peptideshaker: peptide_shaker.xml annotate

annotate peptide_shaker.xml @ 59:943a34df6047 draft

"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 1cb321cbce2a6528764abc9c9431687f56c57588"

author	galaxyp
date	Fri, 21 May 2021 19:13:14 +0000
parents	07ff622ec007
children	a6ff76e057fd

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 $exporting_followup_boolean = False
22 e3be595c0bf5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 5ca27ef280bee8b65fd3d0d2cd5ff280a2cebb3d iracooke parents: 21 diff changeset	29
49 58a3e6cb2598 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6e846f7195a9e939047ac975c6523e8cf99da6b4 galaxyp parents: 46 diff changeset	30 mkdir output_reports &&
58a3e6cb2598 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6e846f7195a9e939047ac975c6523e8cf99da6b4 galaxyp parents: 46 diff changeset	31 cwd=`pwd` &&
58a3e6cb2598 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6e846f7195a9e939047ac975c6523e8cf99da6b4 galaxyp parents: 46 diff changeset	32 export HOME=\$cwd &&
58a3e6cb2598 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6e846f7195a9e939047ac975c6523e8cf99da6b4 galaxyp parents: 46 diff changeset	33
20 2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b iracooke parents: 18 diff changeset	34 ln -s '$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	35
55 bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	36 ## 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	37 ## 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	38 #if $optional_main_parameters.input_optional_identification_parameters:
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	39 cp '${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	40 #else:
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	41 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	42 #end if
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	43 ## 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	44 #if $optional_main_parameters.input_fasta_file:
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	45 ## copy the input .fasta file to the working folder
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	46 cp '${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	47 #end if
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	48 ## 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	49 ## 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	50 #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	51 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	52 #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	53 #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	54 #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	55 #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	56 #set $input_name = $peak_list_file.element_identifier.split('/')[-1].replace(".mzml", "") + ".mzml"
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	57 #end if
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	58 ln -s -f '${peak_list_file}' 'peaklist_input_files/${input_name}' &&
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	59 #end for
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	60 #end if
49 58a3e6cb2598 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6e846f7195a9e939047ac975c6523e8cf99da6b4 galaxyp parents: 46 diff changeset	61
55 bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	62 #if str($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	63 #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	64 #else
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()
55 bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	66 #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	67
18 a5f9b959d5d1 Uploaded iracooke parents: diff changeset	68 ######################
a5f9b959d5d1 Uploaded iracooke parents: diff changeset	69 ## PeptideShakerCLI ##
a5f9b959d5d1 Uploaded iracooke parents: diff changeset	70 ######################
59 943a34df6047 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 1cb321cbce2a6528764abc9c9431687f56c57588" galaxyp parents: 58 diff changeset	71
943a34df6047 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 1cb321cbce2a6528764abc9c9431687f56c57588" galaxyp parents: 58 diff changeset	72 ## TODO: --exec_dir may not be needed anymore. To be tested further (and maybe removed from the Conda package).
943a34df6047 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 1cb321cbce2a6528764abc9c9431687f56c57588" galaxyp parents: 58 diff changeset	73
57 da885ca16cb2 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 44a20633e04b2396fad4b568904a257769b2bbc1" galaxyp parents: 55 diff changeset	74 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	75 -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	76 -temp_folder \$cwd/PeptideShakerCLI
59 943a34df6047 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 1cb321cbce2a6528764abc9c9431687f56c57588" galaxyp parents: 58 diff changeset	77 -use_log_folder 0
55 bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	78 -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	79 -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	80 -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	81 #if $optional_main_parameters.input_fasta_file:
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	82 -fasta_file './input_fasta_file.fasta'
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	83 #end if
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	84 #if str($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	85 -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	86 #end if
58a3e6cb2598 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6e846f7195a9e939047ac975c6523e8cf99da6b4 galaxyp parents: 46 diff changeset	87
55 bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	88 #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	89 -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	90 -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	91 #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	92 -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	93 #end if
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	94 #else:
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	95 #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	96 -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	97 #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	98 #end if
18 a5f9b959d5d1 Uploaded iracooke parents: diff changeset	99
55 bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	100 -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	101
49 58a3e6cb2598 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6e846f7195a9e939047ac975c6523e8cf99da6b4 galaxyp parents: 46 diff changeset	102 ##################################
58a3e6cb2598 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6e846f7195a9e939047ac975c6523e8cf99da6b4 galaxyp parents: 46 diff changeset	103 ## mzidCLI options ##
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
58a3e6cb2598 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6e846f7195a9e939047ac975c6523e8cf99da6b4 galaxyp parents: 46 diff changeset	106 #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	107 -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	108 -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	109 #if $exporting_options.mzidentml_conditional.contact_options.contact_options_selector == "yes":
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	110 -contact_first_name "$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	111 -contact_last_name "$exporting_options.mzidentml_conditional.contact_options.contact_last_name"
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	112 -contact_email "$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	113 -contact_address "$exporting_options.mzidentml_conditional.contact_options.contact_address"
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	114 #if str($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	115 -contact_url = "$exporting_options.mzidentml_conditional.contact_options.contact_url"
49 58a3e6cb2598 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6e846f7195a9e939047ac975c6523e8cf99da6b4 galaxyp parents: 46 diff changeset	116 #end if
55 bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	117 -organization_name "$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	118 -organization_email "$exporting_options.mzidentml_conditional.contact_options.organization_email"
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	119 -organization_address "$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	120 #if str($exporting_options.mzidentml_conditional.contact_options.organization_url).strip() != '':
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	121 -organization_url = "$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	122 #end if
58a3e6cb2598 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6e846f7195a9e939047ac975c6523e8cf99da6b4 galaxyp parents: 46 diff changeset	123 #else:
58a3e6cb2598 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6e846f7195a9e939047ac975c6523e8cf99da6b4 galaxyp parents: 46 diff changeset	124 -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	125 -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	126 -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	127 -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	128 -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	129 -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	130 -organization_address "Minneapolis, MN 55455, Vereinigte Staaten"
18 a5f9b959d5d1 Uploaded iracooke parents: diff changeset	131 #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	132 #end if
18 a5f9b959d5d1 Uploaded iracooke parents: diff changeset	133
55 bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	134 ####################################################################
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	135 ## 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	136 ####################################################################
49 58a3e6cb2598 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6e846f7195a9e939047ac975c6523e8cf99da6b4 galaxyp parents: 46 diff changeset	137 ## 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	138 #if len($output_reports_list) > 0
58a3e6cb2598 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6e846f7195a9e939047ac975c6523e8cf99da6b4 galaxyp parents: 46 diff changeset	139 -out_reports \$cwd/output_reports
58a3e6cb2598 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6e846f7195a9e939047ac975c6523e8cf99da6b4 galaxyp parents: 46 diff changeset	140 -reports #echo ','.join($output_reports_list)#
18 a5f9b959d5d1 Uploaded iracooke parents: diff changeset	141 #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	142
55 bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	143 ####################################################
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	144 ## 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	145 ####################################################
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	146 ## 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	147
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_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	149 #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	150 #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	151 -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	152 #end if
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	153 #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	154 #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	155 -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	156 #end if
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	157 #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	158 #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	159 -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	160 #end if
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	161 #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	162 #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	163 -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	164 #end if
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	165 #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	166 #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	167 -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	168 #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	169 #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	170 #if $progenesis_ptms
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	171 -progenesis_ptms "$progenesis_ptms"
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	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 #end if
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	175 #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	176 #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	177 -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	178 #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	179 #if $peptide_filters
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	180 -inclusion_list_peptide_filters "$peptide_filters"
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	181 #end if
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	182 #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	183 #if $protein_filters
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	184 -inclusion_list_protein_filters "$protein_filters"
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	185 #end if
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	186 #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	187 -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	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 #end if
59 943a34df6047 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 1cb321cbce2a6528764abc9c9431687f56c57588" galaxyp parents: 58 diff changeset	191
943a34df6047 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 1cb321cbce2a6528764abc9c9431687f56c57588" galaxyp parents: 58 diff changeset	192 ## Whilst non-blocking exception " /usr/local/share/peptide-shaker-2.0.25-0/resources/conf/paths.txt (Permission denied)"
943a34df6047 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 1cb321cbce2a6528764abc9c9431687f56c57588" galaxyp parents: 58 diff changeset	193 ## is fixed , we can avoid the process to be stopped by removing that message from the output
943a34df6047 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 1cb321cbce2a6528764abc9c9431687f56c57588" galaxyp parents: 58 diff changeset	194
943a34df6047 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 1cb321cbce2a6528764abc9c9431687f56c57588" galaxyp parents: 58 diff changeset	195 \| grep -v "resources/conf/paths.txt (Permission denied)"
943a34df6047 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 1cb321cbce2a6528764abc9c9431687f56c57588" galaxyp parents: 58 diff changeset	196
53 d67a3c1bfd09 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 1327a0e10d66e5ed6a8b63b211672a724fcac424 galaxyp parents: 52 diff changeset	197 ## 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	198 #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	199 ## 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	200 && 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	201 && 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	202 && 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	203 #end if
d67a3c1bfd09 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 1327a0e10d66e5ed6a8b63b211672a724fcac424 galaxyp parents: 52 diff changeset	204
55 bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	205 ## 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	206 #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	207 && 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	208 && 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	209 && 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	210 && 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	211 #end if
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	212
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	213 ## 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	214 #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	215 #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	216 && 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	217 #end if
58a3e6cb2598 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6e846f7195a9e939047ac975c6523e8cf99da6b4 galaxyp parents: 46 diff changeset	218 #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	219 && 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	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 '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	222 && 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	223 #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	224 #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	225 && 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	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 '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	228 && 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	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 '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	231 && 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	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 '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	234 && 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	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 '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	237 && 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	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 '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	240 && 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	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 '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	243 && 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	244 #end if
58a3e6cb2598 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6e846f7195a9e939047ac975c6523e8cf99da6b4 galaxyp parents: 46 diff changeset	245 #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	246 && 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	247 #end if
58a3e6cb2598 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6e846f7195a9e939047ac975c6523e8cf99da6b4 galaxyp parents: 46 diff changeset	248 #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	249 && 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	250 #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	251 ## 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	252 ## 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	253 ## 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	254 && true
20 2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b iracooke parents: 18 diff changeset	255 #end if
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b iracooke parents: 18 diff changeset	256
55 bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	257 ## 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	258 #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	259 ## 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	260 #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	261 && 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	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_sequences != "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/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	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_proteoforms != "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/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	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 #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	270 && 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	271 #end if
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	272 #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	273 && 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	274 #end if
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	275 #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	276 ]]>
18 a5f9b959d5d1 Uploaded iracooke parents: diff changeset	277 </command>
a5f9b959d5d1 Uploaded iracooke parents: diff changeset	278 <inputs>
21 dfaea053e32f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 327a3944f2f56668d607c3d6cb08ae7d588e208c iracooke parents: 20 diff changeset	279 <param name="searchgui_input" format="searchgui_archive" type="data" label="Compressed SearchGUI results"
24 815f93bb3e1b Uploaded galaxyp parents: 22 diff changeset	280 help="SearchGUI Results from History">
815f93bb3e1b Uploaded galaxyp parents: 22 diff changeset	281 <options options_filter_attribute="metadata.searchgui_major_version" >
815f93bb3e1b Uploaded galaxyp parents: 22 diff changeset	282 <filter type="add_value" value="@SEARCHGUI_MAJOR_VERSION@" />
815f93bb3e1b Uploaded galaxyp parents: 22 diff changeset	283 </options>
815f93bb3e1b Uploaded galaxyp parents: 22 diff changeset	284 </param>
55 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="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	287 <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	288 <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	289 <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	290 </section>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	291
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	292 <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	293
55 bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	294 <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	295 <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	296 <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	297 <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	298 </when>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	299 <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	300 <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	301 <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	302 </when>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	303 </conditional>
49 58a3e6cb2598 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6e846f7195a9e939047ac975c6523e8cf99da6b4 galaxyp parents: 46 diff changeset	304
58a3e6cb2598 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6e846f7195a9e939047ac975c6523e8cf99da6b4 galaxyp parents: 46 diff changeset	305 <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	306 <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	307 <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	308 <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	309
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	310 <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	311 <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	312 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	313 <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	314 <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	315 </param>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	316 <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	317 <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	318 <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	319 <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	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_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	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_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	325 <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	326 </param>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	327 <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	328 <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	329 </param>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	330 <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	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_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	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_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	336 <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	337 </param>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	338 <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	339 <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	340 </param>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	341 <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	342 </param>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	343 </when>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	344 </conditional>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	345
49 58a3e6cb2598 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6e846f7195a9e939047ac975c6523e8cf99da6b4 galaxyp parents: 46 diff changeset	346 </when>
58a3e6cb2598 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6e846f7195a9e939047ac975c6523e8cf99da6b4 galaxyp parents: 46 diff changeset	347 <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	348 </conditional>
58a3e6cb2598 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6e846f7195a9e939047ac975c6523e8cf99da6b4 galaxyp parents: 46 diff changeset	349
55 bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	350 <!-- 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	351 <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	352 <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	353 <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	354 <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	355 </param>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	356 <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	357 <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	358 <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	359 <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	360 <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	361 <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	362 <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	363 <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	364 <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	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_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	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_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	374 <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	375 <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	376 <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	377 <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	378 </param>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	379 <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	380 <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	381 <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	382 </param>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	383 <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	384 <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	385 <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	386 <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	387 <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	388 <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	389 <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	390 </param>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	391 <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	392 <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	393 <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	394 <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	395 <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	396 help="">
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	397 <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	398 </param>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	399 </when>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	400 <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	401 </conditional>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	402 <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	403 <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	404 <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	405 <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	406 <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	407 <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	408 <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	409 </param>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	410 <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	411 <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	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="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	414 <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	415 <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	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_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	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 <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	420 <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	421 <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	422 </param>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	423 <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	424 help=""/>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	425 </when>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	426 <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	427 <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	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="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	430 <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	431 <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	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_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	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 <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	436 <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	437 <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	438 </param>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	439 <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	440 help=""/>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	441 </when>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	442 <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	443 <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	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="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	446 <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	447 <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	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_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	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 <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	452 <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	453 <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	454 </param>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	455 <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	456 help=""/>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	457 </when>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	458 <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	459 <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	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="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	462 <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	463 <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	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_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	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 <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	468 <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	469 <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	470 </param>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	471 <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	472 help=""/>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	473 </when>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	474 <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	475 </conditional>
53 d67a3c1bfd09 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 1327a0e10d66e5ed6a8b63b211672a724fcac424 galaxyp parents: 52 diff changeset	476 </when>
49 58a3e6cb2598 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6e846f7195a9e939047ac975c6523e8cf99da6b4 galaxyp parents: 46 diff changeset	477 </conditional>
58a3e6cb2598 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6e846f7195a9e939047ac975c6523e8cf99da6b4 galaxyp parents: 46 diff changeset	478
55 bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	479 <!-- 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	480 <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	481 <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	482 <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	483 <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	484 <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	485 <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	486 <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	487 <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	488 <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	489 <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	490 <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	491 <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	492 <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	493 </param>
58a3e6cb2598 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6e846f7195a9e939047ac975c6523e8cf99da6b4 galaxyp parents: 46 diff changeset	494
58a3e6cb2598 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6e846f7195a9e939047ac975c6523e8cf99da6b4 galaxyp parents: 46 diff changeset	495 </section>
20 2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b iracooke parents: 18 diff changeset	496
18 a5f9b959d5d1 Uploaded iracooke parents: diff changeset	497 </inputs>
a5f9b959d5d1 Uploaded iracooke parents: diff changeset	498 <outputs>
20 2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b iracooke parents: 18 diff changeset	499 <data format="zip" name="output_zip" from_work_dir="peptideshaker_output.zip" label="${tool.name} on ${on_string}: Archive">
49 58a3e6cb2598 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6e846f7195a9e939047ac975c6523e8cf99da6b4 galaxyp parents: 46 diff changeset	500 <filter>exporting_options['zip_conditional']['zip_output_boolean'] is True</filter>
20 2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b iracooke parents: 18 diff changeset	501 </data>
55 bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	502 <data format="mzid" name="mzidentML" from_work_dir="output.mzid" label="${tool.name} on ${on_string}: mzidentML file">
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	503 <filter>exporting_options['zip_conditional']['zip_output_boolean'] is False and exporting_options['mzidentml_conditional']['mzidentml_creation'] is True</filter>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	504 </data>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	505 <data format="peptideshaker_archive" name="output_psdb" from_work_dir="peptideshaker_output.psdb" label="${tool.name} on ${on_string}: PSDB file">
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	506 <filter>exporting_options['zip_conditional']['zip_output_boolean'] is False and exporting_options['zip_conditional']['export_psdb'] is True</filter>
49 58a3e6cb2598 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6e846f7195a9e939047ac975c6523e8cf99da6b4 galaxyp parents: 46 diff changeset	507 </data>
55 bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	508 <collection name="output_mgf" type="list" label="${tool.name} on ${on_string}: Mgf" >
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	509 <filter>exporting_options['zip_conditional']['zip_output_boolean'] is True and exporting_options['zip_conditional']['export_mgf_when_zip'] is True</filter>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	510 <discover_datasets pattern="__name_and_ext__" directory="output_mgf" ext="mgf"/>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	511 </collection>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	512 <collection name="output_cui" type="list" label="${tool.name} on ${on_string}: Cui" >
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	513 <filter>exporting_options['zip_conditional']['zip_output_boolean'] is True and exporting_options['zip_conditional']['export_mgf_when_zip'] is True</filter>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	514 <discover_datasets pattern="__name_and_ext__" directory="output_cui" ext="cui"/>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	515 </collection>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	516
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	517 <!-- Follow-up analysis -->
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	518 <collection name="output_spectra" type="list" label="${tool.name} on ${on_string}: Spectra" >
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	519 <filter>(exporting_options['zip_conditional']['zip_output_boolean'] is False or exporting_options['zip_conditional']['export_reports_when_zip'] is True) and exporting_options['followup_conditional']['followup_conditional_selector'] == 'yes' and exporting_options['followup_conditional']['followup_export_spectra'] != 'off' </filter>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	520 <discover_datasets pattern="__name_and_ext__" directory="output_reports" ext="mgf"/>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	521 </collection>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	522 <data format="txt" name="output_proteins_accessions" from_work_dir="proteins_accession_numbers.txt" label="${tool.name} on ${on_string}: Proteins Accession Numbers">
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	523 <filter>(exporting_options['zip_conditional']['zip_output_boolean'] is False or exporting_options['zip_conditional']['export_reports_when_zip'] is True) and exporting_options['followup_conditional']['followup_conditional_selector'] == 'yes' and exporting_options['followup_conditional']['followup_export_accession_numbers'] != 'off' </filter>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	524 </data>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	525 <data format="fasta" name="output_proteins_sequences" from_work_dir="proteins_sequences.fasta" label="${tool.name} on ${on_string}: Proteins Sequences">
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	526 <filter>(exporting_options['zip_conditional']['zip_output_boolean'] is False or exporting_options['zip_conditional']['export_reports_when_zip'] is True) and exporting_options['followup_conditional']['followup_conditional_selector'] == 'yes' and exporting_options['followup_conditional']['followup_export_sequences'] != 'off' </filter>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	527 </data>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	528 <data format="txt" name="output_proteoforms" from_work_dir="proteins_proteoforms.txt" label="${tool.name} on ${on_string}: Proteins Proteoforms">
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	529 <filter>(exporting_options['zip_conditional']['zip_output_boolean'] is False or exporting_options['zip_conditional']['export_reports_when_zip'] is True) and exporting_options['followup_conditional']['followup_conditional_selector'] == 'yes' and exporting_options['followup_conditional']['followup_export_proteoforms'] != 'off' </filter>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	530 </data>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	531 <data format="txt" name="output_progenesis" from_work_dir="progenesis.txt" label="${tool.name} on ${on_string}: Progenesis">
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	532 <filter>(exporting_options['zip_conditional']['zip_output_boolean'] is False or exporting_options['zip_conditional']['export_reports_when_zip'] is True) and exporting_options['followup_conditional']['followup_conditional_selector'] == 'yes' and exporting_options['followup_conditional']['followup_export_progenesis_conditional']['followup_export_progenesis_selector'] != 'off' </filter>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	533 </data>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	534 <data format="txt" name="output_inclusion_list" from_work_dir="inclusion_list.txt" label="${tool.name} on ${on_string}: Inclusion/Exclusion List">
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	535 <filter>(exporting_options['zip_conditional']['zip_output_boolean'] is False or exporting_options['zip_conditional']['export_reports_when_zip'] is True) and exporting_options['followup_conditional']['followup_conditional_selector'] == 'yes' and exporting_options['followup_conditional']['followup_export_inclusion_list_conditional']['followup_export_inclusion_list_selector'] != 'off' </filter>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	536 </data>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	537
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	538 <!-- Identification Features outputs -->
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	539 <data format="txt" name="output_certificate" from_work_dir="certificate.txt" label="${tool.name} on ${on_string}: Certificate of Analysis">
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	540 <filter>(exporting_options['zip_conditional']['zip_output_boolean'] is False or exporting_options['zip_conditional']['export_reports_when_zip'] is True) and str(exporting_options['output_reports']) != 'None' and str(exporting_options['output_reports']) != '' and '0' in exporting_options['output_reports']</filter>
18 a5f9b959d5d1 Uploaded iracooke parents: diff changeset	541 </data>
20 2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b iracooke parents: 18 diff changeset	542 <data format="tabular" name="output_hierarchical" from_work_dir="hierarchical.txt" label="${tool.name} on ${on_string}: Hierarchical Report">
55 bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	543 <filter>(exporting_options['zip_conditional']['zip_output_boolean'] is False or exporting_options['zip_conditional']['export_reports_when_zip'] is True) and str(exporting_options['output_reports']) != 'None' and str(exporting_options['output_reports']) != '' and '1' in exporting_options['output_reports']</filter>
20 2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b iracooke parents: 18 diff changeset	544 </data>
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b iracooke parents: 18 diff changeset	545 <data format="tabular" name="output_psm_phosphorylation" from_work_dir="psm_phospho.txt" label="${tool.name} on ${on_string}: PSM Phosphorylation Report">
55 bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	546 <filter>(exporting_options['zip_conditional']['zip_output_boolean'] is False or exporting_options['zip_conditional']['export_reports_when_zip'] is True) and str(exporting_options['output_reports']) != 'None' and str(exporting_options['output_reports']) != '' and '2' in exporting_options['output_reports']</filter>
18 a5f9b959d5d1 Uploaded iracooke parents: diff changeset	547 </data>
20 2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b iracooke parents: 18 diff changeset	548 <data format="tabular" name="output_psm" from_work_dir="psm.txt" label="${tool.name} on ${on_string}: PSM Report">
55 bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	549 <filter>(exporting_options['zip_conditional']['zip_output_boolean'] is False or exporting_options['zip_conditional']['export_reports_when_zip'] is True) and str(exporting_options['output_reports']) != 'None' and str(exporting_options['output_reports']) != '' and '3' in exporting_options['output_reports']</filter>
49 58a3e6cb2598 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6e846f7195a9e939047ac975c6523e8cf99da6b4 galaxyp parents: 46 diff changeset	550 </data>
58a3e6cb2598 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6e846f7195a9e939047ac975c6523e8cf99da6b4 galaxyp parents: 46 diff changeset	551 <data format="tabular" name="output_psm_nonvalidated" from_work_dir="psm_nonvalidated.txt" label="${tool.name} on ${on_string}: PSM Report with non-validated matches">
55 bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	552 <filter>(exporting_options['zip_conditional']['zip_output_boolean'] is False or exporting_options['zip_conditional']['export_reports_when_zip'] is True) and str(exporting_options['output_reports']) != 'None' and str(exporting_options['output_reports']) != '' and '4' in exporting_options['output_reports']</filter>
18 a5f9b959d5d1 Uploaded iracooke parents: diff changeset	553 </data>
30 ad60446b1e93 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit bdb5ee12705a3494eee96d1963f16f68bbe41d5c galaxyp parents: 29 diff changeset	554 <data format="tabular" name="output_extended_psm" from_work_dir="psmx.txt" label="${tool.name} on ${on_string}: Extended PSM Report">
55 bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	555 <filter>(exporting_options['zip_conditional']['zip_output_boolean'] is False or exporting_options['zip_conditional']['export_reports_when_zip'] is True) and str(exporting_options['output_reports']) != 'None' and str(exporting_options['output_reports']) != '' and '11' in exporting_options['output_reports']</filter>
30 ad60446b1e93 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit bdb5ee12705a3494eee96d1963f16f68bbe41d5c galaxyp parents: 29 diff changeset	556 </data>
20 2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b iracooke parents: 18 diff changeset	557 <data format="tabular" name="output_peptides_phosphorylation" from_work_dir="peptides_phospho.txt" label="${tool.name} on ${on_string}: Peptide Phosphorylation Report">
55 bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	558 <filter>(exporting_options['zip_conditional']['zip_output_boolean'] is False or exporting_options['zip_conditional']['export_reports_when_zip'] is True) and str(exporting_options['output_reports']) != 'None' and str(exporting_options['output_reports']) != '' and '5' in exporting_options['output_reports']</filter>
18 a5f9b959d5d1 Uploaded iracooke parents: diff changeset	559 </data>
20 2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b iracooke parents: 18 diff changeset	560 <data format="tabular" name="output_peptides" from_work_dir="peptides.txt" label="${tool.name} on ${on_string}: Peptide Report">
55 bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	561 <filter>(exporting_options['zip_conditional']['zip_output_boolean'] is False or exporting_options['zip_conditional']['export_reports_when_zip'] is True) and str(exporting_options['output_reports']) != 'None' and str(exporting_options['output_reports']) != '' and '6' in exporting_options['output_reports']</filter>
49 58a3e6cb2598 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6e846f7195a9e939047ac975c6523e8cf99da6b4 galaxyp parents: 46 diff changeset	562 </data>
58a3e6cb2598 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6e846f7195a9e939047ac975c6523e8cf99da6b4 galaxyp parents: 46 diff changeset	563 <data format="tabular" name="output_peptides_nonvalidated" from_work_dir="peptides_nonvalidated.txt" label="${tool.name} on ${on_string}: Peptide Report with non-validated matches">
55 bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	564 <filter>(exporting_options['zip_conditional']['zip_output_boolean'] is False or exporting_options['zip_conditional']['export_reports_when_zip'] is True) and str(exporting_options['output_reports']) != 'None' and str(exporting_options['output_reports']) != '' and '7' in exporting_options['output_reports']</filter>
20 2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b iracooke parents: 18 diff changeset	565 </data>
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b iracooke parents: 18 diff changeset	566 <data format="tabular" name="output_proteins_phosphorylation" from_work_dir="proteins_phospho.txt" label="${tool.name} on ${on_string}: Protein Phosphorylation Report">
55 bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	567 <filter>(exporting_options['zip_conditional']['zip_output_boolean'] is False or exporting_options['zip_conditional']['export_reports_when_zip'] is True) and str(exporting_options['output_reports']) != 'None' and str(exporting_options['output_reports']) != '' and '8' in exporting_options['output_reports']</filter>
20 2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b iracooke parents: 18 diff changeset	568 </data>
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b iracooke parents: 18 diff changeset	569 <data format="tabular" name="output_proteins" from_work_dir="proteins.txt" label="${tool.name} on ${on_string}: Protein Report">
55 bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	570 <filter>(exporting_options['zip_conditional']['zip_output_boolean'] is False or exporting_options['zip_conditional']['export_reports_when_zip'] is True) and str(exporting_options['output_reports']) != 'None' and str(exporting_options['output_reports']) != '' and '9' in exporting_options['output_reports']</filter>
49 58a3e6cb2598 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6e846f7195a9e939047ac975c6523e8cf99da6b4 galaxyp parents: 46 diff changeset	571 </data>
55 bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	572 <data format="tabular" name="output_proteins_nonvalidated" from_work_dir="proteins_nonvalidated.txt" label="${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	573 <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	574 </data>
a5f9b959d5d1 Uploaded iracooke parents: diff changeset	575 </outputs>
55 bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	576
18 a5f9b959d5d1 Uploaded iracooke parents: diff changeset	577 <tests>
55 bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	578 <!-- 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	579 <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	580 <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	581 <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	582 <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	583 <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	584 <assert_contents>
07ff622ec007 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0f6ab8b5647a33b2b051d7aa808ef42546436b23" galaxyp parents: 57 diff changeset	585 <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	586 </assert_contents>
07ff622ec007 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0f6ab8b5647a33b2b051d7aa808ef42546436b23" galaxyp parents: 57 diff changeset	587 </output>
55 bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	588 <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	589 <assert_contents>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	590 <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	591 </assert_contents>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	592 </output>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	593 </test>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	594
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	595 <!-- 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	596 <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	597 <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	598 <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	599 <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	600 <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	601 <assert_contents>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	602 <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	603 </assert_contents>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	604 </output>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	605 </test>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	606
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	607 <!-- 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	608 <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	609 <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	610 <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	611 <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	612 <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	613 <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	614 <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	615 <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	616 <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	617 <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	618 <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	619 <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	620 <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	621 <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	622 <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	623 <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	624 <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	625 <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	626 </test>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	627
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	628 <!-- 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	629 <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	630 <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	631 <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	632 <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	633 <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	634 <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	635 <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	636 <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	637 <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	638 <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	639 <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	640 <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	641 <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	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 <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	644 <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	645 <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	646 <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	647 <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	648 </assert_contents>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	649 </element>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	650 </output_collection>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	651 <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	652 <assert_contents>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	653 <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	654 <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	655 <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	656 <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	657 </assert_contents>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	658 </output>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	659 <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	660 <assert_contents>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	661 <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	662 <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	663 <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	664 <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	665 </assert_contents>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	666 </output>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	667 <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	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 <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	670 <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	671 <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	672 <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	673 <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	674 </assert_contents>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	675 </output>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	676 <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	677 <assert_contents>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	678 <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	679 <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	680 <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	681 </assert_contents>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	682 </output>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	683
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	684 </test>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	685
18 a5f9b959d5d1 Uploaded iracooke parents: diff changeset	686 </tests>
a5f9b959d5d1 Uploaded iracooke parents: diff changeset	687 <help>
a5f9b959d5d1 Uploaded iracooke parents: diff changeset	688 What it does
a5f9b959d5d1 Uploaded iracooke parents: diff changeset	689
49 58a3e6cb2598 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6e846f7195a9e939047ac975c6523e8cf99da6b4 galaxyp parents: 46 diff changeset	690 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	691
30 ad60446b1e93 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit bdb5ee12705a3494eee96d1963f16f68bbe41d5c galaxyp parents: 29 diff changeset	692 http://compomics.github.io/projects/peptide-shaker.html
18 a5f9b959d5d1 Uploaded iracooke parents: diff changeset	693
a5f9b959d5d1 Uploaded iracooke parents: diff changeset	694 ----
a5f9b959d5d1 Uploaded iracooke parents: diff changeset	695
55 bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	696 Outputs
18 a5f9b959d5d1 Uploaded iracooke parents: diff changeset	697 =======
a5f9b959d5d1 Uploaded iracooke parents: diff changeset	698
55 bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	699 zip
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
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	702 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	703
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	704 psdb
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
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	707 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	708
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	709 mzIdentML
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	710 -----------
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	711
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	712 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	713
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	714 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	715
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	716 • 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	717 • 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	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 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	721 --------------------
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	722
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	723 Spectra
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	724 '''''''
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	725
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	726 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	727
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	728 • 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	729 • 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	730 • 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	731 • 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	732 • 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	733 • 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	734
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	735 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	736
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	737 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	738 '''''''''''''''''''''''''''
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 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	741
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	742 • 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	743 • 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	744 • 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	745
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	746 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	747
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	748
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	749 Proteins: Sequences
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	750 '''''''''''''''''''
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 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	753
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	754 • 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	755 • 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	756 • 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	757
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	758 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	759
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	760
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	761 Proteins: Proteoforms
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
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	764 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	765
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	766 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	767 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	768
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	769 .. _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	770
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	771
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	772 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	773 '''''''''''''''''''''''''
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	774
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	775 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	776
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	777 • 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	778 • 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	779 • Validated PSMs
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	780 • 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	781
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	782 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	783
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	784
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	785 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	786 ''''''''''''''''''''''''
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	787
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	788 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	789
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	790 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	791
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	792 • Miscleaved Peptides
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	793 • Reactive Peptides
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	794 • Degenerated Peptides.
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 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	797
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	798 • Related Proteins
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	799 • 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	800 • Unrelated Proteins.
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 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	803
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	804 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	805
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 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	809 ---------------------------------
18 a5f9b959d5d1 Uploaded iracooke parents: diff changeset	810
a5f9b959d5d1 Uploaded iracooke parents: diff changeset	811 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	812 ''''''''''
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	813 ============================= ========================================
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	814 Column Description
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	815 ============================= ========================================
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	816 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	817 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	818 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	819 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	820 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	821 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	822 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	823 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	824 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	825 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	826 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	827 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	828 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	829 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	830 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	831 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	832 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	833 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	834 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	835 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	836 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	837 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	838 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	839 ============================= ========================================
18 a5f9b959d5d1 Uploaded iracooke parents: diff changeset	840
55 bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	841
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	842 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	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 Same columns as the original PSM report but also includes non-validated matches.
18 a5f9b959d5d1 Uploaded iracooke parents: diff changeset	846
a5f9b959d5d1 Uploaded iracooke parents: diff changeset	847
55 bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	848 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	849 ''''''''''''''''''''''''''
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	850 ============================= =========================================================
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	851 Column Description
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	852 ============================= =========================================================
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	853 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	854 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	855 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	856 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	857 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	858 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	859 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	860 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	861 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	862 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	863 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	864 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	865 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	866 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	867 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	868 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	869 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	870 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	871 #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	872 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	873 #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	874 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	875 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	876 ============================= =========================================================
18 a5f9b959d5d1 Uploaded iracooke parents: diff changeset	877
55 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 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	880 '''''''''''''''''''
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	881
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	882 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	883
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	884 ============================= =========================================================
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	885 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	886 ============================= =========================================================
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	887 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	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
18 a5f9b959d5d1 Uploaded iracooke parents: diff changeset	891
a5f9b959d5d1 Uploaded iracooke parents: diff changeset	892
a5f9b959d5d1 Uploaded iracooke parents: diff changeset	893 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	894 ''''''''''''''
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	895
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	896 ========================================== =====================================================
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	897 Column Description
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	898 ========================================== =====================================================
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	899 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	900 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	901 #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	902 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	903 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	904 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	905 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	906 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	907 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	908 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	909 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	910 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	911 #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	912 #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	913 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	914 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	915 ========================================== =====================================================
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 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	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 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	922
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 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	925 ''''''''''''''''''''''''''''''
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	926
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	927 ========================================== =====================================================
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	928 Column Description
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	929 ========================================== =====================================================
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	930 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	931 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	932 #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	933 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	934 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	935 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	936 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	937 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	938 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	939 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	940 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	941 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	942 #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	943 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	944 #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	945 #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	946 #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	947 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	948 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	949 ========================================== =====================================================
18 a5f9b959d5d1 Uploaded iracooke parents: diff changeset	950
a5f9b959d5d1 Uploaded iracooke parents: diff changeset	951
55 bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	952 Protein Report
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	953 ''''''''''''''
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	954
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	955 ========================================== =====================================================
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	956 Column Description
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	957 ========================================== =====================================================
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	958 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	959 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	960 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	961 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	962 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	963 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	964 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	965 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	966 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	967 # 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	968 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	969 #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	970 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	971 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	972 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	973 #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	974 #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	975 #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	976 #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	977 #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	978 #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	979 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	980 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	981 ========================================== =====================================================
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 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	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 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	988
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 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	991 ''''''''''''''''''''''''''''''
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	992
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	993 ========================================== =====================================================
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	994 Column Description
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	995 ========================================== =====================================================
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	996 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	997 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	998 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	999 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	1000 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	1001 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	1002 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	1003 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	1004 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	1005 #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	1006 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	1007 #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	1008 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	1009 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	1010 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	1011 #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	1012 #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	1013 #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	1014 #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	1015 #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	1016 #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	1017 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	1018 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	1019 ========================================== =====================================================
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
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	1022 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	1023 '''''''''''''''''''''''
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	1024
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	1025 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	1026
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	1027 * Project Details:
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	1028 ‣ 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	1029 * 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	1030 ‣ 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	1031 * Input Filters:
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	1032 ‣ 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	1033 * Validation Summary:
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	1034 • Proteins:
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	1035 ‣ #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	1036 • Peptides:
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	1037 ‣ #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	1038 • PSMs:
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	1039 ‣ #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	1040 * 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	1041 ‣ 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	1042 * 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	1043 ‣ 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	1044 * Annotation Settings:
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	1045 ‣ Intensity Limit, Automatic Annotation, Selected Ions, Neutral Losses, Neutral Losses Sequence Dependence, Fragment Ion m/z Tolerance.
18 a5f9b959d5d1 Uploaded iracooke parents: diff changeset	1046
a5f9b959d5d1 Uploaded iracooke parents: diff changeset	1047
a5f9b959d5d1 Uploaded iracooke parents: diff changeset	1048 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	1049 ''''''''''''''''''
18 a5f9b959d5d1 Uploaded iracooke parents: diff changeset	1050
55 bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	1051 ========================================== =====================================================
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	1052 Column Description
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	1053 ========================================== =====================================================
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a" galaxyp parents: 54 diff changeset	1054 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	1055 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	1056 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	1057 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	1058 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	1059 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	1060 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	1061 # 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	1062 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	1063 #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	1064 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	1065 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	1066 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	1067 #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	1068 #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	1069 #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	1070 #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	1071 #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	1072 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	1073 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	1074 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	1075 ========================================== =====================================================
18 a5f9b959d5d1 Uploaded iracooke parents: diff changeset	1076
a5f9b959d5d1 Uploaded iracooke parents: diff changeset	1077 ------
a5f9b959d5d1 Uploaded iracooke parents: diff changeset	1078
a5f9b959d5d1 Uploaded iracooke parents: diff changeset	1079 Citation
a5f9b959d5d1 Uploaded iracooke parents: diff changeset	1080
30 ad60446b1e93 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit bdb5ee12705a3494eee96d1963f16f68bbe41d5c galaxyp parents: 29 diff changeset	1081 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	1082
30 ad60446b1e93 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit bdb5ee12705a3494eee96d1963f16f68bbe41d5c galaxyp parents: 29 diff changeset	1083 If you use this tool in Galaxy, please cite Chilton J, Ira Cooke, Bjoern Gruening et al.
18 a5f9b959d5d1 Uploaded iracooke parents: diff changeset	1084 </help>
20 2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b iracooke parents: 18 diff changeset	1085 <expand macro="citations" />
18 a5f9b959d5d1 Uploaded iracooke parents: diff changeset	1086 </tool>

Mercurial > repos > galaxyp > peptideshaker

annotate peptide_shaker.xml @ 59:943a34df6047 draft