msstats: msstats.xml annotate

annotate msstats.xml @ 2:52ac6fde9a5b draft

"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 414edbbd89f9bc83b81289e409c9b688c8c1e40f"

author	galaxyp
date	Fri, 14 Aug 2020 12:19:14 -0400
parents	3e2606fa85bf
children	8212e342e482

rev	line source
1 3e2606fa85bf "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit fa543ac667f63409bfb2e28fd6c711e74d828a79" galaxyp parents: 0 diff changeset	1 <tool id="msstats" name="MSstats" version="@VERSION@.0">
0 80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	2 <description>statistical relative protein significance analysis in DDA, SRM and DIA Mass Spectrometry</description>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	3 <macros>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	4 <token name="@VERSION@">3.20.1</token>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	5 <xml name="useUniquePeptide">
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	6 <param name="useUniquePeptide" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="true" label="remove peptides that are assigned for more than one proteins" help="We assume to use unique peptide for each protein"/>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	7 </xml>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	8 <xml name="summaryforMultipleRows">
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	9 <param name="summaryforMultipleRows" type="select" label="Summary for MultipleRows" help="summaryforMultipleRows - when there are multiple measurements for certain feature and certain run, use highest or sum of all">
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	10 <option value="max" selected="true">max</option>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	11 <option value="sum">sum</option>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	12 </param>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	13 </xml>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	14 <xml name="fewMeasurements">
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	15 <param name="fewMeasurements" type="select" label="Remove the features that have 1 or 2 measurements across runs" help="(fewMeasurements)">
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	16 <option value="remove" selected="true">remove</option>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	17 <option value="keep">keep</option>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	18 </param>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	19 </xml>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	20 <xml name="removeProtein_with1Peptide">
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	21 <param name="removeProtein_with1Peptide" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="false" label="Remove the proteins which have only 1 peptide and charge"/>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	22 </xml>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	23
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	24 </macros>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	25 <requirements>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	26 <requirement type="package" version="@VERSION@">bioconductor-msstats</requirement>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	27 </requirements>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	28 <command detect_errors="exit_code"><![CDATA[
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	29 cat '$msstats_script' > '$r_script' &&
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	30 Rscript '$msstats_script'
1 3e2606fa85bf "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit fa543ac667f63409bfb2e28fd6c711e74d828a79" galaxyp parents: 0 diff changeset	31 && cat msstats*.log > '$log'
0 80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	32 ]]></command>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	33 <configfiles>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	34 <configfile name="msstats_script"><![CDATA[
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	35 library('MSstats', warn.conflicts = F, quietly = T, verbose = F)
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	36
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	37 #if $input.input_src == 'MSstats'
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	38
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	39 #if $input.msstats_input.is_of_type('csv')
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	40 raw <- read.csv("$input.msstats_input")
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	41 #else
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	42 raw <- read.table("$input.msstats_input", sep="\t", header=TRUE)
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	43 #end if
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	44
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	45 #elif $input.input_src == 'MaxQuant'
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	46 \# Read in MaxQuant files
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	47 mq_evidence <- read.table("$input.evidence", sep="\t", header=TRUE)
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	48
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	49 mq_proteinGroups <- read.table("$input.proteinGroups", sep="\t", header=TRUE)
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	50
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	51 \# Read in annotation including condition and biological replicates per run.
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	52 \# Users should make this annotation file. It is not the output from MaxQuant.
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	53 #if $input.annotation.is_of_type('csv')
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	54 annot <- read.csv("$input.annotation", header=TRUE)
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	55 #else
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	56 annot <- read.table("$input.annotation", sep="\t", header=TRUE)
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	57 #end if
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	58
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	59 raw <- MaxQtoMSstatsFormat(evidence=mq_evidence,
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	60 proteinGroups=mq_proteinGroups,
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	61 annotation=annot,
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	62 proteinID="$input.proteinID",
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	63 useUniquePeptide=$input.input_options.useUniquePeptide,
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	64 summaryforMultipleRows=$input.input_options.summaryforMultipleRows,
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	65 fewMeasurements="$input.input_options.fewMeasurements",
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	66 removeMpeptides=$input.input_options.removeMpeptides,
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	67 removeOxidationMpeptides=$input.input_options.removeOxidationMpeptides,
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	68 removeProtein_with1Peptide=$input.input_options.removeProtein_with1Peptide)
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	69
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	70 #elif $input.input_src == 'OpenMS'
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	71
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	72 #if $input.evidence.is_of_type('csv')
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	73 input <- read.csv("$input.evidence", header=TRUE)
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	74 #else
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	75 input <- read.table("$input.evidence", sep="\t", header=TRUE)
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	76 #end if
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	77 #if $input.annotation.is_of_type('csv')
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	78 annot <- read.csv("$input.annotation", header=TRUE)
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	79 #else
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	80 annot <- read.table("$input.annotation", sep="\t", header=TRUE)
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	81 #end if
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	82
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	83 raw <- OpenMStoMSstatsFormat(input,
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	84 annotation=annot,
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	85 useUniquePeptide=$input.input_options.useUniquePeptide,
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	86 summaryforMultipleRows=$input.input_options.summaryforMultipleRows,
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	87 fewMeasurements="$input.input_options.fewMeasurements",
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	88 removeProtein_with1Peptide=$input.input_options.removeProtein_with1Peptide)
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	89
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	90 #elif $input.input_src == 'OpenSWATH'
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	91
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	92 #if $input.evidence.is_of_type('csv')
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	93 input <- read.csv("$input.evidence", header=TRUE)
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	94 #else
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	95 input <- read.table("$input.evidence", sep="\t", header=TRUE)
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	96 #end if
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	97 #if $input.annotation.is_of_type('csv')
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	98 annot <- read.csv("$input.annotation", header=TRUE)
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	99 #else
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	100 annot <- read.table("$input.annotation", sep="\t", header=TRUE)
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	101 #end if
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	102
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	103 raw <- OpenSWATHtoMSstatsFormat(input,
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	104 annotation=annot,
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	105 filter_with_mscore=$input.input_options.filter_with_mscore,
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	106 mscore_cutoff=$input.input_options.mscore_cutoff,
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	107 useUniquePeptide=$input.input_options.useUniquePeptide,
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	108 fewMeasurements="$input.input_options.fewMeasurements",
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	109 removeProtein_with1Feature=$input.input_options.removeProtein_with1Feature,
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	110 summaryforMultipleRows=$input.input_options.summaryforMultipleRows)
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	111
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	112 #end if
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	113
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	114 processed_data <- dataProcess(raw,
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	115 logTrans=$dp_options.logTrans,
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	116 normalization="$dp_options.norm.normalization",
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	117 #if $dp_options.norm.normalization == 'globalStandards'
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	118 nameStandards=c($dp_options.norm.nameStandards),
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	119 #end if
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	120 ## address=$dp_options.address,
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	121 fillIncompleteRows=$dp_options.fillIncompleteRows,
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	122 featureSubset="$dp_options.features.featureSubset",
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	123 #if $dp_options.features.featureSubset == 'topN'
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	124 n_top_feature=$dp_options.features.n_top_feature,
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	125 #end if
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	126 #if $dp_options.features.featureSubset == 'highQuality'
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	127 remove_uninformative_feature_outlier=$dp_options.features.remove_uninformative_feature_outlier,
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	128 #end if
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	129 summaryMethod="$dp_options.summarize.summaryMethod",
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	130 #if $dp_options.summarize.summaryMethod == 'TMP'
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	131 MBimpute=$dp_options.summarize.MBimpute,
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	132 remove50missing=$dp_options.summarize.remove50missing,
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	133 #end if
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	134 #if $dp_options.summarize.summaryMethod == 'linear'
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	135 equalFeatureVar=$dp_options.summarize.equalFeatureVar,
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	136 #end if
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	137 #if $dp_options.censoredInt == 'NULL'
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	138 censoredInt=NULL,
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	139 #else
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	140 censoredInt="$dp_options.censoredInt",
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	141 #end if
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	142 cutoffCensored="$dp_options.cutoffCensored",
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	143 maxQuantileforCensored=$dp_options.maxQuantileforCensored,
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	144 clusters=NULL)
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	145
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	146 #if 'processed_data' in $selected_outputs
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	147 write.table(processed_data\$ProcessedData, "ProcessedData.tsv", sep = "\t", quote = F, row.names = F, dec = ".")
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	148 #end if
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	149 #if 'runlevel_data' in $selected_outputs
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	150 write.table(processed_data\$RunlevelData, "RunlevelData.tsv", sep = "\t", quote = F, row.names = F, dec = ".")
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	151 #end if
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	152
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	153 #if 'qcplot' in $selected_outputs
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	154 dataProcessPlots(data = processed_data, type="QCplot", ylimUp=35,
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	155 width=5, height=5, address="MSStats_only_")
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	156 #end if
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	157
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	158 #if 'profile_plot' in $selected_outputs
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	159 dataProcessPlots(data = processed_data, type="ProfilePlot", ylimUp=35, featureName="NA", width=5, height=5, address="MSStats_only_")
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	160 #end if
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	161
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	162 #if 'condition_plot' in $selected_outputs
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	163 dataProcessPlots(data = processed_data, type="ConditionPlot", width=5, height=5, address="MSStats_only_")
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	164 #end if
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	165
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	166 ## Quantifiaction
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	167 #if 'quant_sample_matrix' in $selected_outputs
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	168 sampleQuantMatrix <- quantification(processed_data, type="Sample")
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	169 write.table(sampleQuantMatrix, "SampleQuantificationMatrix.tsv", sep = "\t", quote = F, row.names = F, dec = ".")
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	170 #end if
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	171
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	172 #if 'quant_sample_long' in $selected_outputs
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	173 sampleQuantLong <- quantification(processed_data, type="Sample", format="long")
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	174 write.table(sampleQuantLong, "SampleQuantificationLong.tsv", sep = "\t", quote = F, row.names = F, dec = ".")
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	175 #end if
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	176
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	177 #if 'quant_group_matrix' in $selected_outputs
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	178 groupQuantMatrix <- quantification(processed_data, type="Group")
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	179 write.table(groupQuantMatrix, "GroupQuantificationMatrix.tsv", sep = "\t", quote = F, row.names = F, dec = ".")
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	180 #end if
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	181
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	182 #if 'quant_group_long' in $selected_outputs
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	183 groupQuantLong <- quantification(processed_data, type="Group", format="long")
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	184 write.table(groupQuantLong, "GroupQuantificationLong.tsv", sep = "\t", quote = F, row.names = F, dec = ".")
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	185 #end if
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	186
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	187 ## Group Comparison
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	188 #if $group.group_comparison == 'yes'
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	189 \# Group Comparison
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	190 #if $group.comparison_matrix.is_of_type('csv')
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	191 comp_matrix <- read.csv("$group.comparison_matrix", header=TRUE)
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	192 #else
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	193 comp_matrix <- read.table("$group.comparison_matrix", sep="\t", header=TRUE)
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	194 #end if
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	195
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	196 ## first columns contains comparison names, use as row name
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	197 comparison <- comp_matrix[,-1]
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	198 row.names(comparison) <- as.character(comp_matrix[,1])
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	199 ## order of conditions has to be the same as they appear in the levels function
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	200 comparison <- as.matrix(comparison[levels(processed_data\$ProcessedData\$GROUP_ORIGINAL)])
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	201
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	202 ## perform group comparison
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	203 comparisons <- groupComparison(contrast.matrix = comparison, data = processed_data)
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	204
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	205 print(comparisons\$fittedmodel)
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	206 #if 'fittedmodel' in $group.select_outputs
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	207 capture.output(print(comparisons\$fittedmodel), file="ComparisonFittedModel.txt")
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	208 #end if
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	209
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	210
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	211 #if 'comparison_result' in $group.select_outputs
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	212 write.table(comparisons\$ComparisonResult, "ComparisonResult.tsv", sep = "\t", quote = F, row.names = F, dec = ".")
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	213 #end if
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	214
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	215 #if 'model_qc' in $group.select_outputs
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	216 write.table(comparisons\$ModelQC, "ModelQC.tsv", sep = "\t", quote = F, row.names = F, dec = ".")
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	217 #end if
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	218
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	219 ## Visualizations:
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	220
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	221 #if 'qqplot' in $group.select_outputs
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	222 \# normal quantile-quantile plots
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	223 modelBasedQCPlots(data=comparisons, type="QQPlots",
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	224 width=5, height=5, address="MSStats_group_")
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	225 #end if
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	226
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	227 #if 'residualplot' in $group.select_outputs
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	228 \# residual plots
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	229 modelBasedQCPlots(data=comparisons, type="ResidualPlots",
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	230 width=5, height=5, address="MSStats_group_")
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	231 #end if
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	232
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	233 #if 'volcanoplot' in $group.select_outputs
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	234 \# volcano plot
2 52ac6fde9a5b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 414edbbd89f9bc83b81289e409c9b688c8c1e40f" galaxyp parents: 1 diff changeset	235 groupComparisonPlots(data = comparisons\$ComparisonResult, type = 'VolcanoPlot',ProteinName=FALSE,
0 80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	236 width=5, height=5, address="MSStats_group_")
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	237 #end if
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	238
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	239 #if 'heatmap' in $group.select_outputs
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	240 \# heatmap - works only for more than 1 comparison
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	241 if (nrow(comparison)>1)
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	242 {
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	243 groupComparisonPlots(data = comparisons\$ComparisonResult, type = 'Heatmap', address="MSStats_group_")
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	244 }
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	245 #end if
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	246
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	247 #if 'comparisonplot' in $group.select_outputs
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	248 \#comparison
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	249 groupComparisonPlots(data=comparisons\$ComparisonResult, type="ComparisonPlot",
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	250 width=5, height=5, address="MSStats_group_")
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	251 #end if
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	252
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	253 #end if
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	254 ]]></configfile>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	255 </configfiles>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	256 <inputs>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	257 <conditional name="input">
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	258 <param name="input_src" type="select" label="input source">
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	259 <option value="MSstats">MStats 10 column format</option>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	260 <option value="MaxQuant">MaxQuant</option>
1 3e2606fa85bf "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit fa543ac667f63409bfb2e28fd6c711e74d828a79" galaxyp parents: 0 diff changeset	261 <!--
0 80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	262 <option value="OpenMS">OpenMS</option>
1 3e2606fa85bf "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit fa543ac667f63409bfb2e28fd6c711e74d828a79" galaxyp parents: 0 diff changeset	263 -->
0 80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	264 <option value="OpenSWATH">OpenSWATH</option>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	265 </param>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	266 <when value="MSstats">
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	267 <param name="msstats_input" type="data" format="tabular,csv" label="MSstats 10-column input"/>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	268 </when>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	269 <when value="MaxQuant">
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	270 <param name="evidence" type="data" format="tabular,csv" label="evidence.txt - feature-level data"/>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	271 <param name="annotation" type="data" format="tabular,csv" label="annotation.txt data which includes Raw.file, Condition, BioReplicate, Run, IsotopeLabelType information"/>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	272 <param name="proteinGroups" type="data" format="tabular,csv" label="proteinGroups.txt" help="It needs to matching protein group ID. If proteinGroups=NULL, use 'Proteins' column in 'evidence.txt'"/>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	273 <param name="proteinID" type="select" label="Select Protein ID in evidence.txt">
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	274 <option value="Proteins">Protein column</option>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	275 <option value="Leading.razor.protein">Leading razor protein column</option>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	276 </param>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	277 <section name="input_options" title="MaxQtoMSstatsFormat Options" expanded="false">
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	278 <expand macro="useUniquePeptide"/>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	279 <expand macro="summaryforMultipleRows"/>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	280 <expand macro="fewMeasurements"/>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	281 <param name="removeMpeptides" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="true" label="Remove the peptides including 'M' sequence"/>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	282 <param name="removeOxidationMpeptides" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="true" label="Remove the peptides including Oxidized 'M' sequence"/>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	283 <expand macro="removeProtein_with1Peptide"/>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	284 </section>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	285 </when>
1 3e2606fa85bf "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit fa543ac667f63409bfb2e28fd6c711e74d828a79" galaxyp parents: 0 diff changeset	286 <!--
0 80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	287 <when value="OpenMS">
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	288 <param name="evidence" type="data" format="tabular,csv" label="OpenSWATH_input"/>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	289 <param name="annotation" type="data" format="tabular,csv" label="OpenSWATH_annotation"/>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	290 <section name="input_options" title="MaxQtoMSstatsFormat Options" expanded="false">
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	291 <expand macro="useUniquePeptide"/>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	292 <expand macro="summaryforMultipleRows"/>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	293 <expand macro="fewMeasurements"/>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	294 <expand macro="removeProtein_with1Peptide"/>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	295 </section>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	296 </when>
1 3e2606fa85bf "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit fa543ac667f63409bfb2e28fd6c711e74d828a79" galaxyp parents: 0 diff changeset	297 -->
0 80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	298 <when value="OpenSWATH">
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	299 <param name="evidence" type="data" format="tabular,csv" label="OpenSWATH_input"/>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	300 <param name="annotation" type="data" format="tabular,csv" label="OpenSWATH_annotation"/>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	301 <section name="input_options" title="OpenSWATHtoMSstatsFormat Options" expanded="false">
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	302 <param name="filter_with_mscore" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="true" label="Remove the peptides including 'M' sequence"/>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	303 <param name="mscore_cutoff" type="float" value="0.01" min="0" max="1.0" label="mscore_cutoff"/>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	304 <expand macro="useUniquePeptide"/>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	305 <expand macro="fewMeasurements"/>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	306 <expand macro="summaryforMultipleRows"/>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	307 <param name="removeProtein_with1Feature" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="false" label="Remove the proteins which have only 1 peptide and charge"/>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	308 </section>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	309 </when>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	310 </conditional>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	311 <section name="dp_options" title="dataProcess Options" expanded="false">
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	312 <param name="logTrans" type="select" label="Log-transform Variable ABUNDANCE with base:" help="(logTrans)">
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	313 <option value="2" selected="true">2</option>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	314 <option value="10">10</option>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	315 </param>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	316 <conditional name="norm">
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	317 <param name="normalization" type="select" label="Normalization to remove systematic bias between MS runs">
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	318 <option value="equalizeMedians" selected="true">equalizeMedians - represents constant normalization</option>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	319 <option value="quantile">quantile - quantile normalization</option>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	320 <option value="globalStandards">globalStandards - normalization with global standards proteins</option>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	321 <option value="FALSE">no normalization is performed</option>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	322 </param>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	323 <when value="equalizeMedians"/>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	324 <when value="quantile"/>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	325 <when value="globalStandards">
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	326 <param name="nameStandards" type="text" value="" label="global standard peptide names">
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	327 <help>peptide names should be double-quoted and separated by commas</help>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	328 <validator type="empty_field" />
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	329 <validator type="regex" message="double-quoted names separated by commas"><![CDATA[^".+"(,".+")*$]]></validator>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	330 </param>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	331 </when>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	332 <when value="FALSE"/>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	333 </conditional>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	334 <param name="fillIncompleteRows" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="true" label="Fill Incomplete Rows" help=" If the input dataset has incomplete rows, TRUE (default) adds the rows with intensity value=NA for missing peaks. FALSE reports error message with list of features which have incomplete rows"/>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	335 <conditional name="features">
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	336 <param name="featureSubset" type="select" label="Features to use">
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	337 <option value="all" selected="true">Use all features that the data set has</option>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	338 <option value="top3">Use the top 3 features which have highest average of log2(intensity) across runs</option>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	339 <option value="topN">Use the top N features which have highest average of log2(intensity) across runs</option>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	340 <option value="highQuality">Flag uninformative feature and outliers</option>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	341 </param>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	342 <when value="all"/>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	343 <when value="top3"/>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	344 <when value="topN">
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	345 <param name="n_top_feature" type="integer" value="3" min="1" label="The number of top features for featureSubset"/>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	346 </when>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	347 <when value="highQuality">
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	348 <param name="remove_uninformative_feature_outlier" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="false" label="Remove features flagged with Uninformative feature_quality"/>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	349 </when>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	350 </conditional>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	351 <conditional name="summarize">
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	352 <param name="summaryMethod" type="select" label="Summary Method">
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	353 <option value="TMP" selected="true">TMP - Tukey's median polish</option>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	354 <option value="linear" selected="true">linear - linear mixed model</option>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	355 </param>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	356 <when value="TMP">
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	357 <param name="MBimpute" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="true" label="Impute Missing Values 'NA' or '0' (depending on censoredInt option) by Accelated failure model" help="(MBimpute) TRUE - inserts 'NA' or '0' (depending on censoredInt option), . FALSE uses the values assigned by cutoffCensored"/>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	358 <param name="remove50missing" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="false" label="Remove runs which have more than 50% missing values"/>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	359 </when>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	360 <when value="linear">
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	361 <param name="equalFeatureVar" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="false" label="Account for heterogeneous variation among intensities from different features" help="(equalFeatureVar) TRUE assumes equal variance among intensities from features. FALSE means that we cannot assume equal variance among intensities from features, then we will account for heterogeneous variation from different features"/>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	362 </when>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	363 </conditional>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	364 <param name="censoredInt" type="select" label="Missing values to censor">
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	365 <help>The output from Skyline and Progenesis should use '0'</help>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	366 <option value="NA" selected="true">Assume that all 'NA's in 'Intensity' column are censored</option>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	367 <option value="0">Use zero intensities '0' as censored intensity</option>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	368 <option value="NULL">Assume all NA intensites are randomly missing</option>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	369 </param>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	370 <param name="cutoffCensored" type="select" label="Cutoff value for censoring">
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	371 <option value="minFeature" selected="true">minimum value for each feature</option>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	372 <option value="minRun">minimum value for each run</option>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	373 <option value="minFeatureNRun">smallest between minimum value of corresponding feature and minimum value of corresponding run</option>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	374 </param>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	375 <param name="maxQuantileforCensored" type="float" value="0.999" min="0.75" max="1.0" label="Maximum quantile for deciding censored missing values"/>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	376 </section>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	377 <param name="selected_outputs" type="select" multiple="true" optional="false" label="Select outputs">
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	378 <option value="log" selected="true">MSstats log</option>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	379 <option value="r_script" selected="false">MSstats Rscript</option>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	380 <option value="processed_data" selected="true">MSstats ProcessedData</option>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	381 <option value="runlevel_data" selected="false">MSstats RunlevelData</option>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	382 <option value="qcplot" selected="true">MSstats QCPlot.pdf</option>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	383 <option value="profile_plot" selected="false">MSstats ProfilePlot.pdf</option>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	384 <option value="profile_wsum_plot" selected="false">MSstats ProfilePlot_wSummarization.pdf</option>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	385 <option value="condition_plot" selected="false">MSstats ConditionPlot.pdf</option>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	386 <option value="quant_sample_matrix" selected="false">Sample Quantification Matrix Table</option>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	387 <option value="quant_sample_long" selected="false">Sample Quantification Long Table</option>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	388 <option value="quant_group_matrix" selected="true">Group Quantification Matrix Table</option>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	389 <option value="quant_group_long" selected="false">Group Quantification Long Table</option>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	390 </param>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	391
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	392 <conditional name="group">
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	393 <param name="group_comparison" type="select" label="Compare Groups">
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	394 <option value="no">No</option>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	395 <option value="yes">Yes</option>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	396 </param>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	397 <when value="no"/>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	398 <when value="yes">
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	399 <param name="comparison_matrix" type="data" format="tabular,csv" label="Comparison Matrix"/>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	400 <param name="select_outputs" type="select" multiple="true" label="Select outputs">
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	401 <help>Heatmap requires more than one comparison</help>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	402 <option value="fittedmodel" selected="true">MSstats ComparisonFittedModel.txt</option>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	403 <option value="comparison_result" selected="true">MSstats ComparisonResult.tsv</option>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	404 <option value="model_qc" selected="false">MSstats ModelQC.tsv</option>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	405 <option value="qqplot" selected="false">MSstats QQPlot.pdf</option>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	406 <option value="residualplot" selected="false">MSstats ResidualPlot.pdf</option>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	407 <option value="volcanoplot" selected="true">MSstats VolcanoPlot.pdf</option>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	408 <option value="heatmap" selected="false">MSstats Heatmap.pdf</option>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	409 <option value="comparisonplot" selected="true">MSstats ComparisonPlot.pdf</option>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	410 </param>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	411 </when>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	412 </conditional>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	413 </inputs>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	414
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	415 <outputs>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	416 <data name="log" format="txt" label="MSstats log">
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	417 <filter>'log' in selected_outputs</filter>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	418 </data>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	419 <data name="r_script" format="txt" label="MSstats Rscript">
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	420 <filter>'r_script' in selected_outputs</filter>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	421 </data>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	422 <data name="processed_data" format="tabular" label="MSstats ProcessedData" from_work_dir="ProcessedData.tsv">
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	423 <filter>'processed_data' in selected_outputs</filter>
1 3e2606fa85bf "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit fa543ac667f63409bfb2e28fd6c711e74d828a79" galaxyp parents: 0 diff changeset	424 <actions>
3e2606fa85bf "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit fa543ac667f63409bfb2e28fd6c711e74d828a79" galaxyp parents: 0 diff changeset	425 <action name="column_names" type="metadata" default="PROTEIN,PEPTIDE,TRANSITION,FEATURE,LABEL,GROUP_ORIGINAL,SUBJECT_ORIGINAL,RUN,GROUP,SUBJECT,INTENSITY,SUBJECT_NESTED,ABUNDANCE,FRACTION,originalRUN,censored" />
3e2606fa85bf "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit fa543ac667f63409bfb2e28fd6c711e74d828a79" galaxyp parents: 0 diff changeset	426 </actions>
0 80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	427 </data>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	428 <data name="runlevel_data" format="tabular" label="MSstats RunlevelData" from_work_dir="RunlevelData.tsv">
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	429 <filter>'runlevel_data' in selected_outputs</filter>
1 3e2606fa85bf "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit fa543ac667f63409bfb2e28fd6c711e74d828a79" galaxyp parents: 0 diff changeset	430 <actions>
3e2606fa85bf "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit fa543ac667f63409bfb2e28fd6c711e74d828a79" galaxyp parents: 0 diff changeset	431 <action name="column_names" type="metadata" default="RUN,Protein,LogIntensities,NumMeasuredFeature,MissingPercentage,more50missing,NumImputedFeature,originalRUN,GROUP,GROUP_ORIGINAL,SUBJECT_ORIGINAL,SUBJECT_NESTED,SUBJECT" />
3e2606fa85bf "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit fa543ac667f63409bfb2e28fd6c711e74d828a79" galaxyp parents: 0 diff changeset	432 </actions>
0 80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	433 </data>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	434 <data name="qcplot" format="pdf" label="MSstats QCPlot.pdf" from_work_dir="MSStats_only_QCPlot.pdf">
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	435 <filter>'qcplot' in selected_outputs</filter>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	436 </data>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	437 <data name="profile_plot" format="pdf" label="MSstats ProfilePlot.pdf" from_work_dir="MSStats_only_ProfilePlot.pdf">
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	438 <filter>'profile_plot' in selected_outputs</filter>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	439 </data>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	440 <data name="profile_wsum_plot" format="pdf" label="MSstats ProfilePlot_wSummarization.pdf" from_work_dir="MSStats_only_ProfilePlot_wSummarization.pdf">
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	441 <filter>'profile_wsum_plot' in selected_outputs</filter>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	442 </data>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	443 <data name="condition_plot" format="pdf" label="MSstats ConditionPlot.pdf" from_work_dir="MSStats_only_ConditionPlot.pdf">
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	444 <filter>'condition_plot' in selected_outputs</filter>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	445 </data>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	446 <data name="quant_sample_matrix" format="tabular" label="MSstats SampleQuantificationMatrix.tsv" from_work_dir="SampleQuantificationMatrix.tsv">
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	447 <filter>'quant_sample_matrix' in selected_outputs</filter>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	448 </data>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	449 <data name="quant_sample_long" format="tabular" label="MSstats SampleQuantificationLong.tsv" from_work_dir="SampleQuantificationLong.tsv">
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	450 <filter>'quant_sample_long' in selected_outputs</filter>
1 3e2606fa85bf "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit fa543ac667f63409bfb2e28fd6c711e74d828a79" galaxyp parents: 0 diff changeset	451 <actions>
3e2606fa85bf "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit fa543ac667f63409bfb2e28fd6c711e74d828a79" galaxyp parents: 0 diff changeset	452 <action name="column_names" type="metadata" default="Protein,Group_Subject,LogIntensity" />
3e2606fa85bf "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit fa543ac667f63409bfb2e28fd6c711e74d828a79" galaxyp parents: 0 diff changeset	453 </actions>
0 80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	454 </data>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	455 <data name="quant_group_matrix" format="tabular" label="MSstats GroupQuantificationMatrix.tsv" from_work_dir="GroupQuantificationMatrix.tsv">
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	456 <filter>'quant_group_matrix' in selected_outputs</filter>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	457 </data>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	458 <data name="quant_group_long" format="tabular" label="MSstats GroupQuantificationLong.tsv" from_work_dir="GroupQuantificationLong.tsv">
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	459 <filter>'quant_group_long' in selected_outputs</filter>
1 3e2606fa85bf "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit fa543ac667f63409bfb2e28fd6c711e74d828a79" galaxyp parents: 0 diff changeset	460 <actions>
3e2606fa85bf "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit fa543ac667f63409bfb2e28fd6c711e74d828a79" galaxyp parents: 0 diff changeset	461 <action name="column_names" type="metadata" default="Protein,Group,LogIntensity" />
3e2606fa85bf "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit fa543ac667f63409bfb2e28fd6c711e74d828a79" galaxyp parents: 0 diff changeset	462 </actions>
0 80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	463 </data>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	464 <data name="comparison_result" format="tabular" label="MSstats ComparisonResult.tsv" from_work_dir="ComparisonResult.tsv">
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	465 <filter> group['group_comparison'] == 'yes' and 'comparison_result' in group['select_outputs']</filter>
1 3e2606fa85bf "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit fa543ac667f63409bfb2e28fd6c711e74d828a79" galaxyp parents: 0 diff changeset	466 <actions>
3e2606fa85bf "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit fa543ac667f63409bfb2e28fd6c711e74d828a79" galaxyp parents: 0 diff changeset	467 <action name="column_names" type="metadata" default="Protein,Label,log2FC,SE,Tvalue,DF,pvalue,adj.pvalue,issue,MissingPercentage,ImputationPercentage" />
3e2606fa85bf "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit fa543ac667f63409bfb2e28fd6c711e74d828a79" galaxyp parents: 0 diff changeset	468 </actions>
0 80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	469 </data>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	470 <data name="fittedmodel" format="txt" label="MSstats ComparisonFittedModel.txt" from_work_dir="ComparisonFittedModel.txt">
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	471 <filter> group['group_comparison'] == 'yes' and 'fittedmodel' in group['select_outputs']</filter>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	472 </data>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	473 <data name="model_qc" format="tabular" label="MSstats ModelQC.tsv" from_work_dir="ModelQC.tsv">
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	474 <filter> group['group_comparison'] == 'yes' and 'model_qc' in group['select_outputs']</filter>
1 3e2606fa85bf "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit fa543ac667f63409bfb2e28fd6c711e74d828a79" galaxyp parents: 0 diff changeset	475 <actions>
3e2606fa85bf "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit fa543ac667f63409bfb2e28fd6c711e74d828a79" galaxyp parents: 0 diff changeset	476 <action name="column_names" type="metadata" default="RUN,PROTEIN,ABUNDANCE,NumMeasuredFeature,MissingPercentage,more50missing,NumImputedFeature,originalRUN,GROUP,GROUP_ORIGINAL,SUBJECT_ORIGINAL,SUBJECT_NESTED,SUBJECT,residuals,fitted" />
3e2606fa85bf "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit fa543ac667f63409bfb2e28fd6c711e74d828a79" galaxyp parents: 0 diff changeset	477 </actions>
0 80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	478 </data>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	479 <data name="qqplot" format="pdf" label="MSstats ModelQQ.pdf" from_work_dir="MSStats_group_QQPlot.pdf">
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	480 <filter> group['group_comparison'] == 'yes' and 'qqplot' in group['select_outputs']</filter>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	481 </data>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	482 <data name="residualplot" format="pdf" label="MSstats ResidualPlot.pdf" from_work_dir="MSStats_group_ResidualPlot.pdf">
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	483 <filter> group['group_comparison'] == 'yes' and 'residualplot' in group['select_outputs']</filter>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	484 </data>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	485 <data name="volcanoplot" format="pdf" label="MSstats VolcanoPlot.pdf" from_work_dir="MSStats_group_VolcanoPlot.pdf">
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	486 <filter> group['group_comparison'] == 'yes' and 'volcanoplot' in group['select_outputs']</filter>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	487 </data>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	488 <data name="heatmap" format="pdf" label="MSstats Heatmap.pdf" from_work_dir="MSStats_group_Heatmap.pdf">
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	489 <filter> group['group_comparison'] == 'yes' and 'heatmap' in group['select_outputs']</filter>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	490 </data>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	491 <data name="comparisonplot" format="pdf" label="MSstats ComparisonPlot.pdf" from_work_dir="MSStats_group_ComparisonPlot.pdf">
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	492 <filter> group['group_comparison'] == 'yes' and 'comparisonplot' in group['select_outputs']</filter>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	493 </data>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	494 </outputs>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	495 <tests>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	496
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	497 <test>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	498 <conditional name="input">
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	499 <param name="input_src" value="MSstats"/>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	500 <param name="msstats_input" ftype="csv" value="msstats_testfile.txt"/>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	501 </conditional>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	502 <param name="selected_outputs" value="processed_data,profile_plot,profile_wsum_plot,quant_sample_matrix,quant_group_long"/>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	503 <output name="processed_data">
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	504 <assert_contents>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	505 <has_text text="D.GPLTGTYR" />
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	506 <has_n_columns n="16" />
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	507 <has_n_lines n="2071" />
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	508 </assert_contents>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	509 </output>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	510 <output name="quant_sample_matrix">
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	511 <assert_contents>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	512 <has_text text="C2_1" />
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	513 <has_n_columns n="7" />
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	514 <has_n_lines n="7" />
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	515 </assert_contents>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	516 </output>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	517 <output name="quant_group_long">
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	518 <assert_contents>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	519 <has_text text="LogIntensity" />
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	520 <has_n_columns n="3" />
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	521 <has_n_lines n="37" />
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	522 </assert_contents>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	523 </output>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	524 <output name="profile_plot" file="MSstats ProfilePlot.pdf" compare="sim_size"/>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	525 <output name="profile_wsum_plot" file="profile_wsum_plot.pdf" compare="sim_size"/>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	526 </test>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	527
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	528 <test>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	529 <conditional name="input">
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	530 <param name="input_src" value="MSstats"/>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	531 <param name="msstats_input" ftype="tabular" value="msstats_testfile.tsv"/>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	532 </conditional>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	533 <conditional name="group">
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	534 <param name="group_comparison" value="yes"/>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	535 <param name="comparison_matrix" ftype="csv" value="comparison_matrix.csv"/>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	536 </conditional>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	537 <param name="select_outputs" value="residualplot,model_qc"/>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	538 <output name="processed_data">
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	539 <assert_contents>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	540 <has_text text="D.GPLTGTYR" />
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	541 <has_n_columns n="16" />
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	542 <has_n_lines n="2071" />
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	543 </assert_contents>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	544 </output>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	545 <output name="model_qc">
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	546 <assert_contents>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	547 <has_text text="MissingPercentage" />
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	548 <has_n_columns n="15" />
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	549 <has_n_lines n="108" />
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	550 </assert_contents>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	551 </output>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	552 <output name="residualplot" file="residual_plot.pdf" compare="sim_size"/>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	553 </test>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	554
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	555 <test>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	556 <conditional name="input">
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	557 <param name="input_src" value="MaxQuant"/>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	558 <param name="evidence" ftype="tabular" value="test_MQ_evidence.tabular"/>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	559 <param name="annotation" ftype="tabular" value="test_MQ_annotation.txt"/>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	560 <param name="proteinGroups" ftype="tabular" value="test_MQ_proteingroups.tabular"/>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	561 </conditional>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	562 <param name="selected_outputs" value="condition_plot,processed_data,runlevel_data"/>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	563 <conditional name="group">
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	564 <param name="group_comparison" value="yes"/>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	565 <param name="comparison_matrix" ftype="csv" value="test_MQ_group12_comparison_matrix.csv"/>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	566 </conditional>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	567 <param name="select_outputs" value="qqplot,comparison_result"/>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	568 <output name="processed_data">
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	569 <assert_contents>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	570 <has_text text="SPILVATAVAAR" />
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	571 <has_n_columns n="16" />
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	572 <has_n_lines n="57" />
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	573 </assert_contents>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	574 </output>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	575 <output name="runlevel_data">
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	576 <assert_contents>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	577 <has_text text="qx017084.raw.thermo" />
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	578 <has_n_columns n="13" />
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	579 <has_n_lines n="13" />
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	580 </assert_contents>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	581 </output>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	582 <output name="comparison_result">
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	583 <assert_contents>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	584 <has_text text="r2-r1" />
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	585 <has_n_columns n="11" />
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	586 <has_n_lines n="4" />
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	587 </assert_contents>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	588 </output>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	589 <output name="condition_plot" file="condition_plot.pdf" compare="sim_size"/>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	590 <output name="qqplot" file="qq_plot.pdf" compare="sim_size"/>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	591 </test>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	592
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	593 <!--
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	594 <test>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	595 <conditional name="input">
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	596 <param name="input_src" value="OpenMS"/>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	597 <param name="evidence" ftype="tabular" value=""/>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	598 <param name="annotation" ftype="tabular" value=""/>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	599 </conditional>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	600 <output name="processed_data">
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	601 <assert_contents>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	602 <has_text text="D.GPLTGTYR" />
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	603 </assert_contents>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	604 </output>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	605 </test>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	606 -->
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	607
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	608 <test>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	609 <conditional name="input">
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	610 <param name="input_src" value="OpenSWATH"/>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	611 <param name="evidence" ftype="tabular" value="test_swath_input_data.tabular"/>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	612 <param name="annotation" ftype="tabular" value="test_swath_annotations.tabular"/>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	613 </conditional>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	614 <output name="processed_data">
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	615 <assert_contents>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	616 <has_text text="GETLGLIGFGR" />
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	617 <has_n_columns n="16" />
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	618 <has_n_lines n="253" />
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	619 </assert_contents>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	620 </output>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	621 <output name="qcplot" file="QC_plot.pdf" compare="sim_size"/>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	622 </test>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	623
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	624 <test>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	625 <conditional name="input">
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	626 <param name="input_src" value="OpenSWATH"/>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	627 <param name="evidence" ftype="tabular" value="test_swath_input_data.tabular"/>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	628 <param name="annotation" ftype="tabular" value="test_swath_annotations.tabular"/>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	629 </conditional>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	630 <param name="selected_outputs" value="r_script,processed_data,quant_sample_long"/>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	631 <conditional name="group">
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	632 <param name="group_comparison" value="yes"/>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	633 <param name="comparison_matrix" ftype="csv" value="test_swath_group12_comparison_matrix.csv"/>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	634 </conditional>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	635 <param name="select_outputs" value="comparison_result,volcanoplot,residualplot"/>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	636 <output name="processed_data">
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	637 <assert_contents>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	638 <has_text text="GETLGLIGFGR" />
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	639 <has_n_columns n="16" />
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	640 <has_n_lines n="253" />
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	641 </assert_contents>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	642 </output>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	643 <output name="quant_sample_long">
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	644 <assert_contents>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	645 <has_text text="NPT_96" />
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	646 <has_n_columns n="3" />
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	647 <has_n_lines n="31" />
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	648 </assert_contents>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	649 </output>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	650 <output name="comparison_result">
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	651 <assert_contents>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	652 <has_text text="Q5VYK3" />
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	653 <has_n_columns n="11" />
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	654 <has_n_lines n="6" />
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	655 </assert_contents>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	656 </output>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	657 <output name="volcanoplot" file="volcanoplot.pdf" compare="sim_size"/>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	658 <output name="residualplot" file="residualplot.pdf" compare="sim_size"/>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	659 </test>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	660
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	661 </tests>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	662 <help><![CDATA[
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	663 MSstats is an open-source R package for statistical relative quantification of proteins and peptides in global, targeted and data-independent proteomics. `More information on MSstats <http://msstats.org/>`_
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	664
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	665 The MSstats Galaxy tool (version @VERSION@) allows the detection of differentially abundant proteins for label-free MS experiments with complex designs on data derived from open-source proteomics software available in Galaxy (e.g. MaxQuant, OpenMS, OpenSWATH). Processing functionalities such as log transformation, normalization, feature selection, missing value imputation and quantification are available as well.
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	666
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	667 -----
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	668
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	669 Input data
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	670
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	671 - Data in tabular or csv format, generated by spectral processing tools such as `MaxQuant <http://coxdocs.org/doku.php?id=maxquant:start/>`_, `OpenSWATH <http://openswath.org/en/latest/>`_ will be automatically converted to 10-column MSstats format
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	672
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	673 - MaxQuant format: evidence.txt, proteinGroups.txt
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	674 - OpenSWATH format: pyprophet export file
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	675 - MSstats format: tabular file with 10 column either manually curated or other sources such as swath2stats tool which is implemented in Pyprophet export in Galaxy. For manual curation: Names of headers are fixed but not case sensitive:
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	676
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	677 - ProteinName: protein ID or peptide ID for peptide-level modeling and analysis; statistical analysis will be done separately for each unique label in this column
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	678 - PeptideSequence: Amino acid sequence for each peptides. If the peptide sequences should be distinguished based on post-translational modifications, this column can be renamed to PeptideModifiedSequence.
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	679 - PrecursorCharge: charge state of precursor.
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	680 - FragmentIon: e.g. b4, y3, if unknown use a single value for all entries.
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	681 - ProductCharge: charge state of product. If unknown use 0 for all entries.
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	682 - IsotopeLabelType: This column indicates whether this measurement is based on the endogenous peptides (use “L”) or labeled reference peptides (use “H”).
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	683 - Condition: For group comparison experiments, this column indicates groups of interest (such as “Disease” or “Control”). For time-course experiments, this column indicates time points (such as “T1”, “T2”, etc). If the experimental design contains both distinct groups of subjects and multiple time points per subject, this column should indicate a combination of these values (such as “Disease_T1”, “Disease_T2”, “Control_T1”, “Control_T2”, etc.).
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	684 - BioReplicate: This column should contain a unique identifier for each biological replicate in the experiment. For example, in a clinical proteomic investigation this should be a unique patient id. Patients from distinct groups should have distinct ids. MSstats does not require the presence of technical replicates in the experiment. If the technical replicates are present, all samples or runs from a same biological replicate should have a same id. MSstats automatically detects the presence of technical replicates and accounts for them in the model-based analysis.
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	685 - Run: This column contains the identifier of a mass spectrometry run. Each mass spectrometry run should have a unique identifier, regardless of the origin of the biological sample. In SRM experiments, if all the transitions of a biological or a technical replicate are split into multiple “methods” due to the technical limitations, each method should have a separate identifier. When processed by Skyline, distinct values of runs correspond to distinct input file names. It is possible to use the actual input file names as values in the column Run.
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	686 - Intensity: This column should contain the quantified signal of a feature in a run without any transformation (in particular, no logarithm transform). The signals can be quantified as the peak height or the peak of area under curve. Any other quantitative representation of abundance can also be used.
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	687 - Example file header:
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	688 ::
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	689
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	690 proteinname peptidesequence precursorcharge fragmention productcharge
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	691 P02768 DLGEENFK 3 y7 0
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	692 P02768 DLGEENFK 3 y8 0
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	693 P02768 ETYGEMADCCAK 2 b3 0
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	694 P02768 ETYGEMADCCAK 2 b4 0
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	695 ... ... ... ... ...
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	696
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	697 isotopelabeltype condition bioreplicate run intensity
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	698 L 1 ReplA 1 4298.12
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	699 H 1 ReplA 1 1974.59
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	700 L 1 ReplA 1 7183.22
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	701 H 1 ReplA 1 8467.58
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	702 ... ... ... ... ...
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	703
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	704
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	705 - Annotations as tabular file are needed for all input options except MSstats format
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	706
2 52ac6fde9a5b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 414edbbd89f9bc83b81289e409c9b688c8c1e40f" galaxyp parents: 1 diff changeset	707 - 4 columns with exactly these headers: Raw.file, Condition, BioReplicate, Run; additional 5th column only for MaxQuant: IsotopeLabelType
0 80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	708
2 52ac6fde9a5b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 414edbbd89f9bc83b81289e409c9b688c8c1e40f" galaxyp parents: 1 diff changeset	709 - Raw.file: File name that has to match exactly as it appears in the other input files (e.g. S1207.raw.thermo; in/AA12_mzML.mzML)
0 80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	710 - all other columns: see description above for MSstats format columns
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	711
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	712 - Comparison matrix as tabular file
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	713
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	714 - 1st column: name of comparison
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	715 - additionally one column for each condition that is present in the tabular file. Use 1 and -1 to indicate the conditions to compare and 0 for conditions that are not compared. Multiple groups can be combined by using 0.5.
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	716 - first row contains the names of the groups, they must exactly match the condition name used in the annotation file
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	717 - each additional row represents one comparison
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	718 - Example for a two group comparison
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	719
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	720 ::
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	721
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	722 names groupA groupB
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	723 groupA-groupB 1 -1
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	724
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	725
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	726 - Example for an experiment with 5 groups and 4 different comparisons
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	727
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	728 ::
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	729
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	730 names G1 G2 G3 G4 G5
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	731 G2-G1 -1 1 0 0 0
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	732 G4-G5 0 0 0 1 -1
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	733 G3-G5 0 0 -1 0 1
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	734 G1+G2-G5 0.5 0.5 0 0 -1
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	735
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	736 Options
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	737
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	738 - data conversion from MaxQuant and OpenSWATH to MSstats format:
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	739
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	740 - MaxQuant input: + Contaminant, + Reverse, + Only.identified.by.site, proteins are automatically removed during conversion
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	741
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	742 - data processing options:
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	743
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	744 - MaxQuant input: Contaminants and reverse and only ID by site) from MaxQuant tool are automatically removed;
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	745 - log transformation
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	746 - normalization of MS runs
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	747 - Feature selection
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	748 - Missing value imputation:
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	749
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	750 - MaxQuant input: All missing values are NA, usecensoredInt must be 'NA'
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	751 - OpenSWATH input: secensoredInt must be '0'
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	752 - Summary method: TMP + censoredInt = NULL: It assumes that all intensities are missing at random, therefore no action with MBimpute = FALSE or error with MBimpute = TRUE
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	753 - censoredInt='NA'or'0'& MBimpute=TRUE: AFT model-based imputation usingcutoffCensoredvalue in the AFT model
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	754 - censoredInt='NA'or'0'&MBimpute=FALSE: censored intensities (hereNA’s) will be replaced withthe value specified incutoffCensored.
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	755 - Summarizing intensities per MS run
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	756 - group comparison: automatic detection of differentially abundant proteins between two conditions, conditions have to be specified with the 'comparison matrix'
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	757 - quantification per sample or group
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	758
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	759 - sample: relative protein abundance in each biological replicate. If there are technical replicates for biological replicates,sample quantification will be the median among technical replicates. If there is no technical replicate for biological replicate (sample), sample quantification will be the same as run-level summarization.
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	760 - group: relative protein abundance in each condition, summarized over the biological replicates (median among sample quantification). In presence of completely missing values in a condition, the estimates will be zero
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	761
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	762 Output options
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	763
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	764 - Different outputs available. Especially for studies with many proteins, it is suggested to select only the necessary pdf outputs as many of them generate one plot per protein.
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	765
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	766 - MSstats log - check log file for warnings and information on the analysis steps (txt)
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	767 - r-script - can be used to re-run analysis outside Galaxy (txt)
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	768 - processed_data - transformed, normalized, imputed intensities (tabular)
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	769 - runlevel_data - summarized intensities per run (tabular)
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	770 - qcplot - log2 intensity boxplot for all proteins and run on first page, followed by one boxplot per protein (pdf)
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	771 - profile_plot - log2 intensity profiles one plot per protein and run (pdf)
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	772 - profile_wsum_plot - log2 intensity profiles one plot per protein and run with run summarization (pdf)
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	773 - condition_plot - log2 intensity range for each protein and condition (pdf)
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	774 - quant_sample_matrix - relative protein abundance in each biological replicate (tabular)
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	775 - quant_sample_long - relative protein abundance in each biological replicate, long format (tabular)
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	776 - quant_group_matrix - relative protein abundance in each condition (tabular)
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	777 - quant_group_long - relative protein abundance in each condition, long format (tabular)
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	778 - comparison_result - summary of statistical results per protein and comparison (tabular)
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	779 - model_qc - summary statistics per run (tabular)
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	780 - qqplot - one QQplot per protein (pdf)
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	781 - residualplot - one residual plot per protein (pdf)
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	782 - volcanoplot - one volcano plot per comparison (pdf)
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	783 - heatmap - needs at least 2 comparisons, one heatmap for all proteins and comparisons (pdf)
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	784 - comparisonplot - log2 intensity range for each protein and comparison (pdf)
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	785
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	786 For additional help please visit the `MSstats documentation <http://msstats.org/msstats-2/>`_
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	787
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	788
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	789 ]]></help>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	790 <citations>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	791 <citation type="doi">10.1093/bioinformatics/btu305</citation>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	792 </citations>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	793 </tool>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	794

Mercurial > repos > galaxyp > msstats

annotate msstats.xml @ 2:52ac6fde9a5b draft