msstats: msstats.xml annotate

annotate msstats.xml @ 0:80b40b9ab835 draft

"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f"

author	galaxyp
date	Sat, 25 Jul 2020 13:21:47 -0400
parents
children	3e2606fa85bf

rev	line source
0 80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	1 <tool id="msstats" name="MSstats" version="@VERSION@.0" python_template_version="3.5">
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 cat '$msstats_script' &&
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	31 Rscript '$msstats_script'
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	32 && cat msstats*.log > $log
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	33 ]]></command>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	34 <configfiles>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	35 <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	36 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	37
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	38 #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	39
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	40 #if $input.msstats_input.is_of_type('csv')
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	41 raw <- read.csv("$input.msstats_input")
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	42 #else
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	43 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	44 #end if
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	45
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	46 #elif $input.input_src == 'MaxQuant'
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	47 \# Read in MaxQuant files
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	48 mq_evidence <- read.table("$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	49
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	50 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	51
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	52 \# 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	53 \# 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	54 #if $input.annotation.is_of_type('csv')
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	55 annot <- read.csv("$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	56 #else
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	57 annot <- read.table("$input.annotation", sep="\t", header=TRUE)
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	58 #end if
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	59
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	60 raw <- MaxQtoMSstatsFormat(evidence=mq_evidence,
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	61 proteinGroups=mq_proteinGroups,
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	62 annotation=annot,
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	63 proteinID="$input.proteinID",
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	64 useUniquePeptide=$input.input_options.useUniquePeptide,
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	65 summaryforMultipleRows=$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	66 fewMeasurements="$input.input_options.fewMeasurements",
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	67 removeMpeptides=$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	68 removeOxidationMpeptides=$input.input_options.removeOxidationMpeptides,
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	69 removeProtein_with1Peptide=$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	70
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	71 #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	72
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	73 #if $input.evidence.is_of_type('csv')
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	74 input <- read.csv("$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	75 #else
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	76 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	77 #end if
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	78 #if $input.annotation.is_of_type('csv')
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	79 annot <- read.csv("$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	80 #else
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	81 annot <- read.table("$input.annotation", sep="\t", header=TRUE)
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	82 #end if
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	83
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	84 raw <- OpenMStoMSstatsFormat(input,
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	85 annotation=annot,
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	86 useUniquePeptide=$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	87 summaryforMultipleRows=$input.input_options.summaryforMultipleRows,
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	88 fewMeasurements="$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	89 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	90
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	91 #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	92
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	93 #if $input.evidence.is_of_type('csv')
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	94 input <- read.csv("$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	95 #else
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	96 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	97 #end if
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	98 #if $input.annotation.is_of_type('csv')
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	99 annot <- read.csv("$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	100 #else
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	101 annot <- read.table("$input.annotation", sep="\t", header=TRUE)
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	102 #end if
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	103
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	104 raw <- OpenSWATHtoMSstatsFormat(input,
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	105 annotation=annot,
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	106 filter_with_mscore=$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	107 mscore_cutoff=$input.input_options.mscore_cutoff,
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	108 useUniquePeptide=$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	109 fewMeasurements="$input.input_options.fewMeasurements",
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	110 removeProtein_with1Feature=$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	111 summaryforMultipleRows=$input.input_options.summaryforMultipleRows)
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	112
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	113 #end if
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	114
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	115 processed_data <- dataProcess(raw,
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	116 logTrans=$dp_options.logTrans,
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	117 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	118 #if $dp_options.norm.normalization == 'globalStandards'
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	119 nameStandards=c($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	120 #end if
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	121 ## address=$dp_options.address,
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	122 fillIncompleteRows=$dp_options.fillIncompleteRows,
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	123 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	124 #if $dp_options.features.featureSubset == 'topN'
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	125 n_top_feature=$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	126 #end if
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	127 #if $dp_options.features.featureSubset == 'highQuality'
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	128 remove_uninformative_feature_outlier=$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	129 #end if
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	130 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	131 #if $dp_options.summarize.summaryMethod == 'TMP'
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	132 MBimpute=$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	133 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	134 #end if
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	135 #if $dp_options.summarize.summaryMethod == 'linear'
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	136 equalFeatureVar=$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	137 #end if
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	138 #if $dp_options.censoredInt == 'NULL'
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	139 censoredInt=NULL,
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	140 #else
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	141 censoredInt="$dp_options.censoredInt",
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	142 #end if
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	143 cutoffCensored="$dp_options.cutoffCensored",
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	144 maxQuantileforCensored=$dp_options.maxQuantileforCensored,
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	145 clusters=NULL)
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	146
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	147 #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	148 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	149 #end if
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	150 #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	151 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	152 #end if
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	153
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	154 #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	155 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	156 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	157 #end if
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	158
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	159 #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	160 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	161 #end if
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	162
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	163 #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	164 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	165 #end if
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	166
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	167 ## Quantifiaction
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	168 #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	169 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	170 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	171 #end if
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	172
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	173 #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	174 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	175 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	176 #end if
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	177
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	178 #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	179 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	180 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	181 #end if
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	182
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	183 #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	184 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	185 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	186 #end if
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	187
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	188 ## Group Comparison
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	189 #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	190 \# Group Comparison
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	191 #if $group.comparison_matrix.is_of_type('csv')
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	192 comp_matrix <- read.csv("$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	193 #else
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	194 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	195 #end if
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	196
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	197 ## 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	198 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	199 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	200 ## 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	201 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	202
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	203 ## perform group comparison
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	204 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	205
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	206 print(comparisons\$fittedmodel)
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	207 #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	208 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	209 #end if
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
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	212 #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	213 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	214 #end if
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	215
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	216 #if 'model_qc' in $group.select_outputs
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	217 write.table(comparisons\$ModelQC, "ModelQC.tsv", sep = "\t", quote = F, row.names = F, dec = ".")
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	218 #end if
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	219
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	220 ## TODO: transform fittedmodel to table
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	221 ##class(DDA2009.comparisons$fittedmodel) # list, probably good to output this somehow
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	222
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	223 ## Visualizations:
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	224
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	225 #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	226 \# 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	227 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	228 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	229 #end if
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	230
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	231 #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	232 \# residual plots
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	233 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	234 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	235 #end if
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	236
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	237 #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	238 \# volcano plot
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	239 groupComparisonPlots(data = comparisons\$ComparisonResult, type = 'VolcanoPlot',
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	240 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	241 #end if
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 #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	244 \# 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	245 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	246 {
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	247 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	248 }
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	249 #end if
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	250
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	251 #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	252 \#comparison
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	253 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	254 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	255 #end if
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	256
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	257 #end if
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	258 ]]></configfile>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	259 </configfiles>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	260 <inputs>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	261 <conditional name="input">
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	262 <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	263 <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	264 <option value="MaxQuant">MaxQuant</option>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	265 <option value="OpenMS">OpenMS</option>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	266 <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	267 </param>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	268 <when value="MSstats">
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	269 <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	270 </when>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	271 <when value="MaxQuant">
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	272 <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	273 <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	274 <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	275 <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	276 <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	277 <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	278 </param>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	279 <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	280 <expand macro="useUniquePeptide"/>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	281 <expand macro="summaryforMultipleRows"/>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	282 <expand macro="fewMeasurements"/>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	283 <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	284 <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	285 <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	286 </section>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	287 </when>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	288 <when value="OpenMS">
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	289 <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	290 <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	291 <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	292 <expand macro="useUniquePeptide"/>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	293 <expand macro="summaryforMultipleRows"/>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	294 <expand macro="fewMeasurements"/>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	295 <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	296 </section>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	297 </when>
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>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	424 </data>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	425 <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	426 <filter>'runlevel_data' 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	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="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	429 <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	430 </data>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	431 <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	432 <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	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="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	435 <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	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="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	438 <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	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="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	441 <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	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="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	444 <filter>'quant_sample_long' 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_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	447 <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	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_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	450 <filter>'quant_group_long' 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	451 </data>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	452 <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	453 <filter> group['group_comparison'] == 'yes' and 'comparison_result' 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	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="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	456 <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	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="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	459 <filter> group['group_comparison'] == 'yes' and 'model_qc' 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	460 </data>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	461 <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	462 <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	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="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	465 <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	466 </data>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	467 <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	468 <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	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="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	471 <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	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="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	474 <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	475 </data>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	476 <!--
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	477 Tabular file (from groupcomparison): "fittedmodel"
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	478 -->
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	479 </outputs>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	480 <tests>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	481
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	482 <test>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	483 <conditional name="input">
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	484 <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	485 <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	486 </conditional>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	487 <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	488 <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	489 <assert_contents>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	490 <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	491 <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	492 <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	493 </assert_contents>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	494 </output>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	495 <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	496 <assert_contents>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	497 <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	498 <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	499 <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	500 </assert_contents>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	501 </output>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	502 <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	503 <assert_contents>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	504 <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	505 <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	506 <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	507 </assert_contents>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	508 </output>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	509 <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	510 <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	511 </test>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	512
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	513 <test>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	514 <conditional name="input">
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	515 <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	516 <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	517 </conditional>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	518 <conditional name="group">
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	519 <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	520 <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	521 </conditional>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	522 <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	523 <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	524 <assert_contents>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	525 <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	526 <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	527 <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	528 </assert_contents>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	529 </output>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	530 <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	531 <assert_contents>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	532 <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	533 <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	534 <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	535 </assert_contents>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	536 </output>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	537 <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	538 </test>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	539
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	540 <test>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	541 <conditional name="input">
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	542 <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	543 <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	544 <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	545 <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	546 </conditional>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	547 <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	548 <conditional name="group">
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	549 <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	550 <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	551 </conditional>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	552 <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	553 <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	554 <assert_contents>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	555 <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	556 <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	557 <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	558 </assert_contents>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	559 </output>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	560 <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	561 <assert_contents>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	562 <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	563 <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	564 <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	565 </assert_contents>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	566 </output>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	567 <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	568 <assert_contents>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	569 <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	570 <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	571 <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	572 </assert_contents>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	573 </output>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	574 <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	575 <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	576 </test>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	577
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	578
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	579
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	580
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	581 <!--
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	582 <test>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	583 <conditional name="input">
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	584 <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	585 <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	586 <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	587 </conditional>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	588 <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	589 <assert_contents>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	590 <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	591 </assert_contents>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	592 </output>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	593 </test>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	594 -->
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	595
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	596 <test>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	597 <conditional name="input">
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	598 <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	599 <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	600 <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	601 </conditional>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	602 <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	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 <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	605 <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	606 <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	607 </assert_contents>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	608 </output>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	609 <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	610 </test>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	611
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	612 <test>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	613 <conditional name="input">
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	614 <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	615 <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	616 <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	617 </conditional>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	618 <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	619 <conditional name="group">
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	620 <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	621 <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	622 </conditional>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	623 <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	624 <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	625 <assert_contents>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	626 <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	627 <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	628 <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	629 </assert_contents>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	630 </output>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	631 <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	632 <assert_contents>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	633 <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	634 <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	635 <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	636 </assert_contents>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	637 </output>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	638 <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	639 <assert_contents>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	640 <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	641 <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	642 <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	643 </assert_contents>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	644 </output>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	645 <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	646 <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	647 </test>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	648
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	649 </tests>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	650 <help><![CDATA[
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	651 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	652
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	653 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	654
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	655 -----
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	656
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	657 Input data
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	658
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	659 - 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	660
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	661 - 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	662 - 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	663 - 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	664
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	665 - 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	666 - 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	667 - 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	668 - 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	669 - 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	670 - 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	671 - 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	672 - 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	673 - 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	674 - 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	675 - Example file header:
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
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	678 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	679 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	680 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	681 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	682 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	683 ... ... ... ... ...
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	684
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	685 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	686 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	687 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	688 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	689 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	690 ... ... ... ... ...
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	691
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	692
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	693 - 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	694
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	695 - 4 columns: Filename, Condition, Bioreplicate, Run; additional 5th column only for MaxQuant: Isotopelabeltype
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 - Filename: the file name has to be exactly as it appears in the other input files (e.g. S1207.raw.thermo; in/AA12_mzML.mzML)
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	698 - 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	699
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	700 - 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	701
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	702 - 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	703 - 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	704 - 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	705 - 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	706 - 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	707
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	708 ::
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	709
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	710 names groupA groupB
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	711 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	712
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 - 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	715
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	716 ::
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	717
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	718 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	719 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	720 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	721 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	722 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	723
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	724 Options
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 - 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	727
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	728 - 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	729
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	730 - data processing options:
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	731
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	732 - 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	733 - log transformation
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	734 - 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	735 - Feature selection
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	736 - Missing value imputation:
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 - 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	739 - 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	740 - 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	741 - 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	742 - 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	743 - 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	744 - 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	745 - 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	746
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	747 - 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	748 - 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	749
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	750 Output options
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	751
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	752 - 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	753
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	754 - 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	755 - 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	756 - 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	757 - 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	758 - 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	759 - 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	760 - 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	761 - 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	762 - 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	763 - 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	764 - 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	765 - 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	766 - 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	767 - 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	768 - 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	769 - 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	770 - 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	771 - 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	772 - 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	773
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	774 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	775
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	776
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	777 ]]></help>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	778 <citations>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	779 <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	780 </citations>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	781 </tool>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	782

Mercurial > repos > galaxyp > msstats

annotate msstats.xml @ 0:80b40b9ab835 draft