession of the protein group.
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	991 Description Description of the protein designed by the main accession.
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	992 Gene Name The gene names of the Ensembl gene ID associated to the main accession.
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	993 Chromosome The chromosome of the Ensembl gene ID associated to the main accession.
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	994 MW (kDa) Molecular Weight.
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	995 Possible Coverage (%) Possible sequence coverage in percent of the protein designed by the main accession according to the search settings.
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	996 Coverage (%) Sequence coverage in percent of the protein designed by the main accession.
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	997 Spectrum Counting NSAF Raw Normalized Spectrum Abundance Factor (NSAF).
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	998 Confident Phosphosites List of the sites where a phosphorylation was confidently localized.
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	999 #Confident Phosphosites Number of sites where a phosphorylation was confidently localized.
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	1000 Ambiguous Phosphosites List of the sites where a phosphorylation was ambiguously localized.
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	1001 #Ambiguous Phosphosites Number of sites where a phosphorylation was ambiguously localized.
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	1002 Protein Inference Protein Inference status of the protein group.
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	1003 Secondary Accessions Other accessions in the protein group (alphabetical order).
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	1004 Protein Group The complete protein group (alphabetical order).
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	1005 #Validated Peptides Number of validated peptides.
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	1006 #Peptides Total number of peptides.
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	1007 #Unique Total number of peptides unique to this protein group.
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	1008 #Validated Unique Total number of peptides unique to this protein group.
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	1009 #Validated PSMs Number of validated PSMs.
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	1010 #PSMs Number of PSMs.
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	1011 Confidence [%] Confidence in percent associated to the protein group.
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	1012 Validation Indicates the validation level of the protein group.
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	1013 ========================================== =====================================================
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	1014
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	1015
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	1016 Certificate of Analysis
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	1017 '''''''''''''''''''''''
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	1018
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	1019 Presents a summary of the most important statistics of the search, grouped by:
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	1020
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	1021 * Project Details:
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	1022 ‣ PeptideShaker Version, Date, Experiment, Sample, Replicate Number, Identification Algorithms.
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	1023 * Database Search Parameters:
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	1024 ‣ Precursor Tolerance Unit, Precursor Ion m/z Tolerance, Fragment Ion Tolerance Unit, Fragment Ion m/z Tolerance, Cleavage, Enzyme, Missed Cleavages, Specificity, Database, Forward Ion, Rewind Ion, Fixed Modifications, Variable Modifications, Refinement Variable Modifications, Refinement Fixed Modifications.
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	1025 * Input Filters:
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	1026 ‣ Minimal Peptide Length, Maximal Peptide Length, Precursor m/z Tolerance, Precursor m/z Tolerance Unit, Unrecognized Modifications Discarded.
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	1027 * Validation Summary:
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	1028 • Proteins:
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	1029 ‣ #Validated, Total Possible TP, FDR Limit [%], FNR Limit [%], Confidence Limit, PEP Limit [%], Confidence Accuracy [%].
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	1030 • Peptides:
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	1031 ‣ #Validated, Total Possible TP, FDR Limit [%], FNR Limit [%], Confidence Limit [%], PEP Limit [%], Confidence Accuracy [%].
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	1032 • PSMs:
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	1033 ‣ #Validated PSM, Total Possible TP, FDR Limit [%]: PSMs, Confidence Limit [%], PEP Limit [%], Confidence Accuracy [%].
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	1034 * PTM Scoring Settings:
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	1035 ‣ Probabilistic Score, Accounting for Neutral Losses, Threshold.
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	1036 * Spectrum Counting Parameters:
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	1037 ‣ Method, Validated Matches Only
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	1038 * Annotation Settings:
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	1039 ‣ Intensity Limit, Automatic Annotation, Selected Ions, Neutral Losses, Neutral Losses Sequence Dependence, Fragment Ion m/z Tolerance.
18 a5f9b959d5d1 Uploaded iracooke parents: diff changeset	1040
a5f9b959d5d1 Uploaded iracooke parents: diff changeset	1041
a5f9b959d5d1 Uploaded iracooke parents: diff changeset	1042 Hierachical Report
55 bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	1043 ''''''''''''''''''
18 a5f9b959d5d1 Uploaded iracooke parents: diff changeset	1044
55 bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	1045 ========================================== =====================================================
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	1046 Column Description
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	1047 ========================================== =====================================================
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	1048 Main Accession Main accession of the protein group.
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	1049 Description Description of the protein designed by the main accession.
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	1050 MW (kDa) Molecular Weight.
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	1051 Possible Coverage (%) Possible sequence coverage in percent of the protein designed by the main accession according to the search settings.
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	1052 Coverage (%) Sequence coverage in percent of the protein designed by the main accession.
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	1053 Spectrum Counting NSAF Normalized Spectrum Abundance Factor (NSAF)
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	1054 Confidently Localized Modification Sites List of the sites where a variable modification was confidently localized.
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	1055 # Confidently Localized Modification Sites Number of sites where a variable modification was confidently localized.
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	1056 Ambiguously Localized Modification Sites List of the sites where ambiguously localized variable modification could possibly be located.
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	1057 #Ambiguously Localized Modification Sites Number of ambiguously localized modifications.
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	1058 Protein Inference Protein Inference status of the protein group.
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	1059 Secondary Accessions Other accessions in the protein group (alphabetical order).
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	1060 Protein Group The complete protein group (alphabetical order).
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	1061 #Validated Peptides Number of validated peptides.
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	1062 #Peptides Total number of peptides.
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	1063 #Unique Total number of peptides unique to this protein group.
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	1064 #Validated PSMs Number of validated PSMs
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	1065 #PSMs Number of PSMs
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	1066 Confidence Confidence in percent associated to the protein group.
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	1067 Decoy Indicates whether the protein group is a decoy (1: yes, 0: no).
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	1068 Validation Indicates the validation level of the protein group.
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	1069 ========================================== =====================================================
18 a5f9b959d5d1 Uploaded iracooke parents: diff changeset	1070
a5f9b959d5d1 Uploaded iracooke parents: diff changeset	1071 ------
a5f9b959d5d1 Uploaded iracooke parents: diff changeset	1072
a5f9b959d5d1 Uploaded iracooke parents: diff changeset	1073 Citation
a5f9b959d5d1 Uploaded iracooke parents: diff changeset	1074
30 ad60446b1e93 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit bdb5ee12705a3494eee96d1963f16f68bbe41d5c galaxyp parents: 29 diff changeset	1075 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	1076
30 ad60446b1e93 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit bdb5ee12705a3494eee96d1963f16f68bbe41d5c galaxyp parents: 29 diff changeset	1077 If you use this tool in Galaxy, please cite Chilton J, Ira Cooke, Bjoern Gruening et al.
18 a5f9b959d5d1 Uploaded iracooke parents: diff changeset	1078 </help>
20 2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b iracooke parents: 18 diff changeset	1079 <expand macro="citations" />
18 a5f9b959d5d1 Uploaded iracooke parents: diff changeset	1080 </tool>

Mercurial > repos > galaxyp > peptideshaker

annotate peptide_shaker.xml @ 58:07ff622ec007 draft