fragpipe: macros.xml annotate

annotate macros.xml @ 1:dc5de2ea607e draft

planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 408c20289d67eb76a2482af828e64265bef29053

author	galaxyp
date	Fri, 12 Jul 2024 18:16:43 +0000
parents	14785481da2b
children	ef46866326ef

rev	line source
0 14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	1 <macros>
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	2 <import>msfragger_macros.xml</import>
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	3 <token name="@TOOL_VERSION@">20.0</token>
1 dc5de2ea607e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 408c20289d67eb76a2482af828e64265bef29053 galaxyp parents: 0 diff changeset	4 <token name="@VERSION_SUFFIX@">1</token>
0 14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	5 <xml name="requirements">
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	6 <requirements>
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	7 <requirement type="package" version="@TOOL_VERSION@">fragpipe</requirement>
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	8 </requirements>
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	9 </xml>
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	10
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	11 <!-- TMT-n uses the following n first labels from TMT-18 -->
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	12 <token name="@TMT_LABELS@">['126', '127N', '127C', '128N', '128C', '129N', '129C', '130N', '130C', '131N', '131C', '132N', '132C', '133N', '133C', '134N', '134C', '135N']</token>
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	13 <token name="@iTRAQ-4_LABELS@">['114', '115', '116', '117']</token>
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	14 <token name="@iTRAQ-8_LABELS@">['113', '114', '115', '116', '117', '118', '119', '121']</token>
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	15
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	16 <!--
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	17 User specifies input file format and selects sample files as are included by the scan_inputs macro
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	18
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	19 User must also supply their own manifest file, a TSV file of the format:
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	20 name, experiment, bioreplicate, data type
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	21 -->
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	22 <xml name="samples">
1 dc5de2ea607e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 408c20289d67eb76a2482af828e64265bef29053 galaxyp parents: 0 diff changeset	23 <param name="inputs" type="data" format="mzml,mzxml" multiple="true" label="Proteomics Spectrum files" help="All input scan files must of a matching format: mzML, mzXML"/>
0 14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	24 <param name="input_prefix" type="text" value="" optional="true" label="File name prefix" help="Names inputs: prefix_rep#.mzXML Leave blank to use History names of inputs">
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	25 <validator type="regex" message="">[a-zA-Z][a-zA-Z0-9_-]*</validator>
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	26 </param>
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	27 <param name="manifest" type="data" format="tabular" label="Manifest file" help="TSV file with entries for each input scan file: Name (Name of input Galaxy history item. Extension in the name must be mzML or mzXML.), Experiment (empty, alphanumeric, or _), Bioreplicate (empty or integer), Data type (DDA, DIA, GPF-DIA, DIA-Quant, or DIA-lib)"/>
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	28 </xml>
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	29
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	30 <!--
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	31 Prepares enviroment variables for FragPipe.
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	32 -->
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	33 <token name="@PREPARE_ENVIRONMENT@"><![CDATA[
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	34 env_location="\$(dirname \$(which philosopher))/.." &&
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	35 cp -r \${env_location}/share/fragpipe*/ fragpipe_local/ &&
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	36 mkdir .cache .config tmp &&
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	37 export XDG_CONFIG_HOME=\$(pwd)/.config &&
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	38 export XDG_CACHE_HOME=\$(pwd)/.cache &&
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	39 export JAVA_OPTS="\$JAVA_OPTS -Djava.io.tmpdir=\$(pwd)/tmp" &&
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	40 export LD_LIBRARY_PATH="\$LD_LIBRARY_PATH:/usr/local/lib" &&
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	41 ]]></token>
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	42
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	43 <!--
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	44 Prepares input scan files.
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	45
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	46 Scans and moved to a scan directory and linked.
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	47
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	48 Annotation files are copied into the scan directory for TMT workflows.
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	49 -->
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	50 <token name="@LINK_SAMPLES@"><![CDATA[
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	51 CWD=\$(pwd \| sed 's@/@\\/@g') &&
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	52
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	53 mkdir -p scans &&
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	54 #if $wf.workflow_name == "TMT10" or $wf.workflow_name == "TMT11"
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	55 cp -p '$wf.annotation' 'scans/annotation.txt' &&
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	56 #end if
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	57
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	58 sed "s@^@\$CWD/scans/@" $manifest > fp.manifest &&
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	59
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	60 #for $sf in $inputs
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	61 #set $i_name = $ln_name($sf)
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	62 ln -s '$sf' 'scans/${i_name}' &&
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	63 #end for
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	64 ]]></token>
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	65
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	66 <!--
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	67 Prepares input files, excluding database.
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	68 -->
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	69 <token name="@PREPARE_INPUTS@"><![CDATA[
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	70 mkdir -p outputs &&
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	71 @CMD_IMPORTS@
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	72 @LINK_SAMPLES@
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	73 ]]></token>
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	74
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	75 <!--
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	76 Prepares database.
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	77
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	78 First genericizes unknown sequence headers in the database.
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	79 Then adds decoys, or decoys and contaminants depending on user selection.
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	80 -->
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	81 <token name="@PREPARE_DATABASE@"><![CDATA[
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	82 '$__tool_directory__/genericize_db.py' $database_name genericized_db.fas &&
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	83
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	84 #if str($database_options) != 'none'
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	85 philosopher workspace --init &&
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	86 philosopher database --custom genericized_db.fas --prefix rev_
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	87 #if str($database_options) != 'decoy_and_contam'
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	88 --contam
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	89 #end if
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	90 --contamprefix &&
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	91 ln -s -decoys-.fas final_db.fas &&
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	92 #else
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	93 ln -s genericized_db.fas final_db.fas &&
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	94 #end if
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	95 ]]></token>
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	96
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	97 <!--
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	98 Prepares outputs.
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	99
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	100 Creates log file symlink, makes a new directory for "combined" outputs and creates "concatenated" results.
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	101 -->
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	102 <token name="@PREPARE_OUTPUTS@"><![CDATA[
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	103 cd outputs &&
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	104
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	105 #if $output_options and 'combined_outputs' in $output_options
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	106 mkdir combined_outputs &&
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	107 find . -name 'combined*tsv' \| xargs -I {} mv {} combined_outputs &&
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	108 #end if
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	109
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	110 ## For each category of results - psm, ion, peptide, protein - this loop concatenates results from each sample into a single result.
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	111 ## For example, the entries sample1/psm.tsv and sample2/psm.tsv would be combined to concat_psm.tsv, a single psm.tsv header as its first line.
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	112 for f in psm.tsv ion.tsv peptide.tsv protein.tsv; do
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	113 n=0;
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	114 for i in \$(find * -name \${f}); do
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	115 d=\${i%/*};
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	116 if [[ \$n == 0 ]]; then
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	117 awk 'NR==1{printf("Experiment\t%s\n",\$0);}' \$i > concat_\${f};
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	118 fi;
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	119 awk 'NR>1{printf("'"\${d}"'\t%s\n",\$0);}' \$i >> concat_\${f}; t=\$(echo \${i} \| tr '/' '.');
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	120 mv \${i} \${t}; n=\$((n+1));
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	121 done;
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	122 done
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	123 ]]></token>
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	124
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	125 <!-- Input database for MSFragger -->
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	126 <xml name="fragger_database">
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	127 <param name="database_name" type="data" format="fasta" label="Proteomics Search Database in FASTA format" help="Generic sequence headers in the input FASTA file that are not formatted according to the UniProt, NCBI, or ENSEMBL formats will be automatically prefixed with '>generic\|' to avoid being misinterpreted by Philosopher."/>
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	128 <!-- Whether to add decoys and contaminants to the database with Philosopher -->
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	129 <param name="database_options"
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	130 type="select"
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	131 label="Decoys and contaminants"
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	132 help="The default decoy prefix is "rev_".">
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	133 <option value="decoy_and_contam" selected="true">Add decoys and contaminants</option>
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	134 <option value="decoy">Add decoys</option>
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	135 <option value="none">Don't add decoys or contaminants</option>
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	136 </param>
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	137
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	138 <!-- Database may be split into chunks for performance benefits -->
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	139 <param name="num_slices" type="integer" label="Split database" value="1" help="The number of chunks in which to split the database."/>
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	140 </xml>
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	141
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	142 <!--
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	143 The following macro allows users to select their FragPipe workfow.
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	144
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	145 For a given workflow selection, the relevant parameter sections are expanded. Options specific to the selected workflow
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	146 are passed to the parameter definitions in the expand element.
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	147
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	148 The Galaxy parameters overwrite a workflow file provided by FragPipe for the selected workflow. As a result, any parameters
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	149 that are not defined in the Galaxy tool will fall back on the FragPipe defaults for that workflow. This logic is defined
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	150 in the <configfile> element.
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	151 -->
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	152 <xml name="workflow">
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	153 <conditional name="wf">
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	154 <param name="workflow_name" type="select" label="Workflow" help="Note: MSBooster is currently disabled in all Galaxy FragPipe workflows.">
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	155 <option value="Default">Default</option>
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	156 <option value="Open">Open</option>
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	157 <option value="Nonspecific-HLA">Nonspecific-HLA</option>
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	158 <option value="LFQ-MBR">LFQ-MBR</option>
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	159 <option value="TMT10">TMT10</option>
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	160 <option value="TMT11">TMT11</option>
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	161 </param>
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	162
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	163 <when value="Default">
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	164 <section name="msfragger" expanded="false" title="MSFragger Options">
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	165 <expand macro="msfragger_default"/>
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	166 </section>
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	167 <expand macro="validation"
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	168 pep="false"
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	169 perc="true"
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	170 boost="false"
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	171 no="false"
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	172 masswidth="5"
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	173 clevel="0"
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	174 accmass="true"
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	175 decoyprobs="true"
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	176 nonparam="true"
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	177 expectscore="true"
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	178 ppm="true"
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	179 combined_pepxml="false"/>
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	180 <expand macro="label_free_quantification" yes="false" no="true"/>
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	181 <expand macro="ptm_shepherd" yes="false" no="true" c="true" z="true"/>
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	182 <expand macro="isobaric_quantification" yes="false" no="true"/>
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	183 </when>
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	184
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	185 <when value="Open">
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	186 <section name="msfragger" expanded="false" title="MSFragger Options">
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	187 <expand macro="msfragger_open"/>
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	188 </section>
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	189 <expand macro="validation"
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	190 pep="true"
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	191 perc="false"
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	192 boost="false"
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	193 no="false"
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	194 masswidth="1000"
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	195 clevel="-2"
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	196 accmass="false"
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	197 decoyprobs="true"
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	198 nonparam="true"
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	199 expectscore="true"
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	200 ppm="false"
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	201 combined_pepxml="true">
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	202 <expand macro="crystalc"/>
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	203 </expand>
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	204 <expand macro="label_free_quantification" yes="false" no="true"/>
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	205 <expand macro="ptm_shepherd" yes="true" no="false"/>
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	206 <expand macro="isobaric_quantification" yes="false" no="true" bridge="false" pool="true"/>
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	207 </when>
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	208
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	209 <when value="Nonspecific-HLA">
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	210 <section name="msfragger" expanded="false" title="MSFragger Options">
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	211 <expand macro="msfragger_nonspecific_HLA"/>
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	212 </section>
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	213 <expand macro="validation"
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	214 pep="false"
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	215 perc="true"
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	216 boost="false"
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	217 no="true"
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	218 masswidth="5"
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	219 clevel="0"
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	220 accmass="true"
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	221 decoyprobs="true"
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	222 nonparam="true"
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	223 expectscore="true"
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	224 ppm="true"
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	225 combined_pepxml="false"/>
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	226 <expand macro="label_free_quantification" yes="false" no="true"/>
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	227 <expand macro="ptm_shepherd" yes="false" no="true"/>
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	228 <expand macro="isobaric_quantification" yes="false" no="true"/>
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	229 </when>
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	230
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	231 <when value="LFQ-MBR">
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	232 <section name="msfragger" expanded="false" title="MSFragger Options">
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	233 <expand macro="msfragger_LFQ_MBR"/>
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	234 </section>
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	235 <!-- MSBooster should be enabled once included in FragPipe Galaxy tool -->
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	236 <expand macro="validation"
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	237 pep="false"
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	238 perc="true"
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	239 boost="false"
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	240 no="true"
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	241 masswidth="5"
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	242 clevel="0"
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	243 accmass="true"
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	244 decoyprobs="true"
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	245 nonparam="true"
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	246 expectscore="true"
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	247 ppm="true"
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	248 combined_pepxml="false"/>
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	249 <expand macro="label_free_quantification" yes="true" no="false"/>
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	250 <expand macro="ptm_shepherd" yes="false" no="true"/>
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	251 <expand macro="isobaric_quantification" yes="false" no="true"/>
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	252 </when>
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	253
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	254 <when value="TMT10">
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	255 <expand macro="tmt_options" plex="TMT-10"/>
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	256 </when>
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	257
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	258 <!-- TMT11 is not in FragPipe GUI -->
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	259 <when value="TMT11">
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	260 <expand macro="tmt_options" plex="TMT-11"/>
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	261 </when>
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	262 </conditional>
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	263 </xml>
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	264
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	265 <!-- Options for TMT workflows -->
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	266 <xml name="tmt_options" token_plex="">
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	267 <param name="annotation" type="data" format="txt" optional="false" label="annotation file" help=""/>
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	268 <section name="msfragger" expanded="false" title="MSFragger Options">
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	269 <expand macro="msfragger_TMT"/>
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	270 </section>
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	271 <expand macro="validation"
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	272 pep="false"
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	273 perc="true"
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	274 boost="false"
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	275 no="false"
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	276 masswidth="5"
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	277 clevel="0"
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	278 accmass="true"
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	279 decoyprobs="true"
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	280 nonparam="true"
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	281 expectscore="true"
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	282 ppm="true"
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	283 combined_pepxml="false"
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	284 protp_minprob="0.5"/>
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	285 <expand macro="isobaric_quantification" yes="true" no="false" plex="@PLEX@" level="2" ref_tag="Bridge" mod_tag="none"/>
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	286 <expand macro="label_free_quantification" yes="false" no="true"/>
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	287 <expand macro="ptm_shepherd" yes="false" no="true" token_unimod="false" token_common="true"/>
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	288 </xml>
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	289
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	290 <!-- Generates the FragPipe workflow-->
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	291 <xml name="workflow_configfile">
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	292 <configfile name="workflow_configfile"><![CDATA[#slurp
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	293 ## Create a fragpipe params dictionary from a file
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	294 #set $comments = []
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	295 #set $wfdict = {}
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	296 #set $wfpath = $__tool_directory__ + '/workflows/' + str($wf.workflow_name) + '.workflow'
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	297 #set $fh = open($wfpath, 'r')
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	298 #for $line in $fh:
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	299 #if $line.startswith('#')
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	300 #silent $comments.append($line)
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	301 #elif $line.strip() != ''
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	302 #set $kv = $line.strip().split('=')
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	303 #if len($kv) < 2
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	304 #silent $kv.append('')
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	305 #end if
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	306 #set $wfdict[$kv[0]] = '='.join($kv[1:])
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	307 #end if
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	308 #end for
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	309
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	310 #set $wfdict['database.db-path'] = 'final_db.fas'
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	311 #set $wfdict['msfragger.misc.slice-db'] = $num_slices
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	312
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	313 ## Get the MSFragger Params (shared with the MSFragger tool)
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	314 #set $prefix = $wf.msfragger
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	315 @MSFRAGGER_PARAM_DICT@
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	316 #if len($vmods) > 0
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	317 #set $msfragger_dict['table.var-mods'] = '; '.join([$re.sub('^(.*,)(\d)$','\\1True,\\2',m) for m in $vmods])
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	318 #end if
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	319 #for $k in $msfragger_dict.keys()
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	320 #set $kv = $k + '=' + str($msfragger_dict[$k])
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	321 #set $wfk = 'msfragger.' + $k
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	322 #set $wfdict[$wfk] = str($msfragger_dict[$k])
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	323 #end for
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	324
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	325 @VALIDATION@
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	326 @PTM_SHEPHERD@
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	327 @LABEL_FREE_QUANTIFICATION@
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	328 @ISOBARIC_QUANTIFICATION@
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	329
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	330 ## Populate the workflow with configuration and comment dictionary entries populated by tool params.
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	331 #for $comment in $comments
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	332 $comment
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	333 #end for
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	334
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	335 #for $k in sorted($wfdict.keys())
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	336 #set $kv = $k + '=' + str($wfdict[$k])
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	337 $kv
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	338 #end for
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	339 #slurp]]></configfile>
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	340 </xml>
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	341
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	342 <!-- Percolator options -->
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	343 <xml name="percolator">
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	344 <section name="percolator" expanded="true" title="Percolator">
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	345 <param name="keep_tsv_files" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Keep intermediate files"/>
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	346 <param name="min_prob" type="float" value="0.5" label="Minimum probability (default 0.5)"/>
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	347 </section>
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	348 </xml>
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	349
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	350 <!-- Set Percolator workflow options -->
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	351 <token name="@PERCOLATOR@"><![CDATA[
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	352 #set $prc = $wf.validation.validation_tab.psm_validation.percolator
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	353 #set $wfdict['run-validation-tab'] = $wf.validation.validation_tab.run_validation
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	354 #set $wfdict['peptide-prophet.run-peptide-prophet'] = 'false'
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	355 #set $wfdict['percolator.run-percolator'] = 'true'
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	356 #set $wfdict['percolator.keep-tsv-files'] = str($prc.keep_tsv_files)
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	357 #set $wfdict['percolator.min-prob'] = str($prc.min_prob)
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	358 ]]></token>
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	359
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	360 <!-- Philosopher Report (phi-report) options -->
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	361 <xml name="phi_report">
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	362 <conditional name="phi_report">
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	363 <param name="run_phi_report" type="select" label="Generate Philosopher Reports">
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	364 <option value="true" selected="true">Yes</option>
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	365 <option value="false">No</option>
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	366 </param>
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	367 <when value="true">
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	368 <section name="phi_report_opts" expanded="false" title="FDR Filter and Report">
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	369 <param name="dont_use_prot_prophet_file" type="boolean" truevalue="true" falsevalue="false" checked="false"/>
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	370 <param name="print_decoys" type="boolean" truevalue="true" falsevalue="false" checked="false"/>
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	371 </section>
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	372 </when>
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	373 <when value="false"/>
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	374 </conditional>
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	375 </xml>
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	376
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	377 <!-- Set Philosopher Report (phi-report) workflow options -->
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	378 <token name="@PHIREPORT@"><![CDATA[
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	379 #set $prfx = $wf.validation.validation_tab.phi_report
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	380 #if $prfx.run_phi_report == 'true'
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	381 #set $wfdict['phi-report.run-report'] = 'true'
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	382 #set $prfx = $wf.validation.validation_tab.phi_report.phi_report_opts
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	383 #set $wfdict['phi-report.print-decoys'] = $prfx.print_decoys
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	384 #else
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	385 #set $wfdict['phi-report.run-report'] = 'false'
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	386 #end if
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	387 ]]></token>
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	388
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	389 <!-- PeptideProphet options -->
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	390 <xml name="peptide_prophet" token_masswidth="5" token_clevel="0" token_accmass="true" token_decoyprobs="true" token_nonparam="true" token_expectscore="true" token_ppm="true" token_combined_pepxml="false">
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	391 <section name="peptide_prophet" expanded="true" title="PeptideProphet">
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	392 <param name="combined_pepxml" type="boolean" truevalue="true" falsevalue="false" checked="@COMBINED_PEPXML@" label="Single combined pepxml per experiment or group"/>
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	393 <param argument="--decoyprobs" type="boolean" truevalue="--decoyprobs" falsevalue="" checked="@DECOYPROBS@" label="compute possible non-zero probabilities for Decoy entries on the last iteration"/>
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	394 <param argument="--ppm" type="boolean" truevalue="--ppm" falsevalue="" checked="@PPM@" label="use PPM mass error instead of Dalton for mass modeling"/>
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	395 <param argument="--accmass" type="boolean" truevalue="--accmass" falsevalue="" checked="@ACCMASS@" label="use Accurate Mass model binning"/>
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	396 <param argument="--nonparam" type="boolean" truevalue="--nonparam" falsevalue="" checked="@NONPARAM@" label="use semi-parametric modeling, must be used in conjunction with --decoy option"/>
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	397 <param argument="--expectscore" type="boolean" truevalue="--expectscore" falsevalue="" checked="@EXPECTSCORE@" label="use expectation value as the only contributor to the f-value for modeling"/>
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	398 <param argument="--masswidth" type="float" value="@MASSWIDTH@" label="model mass width (default 5)"/>
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	399 <param argument="--clevel" type="integer" value="@CLEVEL@" label="set Conservative Level in neg_stdev from the neg_mean, low numbers are less conservative, high numbers are more conservative"/>
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	400 <param argument="--glyc" type="boolean" truevalue="--glyc" falsevalue="" checked="false" label="enable peptide Glyco motif model"/>
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	401 <param argument="--combine" type="boolean" truevalue="--combine" falsevalue="" checked="false" label="combine the results from PeptideProphet into a single result file" />
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	402 <param argument="--minpeplen" type="integer" value="7" label="minimum peptide length not rejected (default 7)" />
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	403 <param argument="--minprob" type="float" value="0.05" label="report results with minimum probability" />
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	404 <param argument="--nomass" type="boolean" truevalue="--nomass" falsevalue="" checked="false" label="disable mass model" />
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	405 <param argument="--nonmc" type="boolean" truevalue="--nonmc" falsevalue="" checked="false" label="disable NMC missed cleavage model" />
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	406 <param argument="--nontt" type="boolean" truevalue="--nontt" falsevalue="" checked="false" label="disable NTT enzymatic termini model" />
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	407 <param argument="--phospho" type="boolean" truevalue="--phospho" falsevalue="" checked="false" label="enable peptide phospho motif model" />
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	408 </section>
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	409 </xml>
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	410 <token name="@PEPTIDEPROPHET@"><![CDATA[
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	411 #set $prfx = $wf.validation.validation_tab.psm_validation.peptide_prophet
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	412 #set $wfdict['peptide-prophet.run-peptide-prophet'] = 'true'
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	413 #set $wfdict['peptide-prophet.combine-pepxml'] = str($prfx.combined_pepxml)
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	414 #set $cmd_opts = [str($prfx.accmass),str($prfx.combine),str($prfx.decoyprobs),str($prfx.expectscore),str($prfx.glyc),str($prfx.nomass),str($prfx.nonmc),str($prfx.nonparam),str($prfx.nontt),str($prfx.phospho),str($prfx.ppm)]
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	415 #silent $cmd_opts.append('--clevel ' + str($prfx.clevel))
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	416 #silent $cmd_opts.append('--masswidth ' + str($prfx.masswidth))
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	417 #silent $cmd_opts.append('--minpeplen ' + str($prfx.minpeplen))
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	418 #silent $cmd_opts.append('--minprob ' + str($prfx.minprob))
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	419 #set $wfdict['peptide-prophet.cmd-opts'] = ' '.join($cmd_opts).strip()
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	420 ]]></token>
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	421
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	422 <!-- CrystalC options -->
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	423 <xml name="crystalc">
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	424 <param name="run_crystalc" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Run Crystal-C" help="Recommend for open searches for additional resuts cleanup"/>
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	425 </xml>
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	426
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	427 <!-- MSBooster options. Disabled until DIA-NN integrated.
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	428 <xml name="msbooster">
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	429 <section name="msbooster" expanded="false" title="MSBooster">
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	430 <param name="predict_rt" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Predict RT"/>
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	431 <param name="predict_spectra" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Predict spectra"/>
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	432 <param name="use_correlated_features" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Use correlated features"/>
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	433 </section>
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	434 </xml>
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	435 -->
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	436
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	437 <!-- Protein Prophet options -->
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	438 <xml name="protein_prophet" token_minprob="0.05">
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	439 <conditional name="protein_prophet">
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	440 <param name="run_protein_prophet" type="select" label="Run Protein Prophet">
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	441 <option value="true" selected="true">Yes</option>
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	442 <option value="false">No</option>
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	443 </param>
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	444 <when value="true">
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	445 <section name="protein_prophet_opts" expanded="true" title="Protein Prophet">
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	446 <param argument="--iprophet" type="boolean" truevalue="--iprophet" falsevalue="" checked="false" label="input is from iProphet" />
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	447 <param argument="--maxppmdiff" type="integer" value="2000000" label="maximum peptide mass difference in ppm (default 2000000)" />
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	448 <param argument="--minprob" type="float" value="@MINPROB@" label="PeptideProphet probability threshold (default 0.05)" />
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	449 <param argument="--nonsp" type="boolean" truevalue="--nonsp" falsevalue="" checked="false" label="do not use NSP model" />
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	450 <param argument="--subgroups" type="boolean" truevalue="--subgroups" falsevalue="" checked="false" label="do not use NOGROUPS" />
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	451 <param argument="--unmapped" type="boolean" truevalue="--unmapped" falsevalue="" checked="false" label="report results for UNMAPPED proteins" />
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	452 </section>
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	453 </when>
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	454 <when value="false"/>
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	455 </conditional>
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	456 </xml>
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	457
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	458 <!-- Set ProteinProphet workflow options -->
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	459 <token name="@PROTEINPROPHET@"><![CDATA[
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	460 #set $prfx = $wf.validation.validation_tab.protein_prophet
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	461 #if $prfx.run_protein_prophet == 'true'
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	462 #set $prfx = $wf.validation.validation_tab.protein_prophet.protein_prophet_opts
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	463 #set $wfdict['protein-prophet.run-protein-prophet'] = 'true'
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	464 #set $cmd_opts = [str($prfx.iprophet),str($prfx.nonsp),str($prfx.subgroups),str($prfx.unmapped)]
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	465 #silent $cmd_opts.append('--maxppmdiff ' + str($prfx.maxppmdiff))
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	466 #silent $cmd_opts.append('--minprob ' + str($prfx.minprob))
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	467 #set $wfdict['protein-prophet.cmd-opts'] = ' '.join($cmd_opts).strip()
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	468 #else
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	469 #set $wfdict[protein-prophet.run-protein-prophet] = 'false'
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	470 #end if
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	471 ]]></token>
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	472
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	473 <!-- Validation options. Includes PeptideProphet, Percolator, MSBooster, ProteinProphet, and CrystalC -->
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	474 <xml name="validation" token_expand="false" token_pep="false" token_perc="false" token_boost="false" token_no="true" token_masswidth="5" token_clevel="0" token_accmass="true" token_decoyprobs="true" token_nonparam="true" token_expectscore="true" token_ppm="true" token_combined_pepxml="false" token_protp_minprob="0.05">
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	475 <section name="validation" expanded="@EXPAND@" title="Validation">
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	476 <conditional name="validation_tab">
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	477 <param name="run_validation" type="select" label="Run Validation">
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	478 <option value="true" selected="true">Yes</option>
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	479 <option value="false">No</option>
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	480 </param>
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	481 <when value="true">
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	482 <yield/> <!-- crystalc -->
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	483 <conditional name="psm_validation">
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	484 <param name="run_psm_validation" type="select" label="PSM Validation">
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	485 <option value="peptide_prophet" selected="@PEP@">Run PeptideProphet</option>
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	486 <option value="percolator" selected="@PERC@">Run Percolator</option>
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	487 <!-- MSBooster disabled until DIA-NN integrated
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	488 <option value="msbooster_percolator" selected="@BOOST@">Run MSBooster and Percolator</option>
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	489 -->
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	490 <option value="no" selected="@NO@">Use workflow values</option>
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	491 </param>
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	492 <when value="peptide_prophet">
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	493 <expand macro="peptide_prophet" masswidth="@MASSWIDTH@" clevel="@CLEVEL@" accmass="@ACCMASS@" decoyprobs="@DECOYPROBS@" nonparam="@NONPARAM@" expectscore="@EXPECTSCORE@" ppm="@PPM@" combined_pepxml="@COMBINED_PEPXML@"/>
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	494 </when>
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	495 <when value="percolator">
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	496 <expand macro="percolator"/>
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	497 </when>
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	498 <!-- MSBooster disabled until DIA-NN integrated
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	499 <when value="msbooster_percolator">
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	500 <expand macro="msbooster"/>
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	501 <expand macro="percolator"/>
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	502 </when>
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	503 -->
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	504 <when value="no">
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	505 </when>
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	506 </conditional>
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	507 <expand macro="protein_prophet" minprob="@PROTP_MINPROB@"/>
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	508 <expand macro="phi_report"/>
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	509 </when>
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	510 <when value="false">
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	511 </when>
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	512 </conditional>
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	513 </section>
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	514 </xml>
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	515
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	516 <!-- Set validation workflow options -->
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	517 <token name="@VALIDATION@"><![CDATA[
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	518 #set $prfx = $wf.validation.validation_tab.psm_validation
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	519 #if $prfx.run_psm_validation == 'peptide_prophet'
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	520 #set $wfdict['run-psm-validation'] = 'true'
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	521 #set $wfdict['msbooster.run-msbooster'] = 'false'
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	522 #set $wfdict['percolator.run-percolator'] = 'false'
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	523 @PEPTIDEPROPHET@
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	524 #elif $prfx.run_psm_validation == 'percolator'
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	525 #set $wfdict['run-psm-validation'] = 'true'
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	526 #set $wfdict['msbooster.run-msbooster'] = 'false'
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	527 @PERCOLATOR@
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	528 ##elif $prfx.run_psm_validation == 'msbooster_percolator'
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	529 # MSBooster disabled until DIA-NN integrated.
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	530 #end if
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	531 @PROTEINPROPHET@
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	532 @PHIREPORT@
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	533 ]]></token>
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	534
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	535 <!-- PTM-Sheperd options -->
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	536 <xml name="ptm_shepherd" token_expand="false" token_yes="true" token_no="false" token_a="false" token_b="true" token_c="false" token_x="false" token_y="true" token_z="false" token_unimod="true" token_common="false" token_glyco="false" token_custom="false">
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	537 <section name="ptms" expanded="false" title="PTMs">
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	538 <conditional name="ptm_shepherd">
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	539 <param name="run_ptm_shepherd" type="select" label="Run PTM Shepherd">
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	540 <option value="yes" selected="@YES@">yes</option>
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	541 <option value="no" selected="@NO@">no</option>
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	542 </param>
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	543 <when value="yes">
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	544 <param name="output_extended" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Extended output"/>
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	545 <section name="ptm_profiling" expanded="false" title="PTM Profiling">
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	546 <param name="histo_smoothbins" type="integer" value="" min="0" optional="true" label="Smoothing factor" help="ptmshepherd.histo_smoothbins"/>
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	547 <param name="precursor_mass_units" type="select" label="Precursor Mass tolerance units" help="ptmshepherd.precursor_mass_units">
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	548 <option value="1" selected="true">ppm</option>
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	549 <option value="0" selected="false">Daltons</option>
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	550 </param>
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	551 <param name="precursor_tol" type="float" value="" min="0" optional="true" label="Precursor tolerance" help="ptmshepherd.precursor_tol"/>
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	552 <param name="peakpicking_promRatio" type="float" value="" min="0" optional="true" label="Prominece ratio" help="ptmshepherd.peakpicking_promRatio"/>
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	553 <param name="peakpicking_mass_units" type="select" label="Peakpicking Mass tolerance units" help="ptmshepherd.peakpicking_mass_units">
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	554 <option value="1" selected="true">ppm</option>
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	555 <option value="0" selected="false">Daltons</option>
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	556 </param>
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	557 <param name="peakpicking_width" type="float" value="" min="0" optional="true" label="Peak picking width" help="ptmshepherd.peakpicking_width"/>
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	558 <param name="peakpicking_minPsm" type="integer" value="" min="0" optional="true" label="Peak minimum PSMs" help="ptmshepherd.peakpicking_minPsm"/>
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	559 <param name="spectra_ppmtol" type="float" value="" min="0" optional="true" label="Fragment Mass tolerance (PPM)" help="ptmshepherd.spectra_ppmtol"/>
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	560 <param name="normalization" type="select" optional="true" label="Normalize data to" help="ptmshepherd.normalization-psms ptmshepherd.normalization-scans">
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	561 <option value="psms" selected="true">PSMs</option>
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	562 <option value="scans" selected="false">MS2 scans</option>
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	563 </param>
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	564 <param name="varmod_masses" type="select" optional="true" label="Custom mass shifts" help="ptmshepherd.varmod_masses">
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	565 <option value="Failed_Carbamidomethylation\:-57.021464">Failed_Carbamidomethylation:-57.021464</option>
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	566 </param>
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	567 </section>
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	568 <section name="ptm_annotation" expanded="true" title="PTM Annotation">
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	569 <param name="annotation_tol" type="float" value="" min="0" optional="true" label="Annotation tolerance (Da)" help="ptmshepherd.annotation_tol"/>
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	570 <conditional name="annotation">
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	571 <param name="annotation_source" type="select" label="Annotation source" help="ptmshepherd.annotation">
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	572 <option value="unimod" selected="@UNIMOD@">Unimod</option>
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	573 <option value="common" selected="@COMMON@">Common mass shifts</option>
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	574 <option value="glyco" selected="@GLYCO@">Glyco mass shifts</option>
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	575 <option value="custom" selected="@CUSTOM@">Custom annotation file</option>
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	576 </param>
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	577 <when value="unimod"/>
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	578 <when value="common"/>
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	579 <when value="glyco"/>
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	580 <when value="custom">
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	581 <param name="annotation_file" type="data" format="txt" label="Custom annotation file"/>
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	582 </when>
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	583 </conditional>
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	584 </section>
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	585 <section name="ptm_localization" expanded="false" title="PTM Localization">
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	586 <param name="nions" type="select" multiple="true" optional="true" label="Use specified N-term ions" help="(default: a,b for CID, c for ETD)">
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	587 <option value="a" selected="@A@">a</option>
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	588 <option value="b" selected="@B@">b</option>
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	589 <option value="c" selected="@C@">c</option>
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	590 </param>
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	591 <param name="cions" type="select" multiple="true" optional="true" label="use specified C-term ions" help="(default: y for CID, z for ETD)">
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	592 <option value="x" selected="@X@">x</option>
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	593 <option value="y" selected="@Y@">y</option>
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	594 <option value="z" selected="@Z@">z</option>
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	595 </param>
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	596 <param name="spectra_maxfragcharge" type="integer" value="" min="0" optional="true" label="Max fragment charge" help="ptmshepherd.spectra_maxfragcharge"/>
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	597 <param name="localization_background" type="integer" value="" min="0" optional="true" label="Localization background" help="ptmshepherd.localization_background"/>
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	598 <param name="localization_allowed_res" type="select" label="Restrict localization to" help="ptmshepherd.localization_allowed_res">
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	599 <option value="" selected="true">none</option>
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	600 <option value="all">all</option>
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	601 <option value="N">N</option>
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	602 <option value="ST">ST</option>
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	603 </param>
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	604 </section>
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	605 <!-- Not yet implemented
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	606 <section name="ion_discovery" expanded="false" title="Diagnostic Ion Discovery">
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	607 </section>
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	608 <section name="glycan" expanded="false" title="Gyclan Assignment and FDR">
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	609 </section>
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	610 -->
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	611 </when>
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	612 <when value="no"/>
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	613 </conditional>
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	614 </section>
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	615 </xml>
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	616
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	617 <!-- Set PTM-Sheperd workflow options -->
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	618 <token name="@PTM_SHEPHERD@"><![CDATA[
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	619 #set $prfx = $wf.ptms.ptm_shepherd
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	620 #if $prfx.run_ptm_shepherd == 'yes'
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	621 #set $wfdict['ptmshepherd.run-shepherd'] = 'true'
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	622 #set $cxt = $prfx.ptm_profiling
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	623 #set $wfdict['ptmshepherd.output_extended'] = $prfx.output_extended
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	624 #if $cxt.histo_smoothbins != ''
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	625 #set $wfdict['ptmshepherd.histo_smoothbins'] = $cxt.histo_smoothbins
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	626 #end if
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	627 #if $cxt.precursor_tol != ''
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	628 #set $wfdict['ptmshepherd.precursor_mass_units'] = $ctx.precursor_mass_units
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	629 #set $wfdict['ptmshepherd.precursor_tol'] = $cxt.precursor_tol
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	630 #end if
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	631 #if $cxt.peakpicking_promRatio != ''
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	632 #set $wfdict['ptmshepherd.peakpicking_promRatio'] = $cxt.peakpicking_promRatio
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	633 #end if
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	634 #if $cxt.peakpicking_width != ''
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	635 #set $wfdict['ptmshepherd.peakpicking_mass_units'] = $ctx.peakpicking_mass_units
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	636 #set $wfdict['ptmshepherd.peakpicking_width'] = $cxt.peakpicking_width
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	637 #end if
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	638 #if $cxt.peakpicking_minPsm != ''
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	639 #set $wfdict['ptmshepherd.peakpicking_minPsm'] = $cxt.peakpicking_minPsm
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	640 #end if
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	641 #if $cxt.spectra_ppmtol != ''
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	642 #set $wfdict['ptmshepherd.spectra_ppmtol'] = $cxt.spectra_ppmtol
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	643 #end if
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	644 #if $cxt.normalization != 'None'
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	645 #if $cxt.normalization == "psms"
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	646 #set $wfdict['ptmshepherd.normalization-psms'] = 'true'
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	647 #set $wfdict['ptmshepherd.normalization-scans'] = 'false'
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	648 #else
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	649 #set $wfdict['ptmshepherd.normalization-psms'] = 'false'
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	650 #set $wfdict['ptmshepherd.normalization-scans'] = 'true'
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	651 #end if
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	652 #end if
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	653 #if $cxt.varmod_masses != 'None'
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	654 #set $wfdict['ptmshepherd.varmod_masses'] = $cxt.varmod_masses
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	655 #end if
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	656 #set $cxt = $prfx.ptm_annotation
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	657 #if $cxt.annotation_tol != ''
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	658 #set $wfdict['ptmshepherd.annotation_tol'] = $cxt.annotation_tol
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	659 #end if
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	660 #if $cxt.annotation.annotation_source == 'unimod'
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	661 #set $wfdict['ptmshepherd.annotation-unimod'] = 'true'
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	662 #set $wfdict['ptmshepherd.annotation-common'] = 'false'
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	663 #set $wfdict['ptmshepherd.annotation-glyco'] = 'false'
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	664 #set $wfdict['ptmshepherd.annotation-custom'] = 'false'
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	665 #elif $cxt.annotation.annotation_source == 'common'
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	666 #set $wfdict['ptmshepherd.annotation-unimod'] = 'false'
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	667 #set $wfdict['ptmshepherd.annotation-common'] = 'true'
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	668 #set $wfdict['ptmshepherd.annotation-glyco'] = 'false'
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	669 #set $wfdict['ptmshepherd.annotation-custom'] = 'false'
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	670 #elif $cxt.annotation.annotation_source == 'glyco'
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	671 #set $wfdict['ptmshepherd.annotation-unimod'] = 'false'
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	672 #set $wfdict['ptmshepherd.annotation-common'] = 'false'
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	673 #set $wfdict['ptmshepherd.annotation-glyco'] = 'true'
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	674 #set $wfdict['ptmshepherd.annotation-custom'] = 'false'
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	675 #elif $cxt.annotation.annotation_source == 'custom'
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	676 #set $wfdict['ptmshepherd.annotation-unimod'] = 'false'
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	677 #set $wfdict['ptmshepherd.annotation-common'] = 'false'
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	678 #set $wfdict['ptmshepherd.annotation-glyco'] = 'false'
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	679 #set $wfdict['ptmshepherd.annotation-custom'] = 'true'
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	680 #set $wfdict['ptmshepherd.annotation_file'] = $cxt.annotation.annotation_file
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	681 #end if
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	682 #set $cxt = $prfx.ptm_localization
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	683 #if $cxt.nions is not None
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	684 #set $wfdict['ptmshepherd.iontype_a'] = str('a' in $cxt.nions).lower()
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	685 #set $wfdict['ptmshepherd.iontype_b'] = str('b' in $cxt.nions).lower()
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	686 #set $wfdict['ptmshepherd.iontype_c'] = str('c' in $cxt.nions).lower()
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	687 #end if
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	688 #if $cxt.cions is not None
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	689 #set $wfdict['ptmshepherd.iontype_x'] = str('x' in $cxt.cions).lower()
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	690 #set $wfdict['ptmshepherd.iontype_y'] = str('y' in $cxt.cions).lower()
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	691 #set $wfdict['ptmshepherd.iontype_z'] = str('z' in $cxt.cions).lower()
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	692 #end if
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	693 #if $cxt.spectra_maxfragcharge != ''
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	694 #set $wfdict['ptmshepherd.spectra_maxfragcharge'] = $cxt.spectra_maxfragcharge
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	695 #end if
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	696 #if $cxt.localization_background != ''
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	697 #set $wfdict['ptmshepherd.localization_background'] = $cxt.localization_background
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	698 #end if
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	699 #set $wfdict['ptmshepherd.localization_allowed_res'] = $cxt.localization_allowed_res
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	700 #else
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	701 #set $wfdict['ptmshepherd.run-shepherd'] = 'false'
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	702 #end if
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	703 ]]></token>
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	704
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	705 <token name="@RE_EXCLUDEMOD@">@RE_AA@,@RE_FLOAT@</token>
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	706 <token name="@RE_EXCLUDEMODS@">@RE_EXCLUDEMOD@(;\s@RE_EXCLUDEMOD@)</token>
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	707
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	708 <!-- Label-free quantification options -->
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	709 <xml name="label_free_quantification" token_expand="false">
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	710 <section name="quant_ms1" expanded="@EXPAND@" title="Quant (MS1)">
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	711 <conditional name="label_free_quantification">
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	712 <param name="label_free_quantification_run" type="select" label="Perform Label-Free Quantification">
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	713 <option value="default" selected="true">Use workflow default</option>
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	714 <option value="no">No Label-Free Quantification</option>
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	715 <option value="ionquant">Run IonQuant</option>
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	716 <option value="freequant">Run FreeQuant</option>
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	717 </param>
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	718 <when value="default"/>
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	719 <when value="no"/>
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	720 <when value="ionquant">
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	721 <section name="ionquant" expanded="false" title="IonQuant Label-Free Quantification">
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	722 <param name="mbr" type="select" optional="true" label="Match between runs (MBR)" help="ionquant.mbr">
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	723 <option value="0">No</option>
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	724 <option value="1">Yes</option>
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	725 </param>
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	726 <param name="normalization" type="select" optional="true" label="Normalize" help="ionquant.normalization">
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	727 <option value="0">No</option>
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	728 <option value="1">Yes</option>
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	729 </param>
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	730 <section name="feature_detection" expanded="false" title="Feature detection">
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	731 <param name="mztol" type="integer" value="" optional="true" label="m/z tolerance in ppm" help="ionquant.mztol (default 10)"/>
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	732 <param name="rttol" type="float" value="" optional="true" label="RT tolerance (minutes)" help="ionquant.rttol (default 0.4)"/>
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	733 <param name="imtol" type="float" value="" optional="true" label="IM tolerance (1/k0)" help="ionquant.imtol (default 0.05)"/>
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	734 </section>
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	735 <section name="mbr" expanded="false" title="Match between runs (MBR)">
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	736 <param name="mbrrttol" type="float" value="" optional="true" label="MBR RT tolerance (minutes)" help="ionquant.mbrrttol"/>
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	737 <param name="mbrimtol" type="float" value="" optional="true" label="MBR IM tolerance (1/k0)" help="ionquant.mbrimtol"/>
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	738 <param name="mbrmincorr" type="float" value="" optional="true" label="MBR min correlation" help="ionquant.mbrmincorr"/>
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	739 <param name="mbrtoprun" type="integer" value="" optional="true" label="MBR top runs" help="ionquant.mbrtoprun"/>
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	740 <param name="ionfdr" type="float" value="" min="0.00001" max="1.0" optional="true" label="MBR ion FDR" help="ionquant.ionfdr"/>
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	741 <param name="peptidefdr" type="float" value="" min="0.00001" max="1.0" optional="true" label="MBR peptide FDR" help="ionquant.peptidefdr"/>
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	742 <param name="proteinfdr" type="float" value="" min="0.00001" max="1.0" optional="true" label="MBR protein FDR" help="ionquant.proteinfdr"/>
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	743 </section>
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	744 <section name="topn" expanded="false" title="Top-N options">
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	745 <param name="tp" type="integer" value="" min="0" optional="true" label="Top N ions" help="ionquant.tp"/>
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	746 <param name="minfreq" type="float" value="" min="0.0" max="1.0" optional="true" label="Min freq" help="ionquant.minfreq"/>
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	747 <param name="minexps" type="integer" value="" optional="true" label="Min exps" help="ionquant.minexps"/>
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	748 </section>
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	749 <conditional name="labeling_conditional">
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	750 <param name="labeling_option" type="select" label="Labeling option">
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	751 <option value="lfq" selected="true">LFQ</option>
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	752 <option value="labeling">Labeling</option>
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	753 </param>
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	754 <when value="lfq">
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	755 <section name="lfq" expanded="false" title="LFQ">
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	756 <param name="maxlfq" type="select" optional="true" label="MaxLFQ" help="ionquant.maxlfq">
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	757 <option value="0">No</option>
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	758 <option value="1">Yes</option>
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	759 </param>
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	760 <param name="minions" type="integer" value="" optional="true" label="Min ions" help="ionquant.minions"/>
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	761 </section>
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	762 </when>
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	763 <when value="labeling">
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	764 <section name="labeling" expanded="false" title="Labeling-based quant">
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	765 <param name="light" type="select" label="Light" help="ionquant.light">
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	766 <option value="" selected="true">none</option>
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	767 <option value="C463.2366">C463.2366</option>
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	768 <option value="C464.28596">C464.28596</option>
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	769 <option value="C561.3387">C561.3387</option>
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	770 <option value="K0;R0">K0;R0</option>
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	771 </param>
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	772 <param name="medium" type="select" label="Medium" help="ionquant.medium">
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	773 <option value="" selected="true">none</option>
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	774 <option value="K4.025107;R6.020129">K4.025107;R6.020129</option>
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	775 </param>
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	776 <param name="heavy" type="select" label="Heavy" help="ionquant.heavy">
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	777 <option value="" selected="true">none</option>
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	778 <option value="C467.2529">C467.2529</option>
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	779 <option value="C470.29977">C470.29977</option>
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	780 <option value="C567.3462">C567.3462</option>
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	781 <option value="K8.014199;R10.008269">K8.014199;R10.008269</option>
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	782 </param>
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	783 <param name="requantify" type="select" label="Re-quantify" help="ionquant.requantify">
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	784 <option value="0">No</option>
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	785 <option value="1" selected="true">Yes</option>
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	786 </param>
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	787 </section>
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	788 </when>
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	789 </conditional>
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	790 <section name="advanced" expanded="false" title="Advanced options">
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	791 <param name="excludemods" type="text" optional="true" label="excludemods" help="ionquant.excludemods">
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	792 <validator type="regex">^\s@RE_EXCLUDEMODS@\s$</validator>
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	793 </param>
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	794 <param name="minscans" type="integer" value="" min="0" optional="true" label="Min scans" help="ionquant.minscans"/>
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	795 <param name="minisotopes" type="integer" value="" min="1" max="3" optional="true" label="Min isotopes" help="ionquant.minisotopes"/>
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	796 <param name="locprob" type="float" value="" min="0.0" max="1.0" optional="true" label="Min site probability" help="ionquant.locprob"/>
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	797 <param name="writeindex" type="select" optional="true" label="Write index" help="ionquant.writeindex">
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	798 <option value="0">No</option>
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	799 <option value="1">Yes</option>
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	800 </param>
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	801 </section>
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	802 </section>
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	803 </when>
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	804 <when value="freequant">
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	805 <section name="freequant" expanded="false" title="IonQuant Label-Free Quantification">
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	806 <param name="rt_tol" type="float" value="" min="0" optional="true" label="RT Window (minutes)"/>
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	807 <param name="mz_tol" type="integer" value="" min="1" optional="true" label="m/z Window (ppm)"/>
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	808 </section>
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	809 </when>
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	810 </conditional>
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	811 </section>
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	812 </xml>
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	813
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	814 <!-- Set label-free quantification workflow options -->
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	815 <token name="@LABEL_FREE_QUANTIFICATION@"><![CDATA[
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	816 #set $prfx = $wf.quant_ms1.label_free_quantification
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	817 #if $prfx.label_free_quantification_run == 'no'
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	818 #set $wfdict['quantitation.run-label-free-quant'] = 'false'
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	819 #elif $prfx.label_free_quantification_run == 'ionquant'
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	820 #set $wfdict['quantitation.run-label-free-quant'] = 'false'
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	821 #set $wfdict['ionquant.run-ionquant'] = 'true'
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	822 #set $wfdict['freequant.run-freequant'] = 'false'
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	823 #set $cxt = $prfx.ionquant
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	824 #if $cxt.mbr != 'None'
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	825 #set $wfdict['ionquant.mbr'] = $cxt.mbr
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	826 #end if
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	827 #if $cxt.maxlfqbr is not None
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	828 #set $wfdict['ionquant.maxlfqbr'] = $cxt.maxlfqbr
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	829 #end if
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	830 #if $cxt.normalization != 'None'
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	831 #set $wfdict['ionquant.normalization'] = $cxt.normalization
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	832 #end if
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	833 #set $cxt = $prfx.ionquant.feature_detection
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	834 #if $cxt.mztol != ''
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	835 #set $wfdict['ionquant.mztol'] = $cxt.mztol
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	836 #end if
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	837 #if $cxt.rttol != ''
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	838 #set $wfdict['ionquant.rttol'] = $cxt.rttol
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	839 #end if
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	840 #if $cxt.imtol != ''
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	841 #set $wfdict['ionquant.imtol'] = $cxt.imtol
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	842 #end if
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	843 #set $cxt = $prfx.ionquant.mbr
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	844 #if $cxt.mbrrttol != ''
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	845 #set $wfdict['ionquant.mbrrttol'] = $cxt.mbrrttol
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	846 #end if
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	847 #if $cxt.mbrimtol != ''
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	848 #set $wfdict['ionquant.mbrimtol'] = $cxt.mbrimtol
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	849 #end if
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	850 #if $cxt.mbrmincorr != ''
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	851 #set $wfdict['ionquant.mbrmincorr'] = $cxt.mbrmincorr
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	852 #end if
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	853 #if $cxt.mbrtoprun != ''
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	854 #set $wfdict['ionquant.mbrtoprun'] = $cxt.mbrtoprun
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	855 #end if
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	856 #if $cxt.ionfdr != ''
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	857 #set $wfdict['ionquant.ionfdr'] = $cxt.ionfdr
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	858 #end if
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	859 #if $cxt.peptidefdr != ''
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	860 #set $wfdict['ionquant.peptidefdr'] = $cxt.peptidefdr
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	861 #end if
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	862 #if $cxt.proteinfdr != ''
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	863 #set $wfdict['ionquant.proteinfdr'] = $cxt.proteinfdr
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	864 #end if
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	865 #set $cxt = $prfx.ionquant.topn
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	866 #if $cxt.tp != ''
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	867 #set $wfdict['ionquant.tp'] = $cxt.tp
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	868 #end if
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	869 #if $cxt.minfreq != ''
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	870 #set $wfdict['ionquant.minfreq'] = $cxt.minfreq
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	871 #end if
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	872 #if $cxt.minexps != ''
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	873 #set $wfdict['ionquant.minexps'] = $cxt.minexps
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	874 #end if
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	875 #set $cxt = $prfx.ionquant.labeling_conditional
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	876 #if $cxt.labeling_option == 'labeling'
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	877 #set $cxt = $prfx.ionquant.labeling_conditional.labeling
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	878 #set $wfdict['ionquant.use-labeling'] = 'true'
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	879 #set $wfdict['ionquant.use-lfq'] = 'false'
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	880 #set $wfdict['ionquant.light'] = $cxt.labeling.light
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	881 #set $wfdict['ionquant.medium'] = $cxt.labeling.medium
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	882 #set $wfdict['ionquant.heavy'] = $cxt.labeling.heavy
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	883 #set $wfdict['ionquant.requantify'] = $cxt.labeling.requantify
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	884 #else
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	885 #set $cxt = $prfx.ionquant.labeling_conditional.lfq
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	886 #set $wfdict['ionquant.use-labeling'] = 'false'
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	887 #set $wfdict['ionquant.use-lfq'] = 'true'
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	888 #if $cxt.maxlfq != 'None'
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	889 #set $wfdict['ionquant.maxlfq'] = $cxt.maxlfq
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	890 #end if
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	891 #if $cxt.minions != ''
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	892 #set $wfdict['ionquant.minions'] = $cxt.minions
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	893 #end if
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	894 #end if
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	895 #set $cxt = $prfx.ionquant.advanced
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	896 #if $cxt.excludemods != ''
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	897 #set $wfdict['ionquant.excludemods'] = $cxt.excludemods
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	898 #end if
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	899 #if $cxt.minscans != ''
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	900 #set $wfdict['ionquant.minscans'] = $cxt.minscans
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	901 #end if
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	902 #if $cxt.minisotopes != ''
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	903 #set $wfdict['ionquant.minisotopes'] = $cxt.minisotopes
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	904 #end if
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	905 #if $cxt.locprob != ''
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	906 #set $wfdict['ionquant.locprob'] = $cxt.locprob
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	907 #end if
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	908 #if $cxt.writeindex != 'None'
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	909 #set $wfdict['ionquant.writeindex'] = $cxt.writeindex
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	910 #end if
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	911 #elif $prfx.label_free_quantification_run == 'freequant'
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	912 #set $wfdict['quantitation.run-label-free-quant'] = 'false'
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	913 #set $wfdict['ionquant.run-ionquant'] = 'false'
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	914 #set $wfdict['freequant.run-freequant'] = 'true'
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	915 #set $cxt = $prfx.freequant
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	916 #if $cxt.rt_tol != ''
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	917 #set $wfdict['freequant.rt-tol'] = $cxt.rt_tol
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	918 #end if
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	919 #if $cxt.mz_tol != ''
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	920 #set $wfdict['freequant.mz-tol'] = $cxt.mz_tol
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	921 #end if
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	922 #end if
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	923 ]]></token>
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	924
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	925 <!--
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	926 Isobaric quantification options
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	927
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	928 TMT-n uses the following n first labels from TMT-18
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	929 TMT-18 "126, 127N, 127C, 128N, 128C, 129N, 129C, 130N, 130C, 131N, 131C, 132N, 132C, 133N, 133C, 134N, 134C, 135N"
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	930 iTRAQ-4 "114, 115, 116, 117"
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	931 iTRAQ-8 "113, 114, 115, 116, 117, 118, 119, 121"
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	932 -->
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	933 <xml name="isobaric_quantification" token_expand="false" token_yes="true" token_no="false" token_plex="" token_level="2" token_virtual="false" token_pool="false" token_bridge="true">
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	934 <section name="quant_iso" expanded="@EXPAND@" title="Quant (Isobaric)">
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	935 <conditional name="isobaric_quantification">
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	936 <param name="isobaric_quantification_step" type="select" label="Perform Isobaric Quantification">
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	937 <option value="default">Use workflow defaults</option>
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	938 <option value="yes" selected="@YES@">yes</option>
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	939 <option value="no" selected="@NO@">no</option>
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	940 </param>
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	941 <when value="default"/>
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	942 <when value="no"/>
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	943 <when value="yes">
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	944 <section name="options" expanded="true" title="Isobaric Quantification">
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	945 <param name="quant_level" type="integer" value="@LEVEL@" min="1" max="3" label="MS level for the quantification"/>
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	946 <param name="channel_num" type="text" value="@PLEX@" optional="true" label="Number of channels">
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	947 <validator type="regex" message="">^TMT-\d?</validator>
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	948 </param>
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	949 <param name="ref_tag" type="select" label="Set Unique tag to identify reference channels">
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	950 <help>Virtual or specify a Reference sample tag: pool or Bridge</help>
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	951 <option value="Virtual" selected="@VIRTUAL@">Virtual - Add an artificial reference channel</option>
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	952 <option value="pool" selected="@POOL@">pool</option>
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	953 <option value="Bridge" selected="@BRIDGE@">Bridge</option>
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	954 </param>
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	955 <param name="groupby" type="select" optional="true" label="Group by level of summarization">
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	956 <option value="0">Gene level</option>
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	957 <option value="1">Protein</option>
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	958 <option value="2">Peptide sequence</option>
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	959 <option value="3">Multiple PTM sites</option>
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	960 <option value="4">Single PTM site</option>
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	961 <option value="-1">All</option>
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	962 </param>
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	963 <param name="log2transformed" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Log2 transform the intensity"/>
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	964 <param name="prot_norm" type="select" optional="true" label="normalization">
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	965 <option value="0">None</option>
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	966 <option value="1">MC (median centering)</option>
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	967 <option value="2">GN (median centering + variance scaling)</option>
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	968 <option value="-1">generate reports with all normalization options</option>
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	969 </param>
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	970 <conditional name="glycan_conditional">
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	971 <param name="use_glycan_composition" type="select" label="Perform Isobaric Quantification">
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	972 <option value="default">Use workflow defaults</option>
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	973 <option value="yes">yes</option>
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	974 </param>
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	975 <when value="default"/>
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	976 <when value="yes">
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	977 <param name="mod_tag" type="select" optional="true" label="PTM Mod tag">
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	978 <option value="none">none</option>
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	979 <option value="N-glyco">N-glyco</option>
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	980 <option value="C(239.1629)">C(239.1629)</option>
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	981 <option value="K(-187.1524)">K(-187.1524)</option>
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	982 <option value="K(-262.1966)">K(-262.1966)</option>
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	983 <option value="K(114.0429),K(-115.12)">K(114.0429),K(-115.12)</option>
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	984 <option value="S(79.9663),T(79.9663),Y(79.9663)">S(79.9663),T(79.9663),Y(79.9663)</option>
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	985 </param>
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	986 <param name="min_site_prob" type="float" min="-1.0" max="1.0" optional="true" label="Minimum site probability">
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	987 <help>site localization confidence thresholdr: -1 for global, 0 for search engine determined, above 0 for probability</help>
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	988 </param>
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	989 <param name="glyco_qval" type="integer" value="-1" optional="true" label="Glycan FDR filter"/>
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	990 </when>
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	991 </conditional>
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	992 <param name="unique_gene" type="select" optional="true" label="Peptide-Gene uniqueness">
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	993 <option value="0">0: allow all PSMs</option>
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	994 <option value="1">1: remove PSMs mapping to more than one GENE with evidence of expression in the dataset</option>
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	995 <option value="2">2: remove all PSMs mapping to more than one GENE in the fasta file</option>
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	996 </param>
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	997 <param name="unique_pep" type="select" optional="true" label="Peptide-Protein uniqueness">
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	998 <option value="false">unique plus razor peptides</option>
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	999 <option value="true">allow PSMs with unique peptides only</option>
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	1000 </param>
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	1001 <param name="min_pep_prob" type="float" min="0" max="1.0" optional="true" label="only use PSMs with a minimum probability score"
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	1002 help="minimum PSM probability threshold (in addition to FDR-based filtering by Philosopher)"/>
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	1003 <param name="min_purity" type="float" min="0" max="1.0" optional="true" label="ion purity threshold (default 0.5)"/>
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	1004 <param name="min_percent" type="float" min="0" max="1.0" optional="true" label="ignore the lower % PSMs based on their summed abundances"
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	1005 help="e.g. value of 0.05 indicates removal of PSMs with the summed TMT reporter ions intensity in the lowest 5% of all PSMs"/>
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	1006 <param name="max_pep_prob_thres" type="float" min="0" max="1.0" optional="true" label="threshold for maximum peptide probability"/>
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	1007 <param name="min_ntt" type="integer" min="0" max="2" optional="true" label="minimum allowed number of enzymatic termini"/>
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	1008 <param name="aggregation_method" type="select" optional="true" label="the aggregation method from the PSM level to the specified level">
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	1009 <option value="0">0: median</option>
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	1010 <option value="1">1: weighted-ratio</option>
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	1011 </param>
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	1012 <param name="prot_exclude" type="text" optional="true" label="Exclude proteins with specified tags at the beginning of the accession number"
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	1013 help="e.g. none: no exclusion; sp\|,tr\| : exclude protein with sp\| or tr\|">
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	1014 <validator type="regex">^(none\|[a-zA-Z]+\\|)$</validator>
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	1015 </param>
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	1016 <param name="best_psm" type="select" optional="true" label="keep the best PSM only (highest summed TMT intensity) among all redundant PSMs within the same LC-MS run">
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	1017 <option value="true">Yes</option>
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	1018 <option value="false">No</option>
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	1019 </param>
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	1020 <param name="psm_norm" type="select" optional="true" label="perform additional retention time-based normalization at the PSM level">
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	1021 <option value="false">No</option>
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	1022 <option value="true">Yes</option>
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	1023 </param>
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	1024 <param name="allow_overlabel" type="select" optional="true" label="allow PSMs with TMT on S (when overlabeling on S was allowed in the database search)">
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	1025 <option value="true">Yes</option>
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	1026 <option value="false">No</option>
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	1027 </param>
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	1028 <param name="allow_unlabeled" type="select" optional="true" label="allow PSMs without TMT tag or acetylation on the peptide n-terminus">
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	1029 <option value="true">Yes</option>
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	1030 <option value="false">No</option>
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	1031 </param>
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	1032 <param name="outlier_removal" type="select" optional="true" label="perform outlier removal">
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	1033 <option value="true">Yes</option>
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	1034 <option value="false">No</option>
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	1035 </param>
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	1036 <param name="ms1_int" type="select" optional="true" label="MS1 precursor ion intensity for reference sample abundance estimation">
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	1037 <option value="true">Yes - use MS1 precursor ion intensity</option>
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	1038 <option value="false">No - use MS2 reference intensity</option>
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	1039 </param>
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	1040 <param name="tolerance" type="integer" optional="true" label="Tolerance"/>
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	1041 <param name="top3_pep" type="select" optional="true" label="use top 3 most intense peptide ions as part of the reference sample abundance estimation">
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	1042 <option value="true">Yes</option>
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	1043 <option value="false">No</option>
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	1044 </param>
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	1045 <param name="print_RefInt" type="select" optional="true" label="print individual reference sample abundance estimates for each multiplex in the final reports">
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	1046 <option value="false">No</option>
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	1047 <option value="true">Yes</option>
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	1048 </param>
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	1049 </section>
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	1050 </when>
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	1051 </conditional>
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	1052 </section>
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	1053 </xml>
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	1054
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	1055 <!-- Set isobaric quantification workflow options -->
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	1056 <token name="@ISOBARIC_QUANTIFICATION@"><![CDATA[
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	1057 #set $prfx = $wf.quant_iso.isobaric_quantification
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	1058 #if $prfx.isobaric_quantification_step == 'no'
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	1059 #set $wfdict['tmtintegrator.run-tmtintegrator'] = 'false'
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	1060 #elif $prfx.isobaric_quantification_step == 'yes'
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	1061 #set $wfdict['tmtintegrator.run-tmtintegrator'] = 'true'
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	1062 #set $wfdict['tmtintegrator.dont-run-fq-lq'] = 'false'
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	1063 #set $cxt = $prfx.options
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	1064 #set $wfdict['tmtintegrator.quant_level'] = $cxt.quant_level
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	1065 #set $wfdict['tmtintegrator.channel_num'] = $cxt.channel_num
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	1066 #if $cxt.ref_tag == 'Virtual'
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	1067 #set $wfdict['tmtintegrator.add_Ref'] = -1
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	1068 #else
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	1069 #set $wfdict['tmtintegrator.add_Ref'] = 1
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	1070 #set $wfdict['tmtintegrator.ref_tag'] = $cxt.ref_tag
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	1071 #end if
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	1072 #if $cxt.groupby != ''
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	1073 #set $wfdict['tmtintegrator.groupby'] = $cxt.groupby
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	1074 #end if
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	1075 #set $wfdict['tmtintegrator.log2transformed'] = $cxt.log2transformed
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	1076 #if $cxt.prot_norm != 'None'
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	1077 #set $wfdict['tmtintegrator.prot_norm'] = $cxt.prot_norm
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	1078 #end if
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	1079 #if $cxt.glycan_conditional.use_glycan_composition == 'yes'
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	1080 #if $cxt.glycan_conditional.mod_tag != 'None'
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	1081 #set $wfdict['tmtintegrator.mod_tag'] = $cxt.glycan_conditional.mod_tag
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	1082 #end if
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	1083 #if $cxt.glycan_conditional.min_site_prob != ''
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	1084 #set $wfdict['tmtintegrator.min_site_prob'] = $cxt.glycan_conditional.min_site_prob
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	1085 #end if
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	1086 #if $cxt.glycan_conditional.glyco_qval != ''
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	1087 #set $wfdict['tmtintegrator.glyco_qval'] = $cxt.glycan_conditional.glyco_qval
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	1088 #end if
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	1089 #end if
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	1090 #if $cxt.unique_gene != 'None'
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	1091 #set $wfdict['tmtintegrator.unique_gene'] = $cxt.unique_gene
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	1092 #end if
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	1093 #if $cxt.unique_pep != 'None'
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	1094 #set $wfdict['tmtintegrator.unique_pep'] = $cxt.unique_pep
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	1095 #end if
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	1096 #if $cxt.min_pep_prob != ''
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	1097 #set $wfdict['tmtintegrator.min_pep_prob'] = $cxt.min_pep_prob
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	1098 #end if
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	1099 #if $cxt.min_purity != ''
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	1100 #set $wfdict['tmtintegrator.min_purity'] = $cxt.min_purity
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	1101 #end if
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	1102 #if $cxt.min_percent != ''
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	1103 #set $wfdict['tmtintegrator.min_percent'] = $cxt.min_percent
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	1104 #end if
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	1105 #if $cxt.max_pep_prob_thres != ''
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	1106 #set $wfdict['tmtintegrator.max_pep_prob_thres'] = $cxt.max_pep_prob_thres
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	1107 #end if
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	1108 #if $cxt.min_ntt != ''
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	1109 #set $wfdict['tmtintegrator.min_ntt'] = $cxt.min_ntt
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	1110 #end if
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	1111 #if $cxt.aggregation_method != 'None'
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	1112 #set $wfdict['tmtintegrator.aggregation_method'] = $cxt.aggregation_method
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	1113 #end if
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	1114 #if $cxt.prot_exclude != ''
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	1115 #set $wfdict['tmtintegrator.prot_exclude'] = $cxt.prot_exclude
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	1116 #end if
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	1117 #if $cxt.best_psm != 'None'
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	1118 #set $wfdict['tmtintegrator.best_psm'] = $cxt.best_psm
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	1119 #end if
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	1120 #if $cxt.psm_norm != 'None'
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	1121 #set $wfdict['tmtintegrator.psm_norm'] = $cxt.psm_norm
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	1122 #end if
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	1123 #if $cxt.allow_overlabel != 'None'
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	1124 #set $wfdict['tmtintegrator.allow_overlabel'] = $cxt.allow_overlabel
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	1125 #end if
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	1126 #if $cxt.allow_unlabeled != 'None'
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	1127 #set $wfdict['tmtintegrator.allow_unlabeled'] = $cxt.allow_unlabeled
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	1128 #end if
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	1129 #if $cxt.outlier_removal != 'None'
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	1130 #set $wfdict['tmtintegrator.outlier_removal'] = $cxt.outlier_removal
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	1131 #end if
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	1132 #if $cxt.ms1_int != 'None'
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	1133 #set $wfdict['tmtintegrator.ms1_int'] = $cxt.ms1_int
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	1134 #end if
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	1135 #if $cxt.tolerance != ''
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	1136 #set $wfdict['tmtintegrator.tolerance'] = $cxt.tolerance
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	1137 #end if
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	1138 #if $cxt.top3_pep != 'None'
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	1139 #set $wfdict['tmtintegrator.top3_pep'] = $cxt.top3_pep
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	1140 #end if
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	1141 #if $cxt.print_RefInt != 'None'
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	1142 #set $wfdict['tmtintegrator.print_RefInt'] = $cxt.print_RefInt
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	1143 #end if
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	1144 #end if
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	1145 ]]></token>
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	1146
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	1147 <!-- License agreement texts. -->
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	1148 <token name="@MSFRAGGER_LICENSE_AGREEMENT@">
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	1149 MSFragger is available freely for academic research and educational purposes only. I have read the ACADEMIC license for MSFragger software: http://msfragger-upgrader.nesvilab.org/upgrader/MSFragger-LICENSE.pdf. This license provides with non-exclusive, non-transferable right to use MSFragger solely for academic research, non-commercial or educational purposes. I agree to be subject to the terms and conditions of this license. I understand that to use MSFragger for other purposes requires a commercial license from the University of Michigan Office of Tech Transfer.
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	1150 </token>
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	1151 <token name="@IONQUANT_LICENSE_AGREEMENT@">
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	1152 IonQuant is available freely for academic research and educational purposes only. I have read the ACADEMIC license for MSFragger software: https://msfragger.arsci.com/ionquant/IonQuant%20Academic%20Use%20License%2005162022.pdf
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	1153 </token>
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	1154 <token name="@THERMO_RAW_READER_LICENSE_AGREEMENT@">
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	1155 I agree to the terms of Thermo (c) Raw File Reader License Agreement: http://msfragger-upgrader.nesvilab.org/upgrader/RawFileRdr_License_Agreement_RevA.pdf
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	1156 </token>
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	1157 <token name="@BRUKER_LICENSE_AGREEMENT@">
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	1158 I agree to the terms of Bruker SDK library distribution conditions: http://msfragger-upgrader.nesvilab.org/upgrader/redist.txt
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	1159 </token>
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	1160 <token name="@LICENSE_AGREEMENTS@">
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	1161 @MSFRAGGER_LICENSE_AGREEMENT@
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	1162 @IONQUANT_LICENSE_AGREEMENT@
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	1163 @THERMO_RAW_READER_LICENSE_AGREEMENT@
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	1164 @BRUKER_LICENSE_AGREEMENT@
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	1165 </token>
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	1166
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	1167 <!-- User must check box agreeing to MSFragger license agreement. -->
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	1168 <xml name="license_agreements">
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	1169 <param name="license_agreements" type="boolean" truevalue="true" falsevalue="false" checked="false" label="I understand that these tools, including MSFragger, IonQuant, Bruker, and Thermo Raw File Reader, are available freely for academic research and educational purposes only, and agree to the following terms.">
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	1170 <validator type="expression" message="You must agree to the MSFragger license!">value == True</validator>
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	1171 <help><![CDATA[
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	1172 @MSFRAGGER_LICENSE_AGREEMENT@
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	1173 <br/><br/>
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	1174 @IONQUANT_LICENSE_AGREEMENT@
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	1175 <br/><br/>
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	1176 @THERMO_RAW_READER_LICENSE_AGREEMENT@
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	1177 <br/><br/>
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	1178 @BRUKER_LICENSE_AGREEMENT@
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	1179 ]]></help>
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	1180 </param>
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	1181 </xml>
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	1182
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	1183 <xml name="citations">
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	1184 <citations>
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	1185 <citation type="doi">10.1038/s41592-020-0912-y</citation>
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	1186 <citation type="doi">10.1038/nmeth.4256</citation>
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	1187 <citation type="doi">10.1038/s41467-020-17921-y</citation>
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	1188 <citation type="doi">10.1038/s41592-020-0967-9</citation>
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	1189 <citation type="doi">10.1021/acs.jproteome.0c00119</citation>
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	1190 <citation type="doi">10.1074/mcp.TIR120.002216</citation>
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	1191 <citation type="doi">10.1074/mcp.TIR120.002048</citation>
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	1192 <citation type="doi">10.1016/j.mcpro.2021.100077</citation>
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	1193 <citation type="doi">10.1021/acs.jproteome.0c00544</citation>
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	1194 <citation type="doi">10.1038/nmeth.3255</citation>
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	1195 <yield />
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	1196 </citations>
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	1197 </xml>
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f galaxyp parents: diff changeset	1198 </macros>

Mercurial > repos > galaxyp > fragpipe

annotate macros.xml @ 1:dc5de2ea607e draft