msstats: msstats.xml annotate

annotate msstats.xml @ 4:593839e1f2c3 draft

"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 4fe4a0b30469f52c937830d2f3c316f6b9667407"

author	galaxyp
date	Thu, 25 Feb 2021 08:41:37 +0000
parents	8212e342e482
children	28434abe6c5c

rev	line source
4 593839e1f2c3 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 4fe4a0b30469f52c937830d2f3c316f6b9667407" galaxyp parents: 3 diff changeset	1 <tool id="msstats" name="MSstats" version="@VERSION@.1">
0 80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	2 <description>statistical relative protein significance analysis in DDA, SRM and DIA Mass Spectrometry</description>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	3 <macros>
3 8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	4 <token name="@VERSION@">3.22.0</token>
0 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">
3 8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 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"/>
0 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">
3 8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	9 <param name="summaryforMultipleRows" type="select" label="Summary for MultipleRows" help="When there are multiple measurements for certain feature and certain run, use highest or sum of all">
0 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">
3 8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	15 <param name="fewMeasurements" type="select" label="Features with few measurements " help="Remove the features that have 1 or 2 measurements across runs or keep all features or keep all features (the latter could give an error in fitting the statistical model)">
0 80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	16 <option value="remove" selected="true">remove</option>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	17 <option value="keep">keep</option>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	18 </param>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	19 </xml>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	20 <xml name="removeProtein_with1Peptide">
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	21 <param name="removeProtein_with1Peptide" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="false" label="Remove the proteins which have only 1 peptide and charge"/>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	22 </xml>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	23
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	24 </macros>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	25 <requirements>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	26 <requirement type="package" version="@VERSION@">bioconductor-msstats</requirement>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	27 </requirements>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	28 <command detect_errors="exit_code"><![CDATA[
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	29 cat '$msstats_script' > '$r_script' &&
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	30 Rscript '$msstats_script'
1 3e2606fa85bf "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit fa543ac667f63409bfb2e28fd6c711e74d828a79" galaxyp parents: 0 diff changeset	31 && cat msstats*.log > '$log'
0 80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	32 ]]></command>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	33 <configfiles>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	34 <configfile name="msstats_script"><![CDATA[
3 8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	35
0 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 $input.annotation.is_of_type('csv')
3 8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	55 annot <- read.csv("$input.annotation", header=TRUE)
0 80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	56 #else
3 8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	57 annot <- read.table("$input.annotation", sep="\t", header=TRUE)
0 80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	58 #end if
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	59
3 8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	60 raw <- MaxQtoMSstatsFormat(evidence=mq_evidence,
0 80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	61 proteinGroups=mq_proteinGroups,
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	62 annotation=annot,
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	63 proteinID="$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
3 8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	73 #if $input.openms_input.is_of_type('csv')
8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	74 input <- read.csv("$input.openms_input", header=TRUE)
0 80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	75 #else
3 8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	76 input <- read.table("$input.openms_input", sep="\t", header=TRUE)
0 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
3 8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	79 #if $input.annotation:
8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	80 #if $input.annotation.is_of_type('csv')
8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	81 annot <- read.csv("$input.annotation", header=TRUE)
8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	82 #else
8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	83 annot <- read.table("$input.annotation", sep="\t", header=TRUE)
8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	84 #end if
8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	85 #end if
8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	86
8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	87 raw <- OpenMStoMSstatsFormat(input,
8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	88 #if $input.annotation:
0 80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	89 annotation=annot,
3 8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	90 #end if
0 80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	91 useUniquePeptide=$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	92 summaryforMultipleRows=$input.input_options.summaryforMultipleRows,
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	93 fewMeasurements="$input.input_options.fewMeasurements",
3 8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	94 removeProtein_with1Feature=$input.input_options.removeProtein_with1Feature)
8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	95
0 80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	96
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	97 #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	98
3 8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	99 #if $input.openswath_input.is_of_type('csv')
8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	100 input <- read.csv("$input.openswath_input", header=TRUE)
0 80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	101 #else
3 8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	102 input <- read.table("$input.openswath_input", sep="\t", header=TRUE)
0 80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	103 #end if
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	104 #if $input.annotation.is_of_type('csv')
3 8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	105 annot <- read.csv("$input.annotation", header=TRUE)
0 80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	106 #else
3 8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	107 annot <- read.table("$input.annotation", sep="\t", header=TRUE)
0 80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	108 #end if
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	109
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	110 raw <- OpenSWATHtoMSstatsFormat(input,
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	111 annotation=annot,
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	112 filter_with_mscore=$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	113 mscore_cutoff=$input.input_options.mscore_cutoff,
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	114 useUniquePeptide=$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	115 fewMeasurements="$input.input_options.fewMeasurements",
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	116 removeProtein_with1Feature=$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	117 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	118
3 8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	119 #elif $input.input_src == 'Skyline'
8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	120
8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	121 #if $input.skyline_input.is_of_type('csv')
8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	122 input <- read.csv("$input.skyline_input", header=TRUE)
8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	123 #else
8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	124 input <- read.table("$input.skyline_input", sep="\t", header=TRUE)
8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	125 #end if
8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	126
8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	127 #if $input.annotation:
8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	128 #if $input.annotation.is_of_type('csv')
8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	129 annot <- read.csv("$input.annotation", header=TRUE)
8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	130 #else
8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	131 annot <- read.table("$input.annotation", sep="\t", header=TRUE)
8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	132 #end if
8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	133 #end if
8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	134
8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	135 raw <- SkylinetoMSstatsFormat(input,
8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	136 #if $input.annotation:
8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	137 annotation = annot,
8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	138 #end if
8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	139 removeiRT = $input.input_options.removeiRT,
8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	140 filter_with_Qvalue = $input.input_options.filter_with_Qvalue,
8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	141 qvalue_cutoff = $input.input_options.qvalue_cutoff,
8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	142 useUniquePeptide = $input.input_options.useUniquePeptide,
8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	143 fewMeasurements="$input.input_options.fewMeasurements",
8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	144 removeOxidationMpeptides = $input.input_options.removeOxidationMpeptides,
8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	145 removeProtein_with1Feature = $input.input_options.removeProtein_with1Feature)
8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	146
0 80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	147 #end if
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	148
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	149 processed_data <- dataProcess(raw,
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	150 logTrans=$dp_options.logTrans,
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	151 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	152 #if $dp_options.norm.normalization == 'globalStandards'
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	153 nameStandards=c($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	154 #end if
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	155 fillIncompleteRows=$dp_options.fillIncompleteRows,
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	156 featureSubset="$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	157 #if $dp_options.features.featureSubset == 'topN'
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	158 n_top_feature=$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	159 #end if
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	160 #if $dp_options.features.featureSubset == 'highQuality'
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	161 remove_uninformative_feature_outlier=$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	162 #end if
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	163 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	164 #if $dp_options.summarize.summaryMethod == 'TMP'
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	165 MBimpute=$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	166 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	167 #end if
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	168 #if $dp_options.summarize.summaryMethod == 'linear'
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	169 equalFeatureVar=$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	170 #end if
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	171 #if $dp_options.censoredInt == 'NULL'
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	172 censoredInt=NULL,
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	173 #else
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	174 censoredInt="$dp_options.censoredInt",
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	175 #end if
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	176 cutoffCensored="$dp_options.cutoffCensored",
4 593839e1f2c3 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 4fe4a0b30469f52c937830d2f3c316f6b9667407" galaxyp parents: 3 diff changeset	177 #if $dp_options.maxQuantileforCensored == ''
593839e1f2c3 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 4fe4a0b30469f52c937830d2f3c316f6b9667407" galaxyp parents: 3 diff changeset	178 maxQuantileforCensored = NULL)
593839e1f2c3 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 4fe4a0b30469f52c937830d2f3c316f6b9667407" galaxyp parents: 3 diff changeset	179 #else
3 8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	180 maxQuantileforCensored = $dp_options.maxQuantileforCensored)
4 593839e1f2c3 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 4fe4a0b30469f52c937830d2f3c316f6b9667407" galaxyp parents: 3 diff changeset	181 #end if
593839e1f2c3 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 4fe4a0b30469f52c937830d2f3c316f6b9667407" galaxyp parents: 3 diff changeset	182
593839e1f2c3 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 4fe4a0b30469f52c937830d2f3c316f6b9667407" galaxyp parents: 3 diff changeset	183 #if 'raw_data' in $dp_options.selected_outputs
593839e1f2c3 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 4fe4a0b30469f52c937830d2f3c316f6b9667407" galaxyp parents: 3 diff changeset	184 write.table(raw, "raw.tsv", sep = "\t", quote = F, row.names = F, dec = ".")
593839e1f2c3 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 4fe4a0b30469f52c937830d2f3c316f6b9667407" galaxyp parents: 3 diff changeset	185 #end if
593839e1f2c3 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 4fe4a0b30469f52c937830d2f3c316f6b9667407" galaxyp parents: 3 diff changeset	186
593839e1f2c3 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 4fe4a0b30469f52c937830d2f3c316f6b9667407" galaxyp parents: 3 diff changeset	187 #if 'processed_data' in $dp_options.selected_outputs
0 80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	188 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	189 #end if
4 593839e1f2c3 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 4fe4a0b30469f52c937830d2f3c316f6b9667407" galaxyp parents: 3 diff changeset	190
593839e1f2c3 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 4fe4a0b30469f52c937830d2f3c316f6b9667407" galaxyp parents: 3 diff changeset	191 #if 'runlevel_data' in $dp_options.selected_outputs
0 80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	192 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	193 #end if
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	194
4 593839e1f2c3 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 4fe4a0b30469f52c937830d2f3c316f6b9667407" galaxyp parents: 3 diff changeset	195 #for $plot_type in $dp_options.out_plots_opt.selected_vis_outputs
593839e1f2c3 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 4fe4a0b30469f52c937830d2f3c316f6b9667407" galaxyp parents: 3 diff changeset	196
593839e1f2c3 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 4fe4a0b30469f52c937830d2f3c316f6b9667407" galaxyp parents: 3 diff changeset	197
3 8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	198 #if $plot_type[-4:] == "Plot"
0 80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	199
3 8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	200 dataProcessPlots(data = processed_data,
8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	201 type = '$plot_type',
4 593839e1f2c3 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 4fe4a0b30469f52c937830d2f3c316f6b9667407" galaxyp parents: 3 diff changeset	202 featureName = "$dp_options.out_plots_opt.proc_plots_advanced.featureName",
593839e1f2c3 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 4fe4a0b30469f52c937830d2f3c316f6b9667407" galaxyp parents: 3 diff changeset	203 #if $dp_options.out_plots_opt.proc_plots_advanced.ylimUp:
593839e1f2c3 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 4fe4a0b30469f52c937830d2f3c316f6b9667407" galaxyp parents: 3 diff changeset	204 ylimUp = $dp_options.out_plots_opt.proc_plots_advanced.ylimUp,
3 8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	205 #end if
4 593839e1f2c3 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 4fe4a0b30469f52c937830d2f3c316f6b9667407" galaxyp parents: 3 diff changeset	206 #if $dp_options.out_plots_opt.proc_plots_advanced.ylimDown:
593839e1f2c3 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 4fe4a0b30469f52c937830d2f3c316f6b9667407" galaxyp parents: 3 diff changeset	207 ylimDown = $dp_options.out_plots_opt.proc_plots_advanced.ylimDown,
3 8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	208 #end if
4 593839e1f2c3 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 4fe4a0b30469f52c937830d2f3c316f6b9667407" galaxyp parents: 3 diff changeset	209 scale = $dp_options.out_plots_opt.proc_plots_advanced.scale,
593839e1f2c3 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 4fe4a0b30469f52c937830d2f3c316f6b9667407" galaxyp parents: 3 diff changeset	210 interval = "$dp_options.out_plots_opt.proc_plots_advanced.interval",
593839e1f2c3 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 4fe4a0b30469f52c937830d2f3c316f6b9667407" galaxyp parents: 3 diff changeset	211 x.axis.size = $dp_options.out_plots_opt.proc_plots_advanced.x_axis_size,
593839e1f2c3 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 4fe4a0b30469f52c937830d2f3c316f6b9667407" galaxyp parents: 3 diff changeset	212 y.axis.size = $dp_options.out_plots_opt.proc_plots_advanced.y_axis_size,
593839e1f2c3 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 4fe4a0b30469f52c937830d2f3c316f6b9667407" galaxyp parents: 3 diff changeset	213 text.size = $dp_options.out_plots_opt.proc_plots_advanced.text_size,
593839e1f2c3 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 4fe4a0b30469f52c937830d2f3c316f6b9667407" galaxyp parents: 3 diff changeset	214 text.angle = $dp_options.out_plots_opt.proc_plots_advanced.text_angle,
593839e1f2c3 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 4fe4a0b30469f52c937830d2f3c316f6b9667407" galaxyp parents: 3 diff changeset	215 legend.size = $dp_options.out_plots_opt.proc_plots_advanced.legend_size,
593839e1f2c3 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 4fe4a0b30469f52c937830d2f3c316f6b9667407" galaxyp parents: 3 diff changeset	216 dot.size.profile = $dp_options.out_plots_opt.proc_plots_advanced.dot_size_profile,
593839e1f2c3 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 4fe4a0b30469f52c937830d2f3c316f6b9667407" galaxyp parents: 3 diff changeset	217 dot.size.condition = $dp_options.out_plots_opt.proc_plots_advanced.dot_size_condition,
593839e1f2c3 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 4fe4a0b30469f52c937830d2f3c316f6b9667407" galaxyp parents: 3 diff changeset	218 width = $dp_options.out_plots_opt.width,
593839e1f2c3 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 4fe4a0b30469f52c937830d2f3c316f6b9667407" galaxyp parents: 3 diff changeset	219 height = $dp_options.out_plots_opt.height,
593839e1f2c3 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 4fe4a0b30469f52c937830d2f3c316f6b9667407" galaxyp parents: 3 diff changeset	220 #if $dp_options.out_plots_opt.which_Protein.select != 'list'
593839e1f2c3 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 4fe4a0b30469f52c937830d2f3c316f6b9667407" galaxyp parents: 3 diff changeset	221 which.Protein = "$dp_options.out_plots_opt.which_Protein.select",
3 8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	222 #else
4 593839e1f2c3 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 4fe4a0b30469f52c937830d2f3c316f6b9667407" galaxyp parents: 3 diff changeset	223 which.Protein = unlist(read.table("$dp_options.out_plots_opt.which_Protein.protein_list", sep = "\n", header = FALSE), use.names = FALSE),
3 8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	224 #end if
4 593839e1f2c3 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 4fe4a0b30469f52c937830d2f3c316f6b9667407" galaxyp parents: 3 diff changeset	225 remove_uninformative_feature_outlier = $dp_options.out_plots_opt.proc_plots_advanced.remove_uninformative_feature_outlier,
3 8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	226 address="MSStats_only_")
0 80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	227
3 8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	228 #end if
8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	229 #end for
0 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 ## Quantifiaction
4 593839e1f2c3 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 4fe4a0b30469f52c937830d2f3c316f6b9667407" galaxyp parents: 3 diff changeset	232 #if 'quant_sample_matrix' in $dp_options.selected_outputs
0 80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	233 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	234 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	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
4 593839e1f2c3 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 4fe4a0b30469f52c937830d2f3c316f6b9667407" galaxyp parents: 3 diff changeset	237 #if 'quant_sample_long' in $dp_options.selected_outputs
0 80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	238 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	239 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	240 #end if
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	241
4 593839e1f2c3 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 4fe4a0b30469f52c937830d2f3c316f6b9667407" galaxyp parents: 3 diff changeset	242 #if 'quant_group_matrix' in $dp_options.selected_outputs
0 80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	243 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	244 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	245 #end if
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	246
4 593839e1f2c3 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 4fe4a0b30469f52c937830d2f3c316f6b9667407" galaxyp parents: 3 diff changeset	247 #if 'quant_group_long' in $dp_options.selected_outputs
0 80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	248 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	249 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	250 #end if
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	251
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	252 ## Group Comparison
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	253 #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	254 \# Group Comparison
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	255 #if $group.comparison_matrix.is_of_type('csv')
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	256 comp_matrix <- read.csv("$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	257 #else
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	258 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	259 #end if
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	260
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	261 ## 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	262 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	263 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	264 ## 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	265 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	266
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	267 ## perform group comparison
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	268 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	269
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	270 print(comparisons\$fittedmodel)
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	271 #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	272 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	273 #end if
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	274
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	275
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	276 #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	277 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	278 #end if
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	279
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	280 #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	281 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	282 #end if
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	283
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	284 ## Visualizations:
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	285
4 593839e1f2c3 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 4fe4a0b30469f52c937830d2f3c316f6b9667407" galaxyp parents: 3 diff changeset	286 #for $plot_type in $group.comparison_plots_opt.select_comparison_plots
593839e1f2c3 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 4fe4a0b30469f52c937830d2f3c316f6b9667407" galaxyp parents: 3 diff changeset	287
3 8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	288
8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	289 #if $plot_type == "QQPlots" or $plot_type == "ResidualPlots"
0 80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	290
3 8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	291 modelBasedQCPlots(data = comparisons,
8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	292 type = "$plot_type",
4 593839e1f2c3 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 4fe4a0b30469f52c937830d2f3c316f6b9667407" galaxyp parents: 3 diff changeset	293 axis.size = $group.comparison_plots_opt.comparison_vis_options.axis_size,
593839e1f2c3 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 4fe4a0b30469f52c937830d2f3c316f6b9667407" galaxyp parents: 3 diff changeset	294 dot.size = $group.comparison_plots_opt.comparison_vis_options.dot_size,
593839e1f2c3 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 4fe4a0b30469f52c937830d2f3c316f6b9667407" galaxyp parents: 3 diff changeset	295 text.size = $group.comparison_plots_opt.comparison_vis_options.text_size,
593839e1f2c3 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 4fe4a0b30469f52c937830d2f3c316f6b9667407" galaxyp parents: 3 diff changeset	296 legend.size = $group.comparison_plots_opt.comparison_vis_options.legend_size,
593839e1f2c3 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 4fe4a0b30469f52c937830d2f3c316f6b9667407" galaxyp parents: 3 diff changeset	297 width = $group.comparison_plots_opt.width,
593839e1f2c3 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 4fe4a0b30469f52c937830d2f3c316f6b9667407" galaxyp parents: 3 diff changeset	298 height = $group.comparison_plots_opt.height,
593839e1f2c3 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 4fe4a0b30469f52c937830d2f3c316f6b9667407" galaxyp parents: 3 diff changeset	299 #if $group.comparison_plots_opt.which_Protein.select != 'list'
593839e1f2c3 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 4fe4a0b30469f52c937830d2f3c316f6b9667407" galaxyp parents: 3 diff changeset	300 which.Protein = "$group.comparison_plots_opt.which_Protein.select",
3 8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	301 #else
4 593839e1f2c3 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 4fe4a0b30469f52c937830d2f3c316f6b9667407" galaxyp parents: 3 diff changeset	302 which.Protein = unlist(read.table("$group.comparison_plots_opt.which_Protein.protein_list", sep = "\n", header = FALSE), use.names = FALSE),
3 8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	303 #end if
8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	304 address="MSStats_group_")
8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	305
8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	306
8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	307 #elif $plot_type == "VolcanoPlot" or $plot_type == "Heatmap" or $plot_type == "ComparisonPlot"
0 80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	308
3 8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	309 groupComparisonPlots(data = comparisons\$ComparisonResult,
8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	310 type = "$plot_type",
4 593839e1f2c3 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 4fe4a0b30469f52c937830d2f3c316f6b9667407" galaxyp parents: 3 diff changeset	311 sig = $group.comparison_plots_opt.comparison_vis_options.sig,
593839e1f2c3 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 4fe4a0b30469f52c937830d2f3c316f6b9667407" galaxyp parents: 3 diff changeset	312 #if $group.comparison_plots_opt.comparison_vis_options.FCcutoff:
593839e1f2c3 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 4fe4a0b30469f52c937830d2f3c316f6b9667407" galaxyp parents: 3 diff changeset	313 FCcutoff = $group.comparison_plots_opt.comparison_vis_options.FCcutoff,
3 8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	314 #end if
4 593839e1f2c3 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 4fe4a0b30469f52c937830d2f3c316f6b9667407" galaxyp parents: 3 diff changeset	315 logBase.pvalue = $group.comparison_plots_opt.comparison_vis_options.logBase_pvalue,
593839e1f2c3 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 4fe4a0b30469f52c937830d2f3c316f6b9667407" galaxyp parents: 3 diff changeset	316 #if $group.comparison_plots_opt.comparison_vis_options.ylimUp:
593839e1f2c3 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 4fe4a0b30469f52c937830d2f3c316f6b9667407" galaxyp parents: 3 diff changeset	317 ylimUp = $group.comparison_plots_opt.comparison_vis_options.ylimUp,
3 8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	318 #end if
4 593839e1f2c3 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 4fe4a0b30469f52c937830d2f3c316f6b9667407" galaxyp parents: 3 diff changeset	319 #if $group.comparison_plots_opt.comparison_vis_options.ylimDown:
593839e1f2c3 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 4fe4a0b30469f52c937830d2f3c316f6b9667407" galaxyp parents: 3 diff changeset	320 ylimDown = $group.comparison_plots_opt.comparison_vis_options.ylimDown,
3 8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	321 #end if
4 593839e1f2c3 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 4fe4a0b30469f52c937830d2f3c316f6b9667407" galaxyp parents: 3 diff changeset	322 x.axis.size = $group.comparison_plots_opt.comparison_vis_options.x_axis_size,
593839e1f2c3 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 4fe4a0b30469f52c937830d2f3c316f6b9667407" galaxyp parents: 3 diff changeset	323 y.axis.size = $group.comparison_plots_opt.comparison_vis_options.y_axis_size,
593839e1f2c3 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 4fe4a0b30469f52c937830d2f3c316f6b9667407" galaxyp parents: 3 diff changeset	324 dot.size = $group.comparison_plots_opt.comparison_vis_options.dot_size,
593839e1f2c3 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 4fe4a0b30469f52c937830d2f3c316f6b9667407" galaxyp parents: 3 diff changeset	325 text.size = $group.comparison_plots_opt.comparison_vis_options.text_size,
593839e1f2c3 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 4fe4a0b30469f52c937830d2f3c316f6b9667407" galaxyp parents: 3 diff changeset	326 text.angle = $group.comparison_plots_opt.comparison_vis_options.text_angle,
593839e1f2c3 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 4fe4a0b30469f52c937830d2f3c316f6b9667407" galaxyp parents: 3 diff changeset	327 legend.size = $group.comparison_plots_opt.comparison_vis_options.legend_size,
593839e1f2c3 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 4fe4a0b30469f52c937830d2f3c316f6b9667407" galaxyp parents: 3 diff changeset	328 ProteinName = $group.comparison_plots_opt.comparison_vis_options.ProteinName,
593839e1f2c3 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 4fe4a0b30469f52c937830d2f3c316f6b9667407" galaxyp parents: 3 diff changeset	329 colorkey = $group.comparison_plots_opt.comparison_vis_options.colorkey,
593839e1f2c3 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 4fe4a0b30469f52c937830d2f3c316f6b9667407" galaxyp parents: 3 diff changeset	330 numProtein = $group.comparison_plots_opt.comparison_vis_options.numProtein,
593839e1f2c3 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 4fe4a0b30469f52c937830d2f3c316f6b9667407" galaxyp parents: 3 diff changeset	331 clustering = "$group.comparison_plots_opt.comparison_vis_options.clustering",
593839e1f2c3 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 4fe4a0b30469f52c937830d2f3c316f6b9667407" galaxyp parents: 3 diff changeset	332 width = $group.comparison_plots_opt.width,
593839e1f2c3 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 4fe4a0b30469f52c937830d2f3c316f6b9667407" galaxyp parents: 3 diff changeset	333 height = $group.comparison_plots_opt.height,
593839e1f2c3 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 4fe4a0b30469f52c937830d2f3c316f6b9667407" galaxyp parents: 3 diff changeset	334 #if $group.comparison_plots_opt.which_Protein.select != 'list'
593839e1f2c3 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 4fe4a0b30469f52c937830d2f3c316f6b9667407" galaxyp parents: 3 diff changeset	335 which.Protein = "$group.comparison_plots_opt.which_Protein.select",
3 8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	336 #else
4 593839e1f2c3 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 4fe4a0b30469f52c937830d2f3c316f6b9667407" galaxyp parents: 3 diff changeset	337 which.Protein = unlist(read.table("$group.comparison_plots_opt.which_Protein.protein_list", sep = "\n", header = FALSE), use.names = FALSE),
3 8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	338 #end if
4 593839e1f2c3 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 4fe4a0b30469f52c937830d2f3c316f6b9667407" galaxyp parents: 3 diff changeset	339 #if $group.comparison_plots_opt.comparison_vis_options.which_Comparison.select != 'list'
593839e1f2c3 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 4fe4a0b30469f52c937830d2f3c316f6b9667407" galaxyp parents: 3 diff changeset	340 which.Comparison = "$group.comparison_plots_opt.comparison_vis_options.which_Comparison.select",
3 8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	341 #else
4 593839e1f2c3 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 4fe4a0b30469f52c937830d2f3c316f6b9667407" galaxyp parents: 3 diff changeset	342 which.Comparison = unlist(read.table("$group.comparison_plots_opt.comparison_vis_options.which_Comparison.comparison_list", sep = "\n", header = FALSE), use.names = FALSE),
3 8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	343 #end if
8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	344 address="MSStats_group_")
0 80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	345
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	346
3 8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	347 #end if
8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	348 #end for
0 80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	349
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	350 #end if
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	351 ]]></configfile>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	352 </configfiles>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	353 <inputs>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	354 <conditional name="input">
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	355 <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	356 <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	357 <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	358 <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	359 <option value="OpenSWATH">OpenSWATH</option>
3 8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	360 <!--option value="DIAUmpire">DIA-Umpire</option-->
8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	361 <option value="Skyline">Skyline</option>
0 80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	362 </param>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	363 <when value="MSstats">
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	364 <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	365 </when>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	366 <when value="MaxQuant">
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	367 <param name="evidence" type="data" format="tabular,csv" label="evidence.txt - feature-level data"/>
4 593839e1f2c3 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 4fe4a0b30469f52c937830d2f3c316f6b9667407" galaxyp parents: 3 diff changeset	368 <param name="proteinGroups" type="data" format="tabular,csv" label="proteinGroups.txt - protein-level data" help="It needs to match protein group ID. If not selected use Proteins in 'evidence.txt'"/>
3 8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	369 <param name="annotation" type="data" format="tabular,csv" label="annotation file" help="Columns: Raw.file, Condition (the name of the condition is not allowed to start with a number or contain any special characters.), BioReplicate, Run, IsotopeLabelType information"/>
8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	370
0 80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	371 <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	372 <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	373 <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	374 </param>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	375 <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	376 <expand macro="useUniquePeptide"/>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	377 <expand macro="summaryforMultipleRows"/>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	378 <expand macro="fewMeasurements"/>
3 8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	379 <param name="removeMpeptides" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="false" label="Remove the peptides including 'M' sequence"/>
8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	380 <param name="removeOxidationMpeptides" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="false" label="Remove the peptides including Oxidized 'M' sequence"/>
0 80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	381 <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	382 </section>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	383 </when>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	384 <when value="OpenMS">
3 8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	385 <param name="openms_input" type="data" format="tabular,csv" label="OpenMS input (e.g. output of MSstatsConverter)"/>
8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	386 <param name="annotation" type="data" format="tabular,csv" optional="true" label="If annotation is not yet complete in OpenMS, use annotation with Raw.file, Condition (the name of the condition is not allowed to start with a number or contain any special characters), BioReplicate, and Runinformation"/>
8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	387 <section name="input_options" title="OpenMStoMSstatsFormat Options" expanded="false">
0 80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	388 <expand macro="useUniquePeptide"/>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	389 <expand macro="summaryforMultipleRows"/>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	390 <expand macro="fewMeasurements"/>
3 8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	391 <param name="removeProtein_with1Feature" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="false" label="Remove the proteins which have only 1 peptide and charge"/>
0 80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	392 </section>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	393 </when>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	394 <when value="OpenSWATH">
3 8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	395 <param name="openswath_input" type="data" format="tabular,csv" label="OpenSWATH_input"/>
8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	396 <param name="annotation" type="data" format="tabular,csv" label="annotation file"/>
0 80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	397 <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	398 <param name="filter_with_mscore" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="true" label="Remove the peptides including 'M' sequence"/>
3 8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	399 <param name="mscore_cutoff" type="float" value="0.01" min="0" max="1.0" label="m_score cutoff"/>
0 80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	400 <expand macro="useUniquePeptide"/>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	401 <expand macro="fewMeasurements"/>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	402 <expand macro="summaryforMultipleRows"/>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	403 <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	404 </section>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	405 </when>
3 8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	406 <when value="Skyline">
8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	407 <param name="skyline_input" type="data" format="tabular,csv" label="Skyline input"/>
8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	408 <param name="annotation" type="data" optional="true" format="tabular,csv" label="annotation file"/>
8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	409 <section name="input_options" title="SkylinetoMSstatsFormat Options" expanded="false">
8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	410 <param name="removeiRT" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="true" label="Remove iRT" help="Yes (default) will remove the proteins or peptides which are labeld ’iRT’ in ’StandardType’ column. No will keep them."/>
8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	411 <param name="filter_with_Qvalue" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="true" label="Filter with Qvalue" help="Yes (default) will filter out the intensities that have greater than qvalue_cutoff in Detection QValue column. Those intensities will be replaced with zero and will be considered as censored missing values for imputation purpose."/>
8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	412 <param name="qvalue_cutoff" type="float" value="0.01" min="0" max="1.0" label="Cutoff for Detection QValue."/>
8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	413 <expand macro="removeProtein_with1Peptide"/>
8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	414 <expand macro="useUniquePeptide"/>
8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	415 <expand macro="fewMeasurements"/>
8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	416 <param name="removeOxidationMpeptides" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="false" label="Remove Oxidation M peptides" help="Yes will remove the peptides including ’oxidation (M)’ in modification."/>
8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	417 <param name="removeProtein_with1Feature" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="false" label="Remove proteins with 1 feature" help="Yes will remove the proteins which have only 1 peptide and charge."/>
8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	418 </section>
8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	419 </when>
8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	420 </conditional>
8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	421
4 593839e1f2c3 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 4fe4a0b30469f52c937830d2f3c316f6b9667407" galaxyp parents: 3 diff changeset	422 <section name="dp_options" title="dataProcess Options" expanded="true">
593839e1f2c3 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 4fe4a0b30469f52c937830d2f3c316f6b9667407" galaxyp parents: 3 diff changeset	423 <param name="selected_outputs" type="select" display="checkboxes" multiple="true" label="Select outputs">
593839e1f2c3 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 4fe4a0b30469f52c937830d2f3c316f6b9667407" galaxyp parents: 3 diff changeset	424 <option value="log" selected="true">MSstats log</option>
593839e1f2c3 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 4fe4a0b30469f52c937830d2f3c316f6b9667407" galaxyp parents: 3 diff changeset	425 <option value="r_script" selected="false">MSstats Rscript</option>
593839e1f2c3 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 4fe4a0b30469f52c937830d2f3c316f6b9667407" galaxyp parents: 3 diff changeset	426 <option value="raw_data" selected="true">MSstats RawData</option>
593839e1f2c3 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 4fe4a0b30469f52c937830d2f3c316f6b9667407" galaxyp parents: 3 diff changeset	427 <option value="processed_data" selected="true">MSstats ProcessedData</option>
593839e1f2c3 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 4fe4a0b30469f52c937830d2f3c316f6b9667407" galaxyp parents: 3 diff changeset	428 <option value="runlevel_data" selected="false">MSstats RunlevelData</option>
593839e1f2c3 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 4fe4a0b30469f52c937830d2f3c316f6b9667407" galaxyp parents: 3 diff changeset	429 <option value="quant_sample_matrix" selected="false">Sample Quantification Matrix Table</option>
593839e1f2c3 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 4fe4a0b30469f52c937830d2f3c316f6b9667407" galaxyp parents: 3 diff changeset	430 <option value="quant_sample_long" selected="false">Sample Quantification Long Table</option>
593839e1f2c3 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 4fe4a0b30469f52c937830d2f3c316f6b9667407" galaxyp parents: 3 diff changeset	431 <option value="quant_group_matrix" selected="true">Group Quantification Matrix Table</option>
593839e1f2c3 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 4fe4a0b30469f52c937830d2f3c316f6b9667407" galaxyp parents: 3 diff changeset	432 <option value="quant_group_long" selected="false">Group Quantification Long Table</option>
593839e1f2c3 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 4fe4a0b30469f52c937830d2f3c316f6b9667407" galaxyp parents: 3 diff changeset	433 </param>
3 8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	434 <param name="logTrans" type="select" label="logarithm transformation of intensities with base 2 or 10." help="Intensities for original intensity between 0 and 1 will be replaced with zero value after normalization.">
0 80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	435 <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	436 <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	437 </param>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	438 <conditional name="norm">
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	439 <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	440 <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	441 <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	442 <option value="globalStandards">globalStandards - normalization with global standards proteins</option>
3 8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	443 <option value="FALSE">false - no normalization is performed</option>
0 80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	444 </param>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	445 <when value="equalizeMedians"/>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	446 <when value="quantile"/>
3 8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	447 <when value="globalStandards">
8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	448 <param name="nameStandards" type="text" value="" label="global standard peptide names" help="Peptide names should be double-quoted and separated by commas">
0 80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	449 <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	450 <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	451 </param>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	452 </when>
3 8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	453 <when value="FALSE"/>
0 80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	454 </conditional>
3 8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	455 <param name="fillIncompleteRows" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="true" label="Fill Incomplete Rows" help="If the input dataset has incomplete rows, 'Yes' (default) adds the rows with intensity value=NA for missing peaks. 'No' reports error message with list of features which have incomplete rows"/>
0 80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	456 <conditional name="features">
3 8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	457 <param name="featureSubset" type="select" label="Feature Subset">
0 80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	458 <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	459 <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	460 <option value="topN">Use the top N features which have highest average of log2(intensity) across runs</option>
3 8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	461 <option value="highQuality">High quality: Flag uninformative feature and outliers</option>
0 80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	462 </param>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	463 <when value="all"/>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	464 <when value="top3"/>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	465 <when value="topN">
3 8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	466 <param name="n_top_feature" type="integer" value="3" min="1" label="The number of top features for Feature Subset"/>
0 80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	467 </when>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	468 <when value="highQuality">
3 8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	469 <param name="remove_uninformative_feature_outlier" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="false" label="Remove features flagged with uninformative feature quality"/>
0 80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	470 </when>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	471 </conditional>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	472 <conditional name="summarize">
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	473 <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	474 <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	475 <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	476 </param>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	477 <when value="TMP">
3 8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	478 <param name="MBimpute" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="true" label="Impute Missing Values" help="Yes: inserts 'NA' or '0' (depending on censored intensity), No: uses the values assigned by cutoff value for censoring"/>
0 80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	479 <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	480 </when>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	481 <when value="linear">
4 593839e1f2c3 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 4fe4a0b30469f52c937830d2f3c316f6b9667407" galaxyp parents: 3 diff changeset	482 <param name="equalFeatureVar" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="true" label="Account for heterogeneous variation among intensities from different features" help="Yes: assumes equal variance among intensities from features. No: means that we cannot assume equal variance among intensities from features, then we will account for heterogeneous variation from different features"/>
0 80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	483 </when>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	484 </conditional>
3 8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	485 <param name="censoredInt" type="select" label="Censored intensity">
4 593839e1f2c3 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 4fe4a0b30469f52c937830d2f3c316f6b9667407" galaxyp parents: 3 diff changeset	486 <help>The processing tools report missing values differently. This option is for distinguish which value should be considered as missing, and further whether it is censored or at random. Skyline and OpenSWATH input should use '0'. MaxQuant input should use 'NA'</help>
3 8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	487 <option value="NA" selected="true">NA - Assume that all 'NA's in 'Intensity' column are censored</option>
8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	488 <option value="0">0 - Use zero intensities '0' as censored intensity</option>
8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	489 <option value="NULL">NULL - Assume all NA intensites are randomly missing</option>
0 80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	490 </param>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	491 <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	492 <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	493 <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	494 <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	495 </param>
4 593839e1f2c3 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 4fe4a0b30469f52c937830d2f3c316f6b9667407" galaxyp parents: 3 diff changeset	496 <param name="maxQuantileforCensored" type="float" optional="true" value="0.999" min="0" max="1.0" label="Maximum quantile for deciding censored missing values." help="If you don't want to apply the threshold of noise intensity in your data, remove the value (empty field)"/>
593839e1f2c3 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 4fe4a0b30469f52c937830d2f3c316f6b9667407" galaxyp parents: 3 diff changeset	497
593839e1f2c3 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 4fe4a0b30469f52c937830d2f3c316f6b9667407" galaxyp parents: 3 diff changeset	498
593839e1f2c3 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 4fe4a0b30469f52c937830d2f3c316f6b9667407" galaxyp parents: 3 diff changeset	499 <section name="out_plots_opt" title="DataProcess Plot Options" expanded="false">
593839e1f2c3 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 4fe4a0b30469f52c937830d2f3c316f6b9667407" galaxyp parents: 3 diff changeset	500 <param name="selected_vis_outputs" type="select" display="checkboxes" multiple="true" label="Select visualization outputs">
593839e1f2c3 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 4fe4a0b30469f52c937830d2f3c316f6b9667407" galaxyp parents: 3 diff changeset	501 <option value="QCPlot" selected="false">MSstats QCPlot</option>
593839e1f2c3 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 4fe4a0b30469f52c937830d2f3c316f6b9667407" galaxyp parents: 3 diff changeset	502 <option value="ProfilePlot" selected="false">MSstats ProfilePlot</option>
593839e1f2c3 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 4fe4a0b30469f52c937830d2f3c316f6b9667407" galaxyp parents: 3 diff changeset	503 <option value="profile_wsum_plot" selected="false">MSstats ProfilePlot_wSummarization</option>
593839e1f2c3 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 4fe4a0b30469f52c937830d2f3c316f6b9667407" galaxyp parents: 3 diff changeset	504 <option value="ConditionPlot" selected="false">MSstats ConditionPlot</option>
593839e1f2c3 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 4fe4a0b30469f52c937830d2f3c316f6b9667407" galaxyp parents: 3 diff changeset	505 </param>
3 8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	506 <conditional name="which_Protein">
8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	507 <param name="select" type="select" label="Select protein IDs to draw plots">
8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	508 <option value="all" selected="true">generate all plots for each protein</option>
8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	509 <option value="allonly">Option for QC plot: "allonly" will generate one QC plot with all proteins</option>
8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	510 <option value="list">Protein IDs as tabular input</option>
8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	511 </param>
8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	512 <when value="all"/>
8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	513 <when value="allonly"/>
8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	514 <when value="list">
8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	515 <param name="protein_list" type="data" format="tabular" label="List of proteins"/>
8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	516 </when>
8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	517 </conditional>
4 593839e1f2c3 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 4fe4a0b30469f52c937830d2f3c316f6b9667407" galaxyp parents: 3 diff changeset	518 <param name="width" type="integer" min="1" value="8" label="Width of the saved pdf file"/>
593839e1f2c3 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 4fe4a0b30469f52c937830d2f3c316f6b9667407" galaxyp parents: 3 diff changeset	519 <param name="height" type="integer" min="1" value="5" label="Height of the saved pdf file"/>
593839e1f2c3 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 4fe4a0b30469f52c937830d2f3c316f6b9667407" galaxyp parents: 3 diff changeset	520
593839e1f2c3 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 4fe4a0b30469f52c937830d2f3c316f6b9667407" galaxyp parents: 3 diff changeset	521 <section name="proc_plots_advanced" title="Advanced visualization parameters" expanded="false">
593839e1f2c3 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 4fe4a0b30469f52c937830d2f3c316f6b9667407" galaxyp parents: 3 diff changeset	522 <param name="featureName" type="select" display="radio" label="Feature name for Profile Plot" help="Transition means printing feature legend intransition-level; Peptide means printing feature legend in peptide-level; NA means no feature legend printing.">
593839e1f2c3 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 4fe4a0b30469f52c937830d2f3c316f6b9667407" galaxyp parents: 3 diff changeset	523 <option value="Transition" selected="true">Transition</option>
593839e1f2c3 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 4fe4a0b30469f52c937830d2f3c316f6b9667407" galaxyp parents: 3 diff changeset	524 <option value="Peptide">Peptide</option>
593839e1f2c3 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 4fe4a0b30469f52c937830d2f3c316f6b9667407" galaxyp parents: 3 diff changeset	525 <option value="NA">NA</option>
593839e1f2c3 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 4fe4a0b30469f52c937830d2f3c316f6b9667407" galaxyp parents: 3 diff changeset	526 </param>
593839e1f2c3 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 4fe4a0b30469f52c937830d2f3c316f6b9667407" galaxyp parents: 3 diff changeset	527 <param name="ylimUp" type="float" optional="true" label="For all three plots, upper limit for y-axis." help="Empty (default) for Profile Plot and QC Plot uses the upper limit as rounded off maximum of log2(intensities) after normalization + 3; for Condition Plot maximum of log ratio + SD or CI. Alternatively, insert specific value of y-axis limit."/>
593839e1f2c3 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 4fe4a0b30469f52c937830d2f3c316f6b9667407" galaxyp parents: 3 diff changeset	528 <param name="ylimDown" type="float" optional="true" label="For all three plots, lower limit for y-axis in the log scale" help="Empty (default) for Profile Plot and QCPlot uses 0; for Condition Plot is minimum of log ratio - SD or CI. Alternatively, insert specific value of lower y-axis limit. "/>
593839e1f2c3 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 4fe4a0b30469f52c937830d2f3c316f6b9667407" galaxyp parents: 3 diff changeset	529
593839e1f2c3 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 4fe4a0b30469f52c937830d2f3c316f6b9667407" galaxyp parents: 3 diff changeset	530 <param name="scale" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="false" label="Scale for Condition Plot" help=" No (Default) means each conditional level is not scaled at x-axis according to its actual value (equal space at x-axis). Yes means each conditional level is scaled at x-axis according to its actual value (unequal space at x-axis)."/>
593839e1f2c3 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 4fe4a0b30469f52c937830d2f3c316f6b9667407" galaxyp parents: 3 diff changeset	531 <param name="interval" type="select" display="radio" label="Interval for Condition Plot" help="CI (default) uses confidence interval with 0.95 significant level for the width of error bar. SD uses standard deviation for the width of error bar.">
593839e1f2c3 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 4fe4a0b30469f52c937830d2f3c316f6b9667407" galaxyp parents: 3 diff changeset	532 <option value="CI" selected="true">CI - confidence interval</option>
593839e1f2c3 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 4fe4a0b30469f52c937830d2f3c316f6b9667407" galaxyp parents: 3 diff changeset	533 <option value="SD">SD - standard deviation</option>
593839e1f2c3 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 4fe4a0b30469f52c937830d2f3c316f6b9667407" galaxyp parents: 3 diff changeset	534 </param>
593839e1f2c3 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 4fe4a0b30469f52c937830d2f3c316f6b9667407" galaxyp parents: 3 diff changeset	535 <param name="x_axis_size" type="integer" min="1" value="10" label="Size of x-axis labeling for 'Run' in Profile Plot and QC Plot, and 'Condition' in Condition Plot"/>
593839e1f2c3 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 4fe4a0b30469f52c937830d2f3c316f6b9667407" galaxyp parents: 3 diff changeset	536 <param name="y_axis_size" type="integer" min="1" value="10" label="Size of y-axis labeling"/>
593839e1f2c3 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 4fe4a0b30469f52c937830d2f3c316f6b9667407" galaxyp parents: 3 diff changeset	537 <param name="text_size" type="integer" min="1" value="4" label="Size of labeling for feature names in normal QQPlots separately for each feature and size of labels represented each condition at the top of graph in Profile Plot and QC plot."/>
593839e1f2c3 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 4fe4a0b30469f52c937830d2f3c316f6b9667407" galaxyp parents: 3 diff changeset	538 <param name="text_angle" type="integer" min="0" max="360" value="90" label="Angle of labels represented each condition at the top of graph in Profile Plot and QC plot or x-axis labeling in Condition plot."/>
593839e1f2c3 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 4fe4a0b30469f52c937830d2f3c316f6b9667407" galaxyp parents: 3 diff changeset	539 <param name="legend_size" type="integer" min="1" value="7" label="Size of feature names in residual plots and feature legend (transition-level or peptide-level) above graph in Profile Plot. "/>
593839e1f2c3 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 4fe4a0b30469f52c937830d2f3c316f6b9667407" galaxyp parents: 3 diff changeset	540 <param name="dot_size_profile" type="integer" min="1" value="2" label="Size of dots in Profile plot"/>
593839e1f2c3 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 4fe4a0b30469f52c937830d2f3c316f6b9667407" galaxyp parents: 3 diff changeset	541 <param name="dot_size_condition" type="integer" min="1" value="3" label="Size of dots in Condition plot"/>
593839e1f2c3 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 4fe4a0b30469f52c937830d2f3c316f6b9667407" galaxyp parents: 3 diff changeset	542
593839e1f2c3 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 4fe4a0b30469f52c937830d2f3c316f6b9667407" galaxyp parents: 3 diff changeset	543 <param name="remove_uninformative_feature_outlier" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="false" label="Remove uninformative feature outlier in profile plots" help="It only works after when feature subset high Quality was used in dataProcess options. Yes allows to remove 1) the features are flagged in the column, feature_quality=Uninformative which are features with bad quality, 2) outliers that are flagged in the column, is_outlier=TRUE in profile plots. No (default) shows all features and intensities in profile plots."/>
593839e1f2c3 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 4fe4a0b30469f52c937830d2f3c316f6b9667407" galaxyp parents: 3 diff changeset	544 </section>
593839e1f2c3 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 4fe4a0b30469f52c937830d2f3c316f6b9667407" galaxyp parents: 3 diff changeset	545 </section>
593839e1f2c3 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 4fe4a0b30469f52c937830d2f3c316f6b9667407" galaxyp parents: 3 diff changeset	546 </section>
593839e1f2c3 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 4fe4a0b30469f52c937830d2f3c316f6b9667407" galaxyp parents: 3 diff changeset	547
0 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" 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	550 <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	551 <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	552 </param>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	553 <when value="no"/>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	554 <when value="yes">
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	555 <param name="comparison_matrix" type="data" format="tabular,csv" label="Comparison Matrix"/>
4 593839e1f2c3 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 4fe4a0b30469f52c937830d2f3c316f6b9667407" galaxyp parents: 3 diff changeset	556 <param name="select_outputs" type="select" display="checkboxes" multiple="true" label="Select outputs">
593839e1f2c3 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 4fe4a0b30469f52c937830d2f3c316f6b9667407" galaxyp parents: 3 diff changeset	557 <option value="comparison_result" selected="true">MSstats ComparisonResult.tsv</option>
3 8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	558 <option value="fittedmodel" selected="false">MSstats ComparisonFittedModel.txt</option>
0 80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	559 <option value="model_qc" selected="false">MSstats ModelQC.tsv</option>
4 593839e1f2c3 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 4fe4a0b30469f52c937830d2f3c316f6b9667407" galaxyp parents: 3 diff changeset	560 </param>
593839e1f2c3 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 4fe4a0b30469f52c937830d2f3c316f6b9667407" galaxyp parents: 3 diff changeset	561
593839e1f2c3 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 4fe4a0b30469f52c937830d2f3c316f6b9667407" galaxyp parents: 3 diff changeset	562 <section name="comparison_plots_opt" title="Comparison Visualization Options" expanded="false">
593839e1f2c3 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 4fe4a0b30469f52c937830d2f3c316f6b9667407" galaxyp parents: 3 diff changeset	563 <param name="select_comparison_plots" type="select" display="checkboxes" multiple="true" label="Select visualization outputs">
593839e1f2c3 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 4fe4a0b30469f52c937830d2f3c316f6b9667407" galaxyp parents: 3 diff changeset	564 <option value="VolcanoPlot" selected="false">MSstats VolcanoPlot</option>
593839e1f2c3 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 4fe4a0b30469f52c937830d2f3c316f6b9667407" galaxyp parents: 3 diff changeset	565 <option value="ComparisonPlot" selected="false">MSstats ComparisonPlot</option>
3 8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	566 <option value="QQPlots" selected="false">MSstats QQPlot</option>
8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	567 <option value="ResidualPlots" selected="false">MSstats ResidualPlot</option>
4 593839e1f2c3 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 4fe4a0b30469f52c937830d2f3c316f6b9667407" galaxyp parents: 3 diff changeset	568 <option value="Heatmap" selected="false">MSstats Heatmap (only possible for at least 2 comparisons)</option>
0 80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	569 </param>
4 593839e1f2c3 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 4fe4a0b30469f52c937830d2f3c316f6b9667407" galaxyp parents: 3 diff changeset	570 <param name="width" type="integer" min="1" value="8" label="Width of the saved pdf file"/>
593839e1f2c3 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 4fe4a0b30469f52c937830d2f3c316f6b9667407" galaxyp parents: 3 diff changeset	571 <param name="height" type="integer" min="1" value="5" label="Height of the saved pdf file"/>
593839e1f2c3 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 4fe4a0b30469f52c937830d2f3c316f6b9667407" galaxyp parents: 3 diff changeset	572 <conditional name="which_Protein">
593839e1f2c3 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 4fe4a0b30469f52c937830d2f3c316f6b9667407" galaxyp parents: 3 diff changeset	573 <param name="select" type="select" label="Select protein IDs to draw plots">
593839e1f2c3 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 4fe4a0b30469f52c937830d2f3c316f6b9667407" galaxyp parents: 3 diff changeset	574 <option value="all" selected="true">generate all plots for each protein</option>
593839e1f2c3 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 4fe4a0b30469f52c937830d2f3c316f6b9667407" galaxyp parents: 3 diff changeset	575 <option value="list">Protein IDs as tabular input</option>
593839e1f2c3 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 4fe4a0b30469f52c937830d2f3c316f6b9667407" galaxyp parents: 3 diff changeset	576 </param>
593839e1f2c3 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 4fe4a0b30469f52c937830d2f3c316f6b9667407" galaxyp parents: 3 diff changeset	577 <when value="all"/>
593839e1f2c3 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 4fe4a0b30469f52c937830d2f3c316f6b9667407" galaxyp parents: 3 diff changeset	578 <when value="list">
593839e1f2c3 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 4fe4a0b30469f52c937830d2f3c316f6b9667407" galaxyp parents: 3 diff changeset	579 <param name="protein_list" type="data" format="tabular" label="List of proteins"/>
593839e1f2c3 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 4fe4a0b30469f52c937830d2f3c316f6b9667407" galaxyp parents: 3 diff changeset	580 </when>
593839e1f2c3 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 4fe4a0b30469f52c937830d2f3c316f6b9667407" galaxyp parents: 3 diff changeset	581 </conditional>
593839e1f2c3 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 4fe4a0b30469f52c937830d2f3c316f6b9667407" galaxyp parents: 3 diff changeset	582
593839e1f2c3 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 4fe4a0b30469f52c937830d2f3c316f6b9667407" galaxyp parents: 3 diff changeset	583 <section name="comparison_vis_options" title="Advanced visualization parameters">
593839e1f2c3 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 4fe4a0b30469f52c937830d2f3c316f6b9667407" galaxyp parents: 3 diff changeset	584
593839e1f2c3 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 4fe4a0b30469f52c937830d2f3c316f6b9667407" galaxyp parents: 3 diff changeset	585 <param name="sig" type="float" min="0" max="1" value="0.05" label="FDR cutoff for the adjusted p-values in heatmap and volcano plot" help="Level of significance for comparison plot. 100(1-sig)% confidence interval will be drawn."/>
593839e1f2c3 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 4fe4a0b30469f52c937830d2f3c316f6b9667407" galaxyp parents: 3 diff changeset	586 <param name="FCcutoff" type="float" optional="true" label="Involve fold change cutoff or not for volcano plot or heatmap." help="Empty (default) means no fold change cutoff is applied for significance analysis. Specific value means specific fold change cutoff is applied"/>
593839e1f2c3 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 4fe4a0b30469f52c937830d2f3c316f6b9667407" galaxyp parents: 3 diff changeset	587 <param name="logBase_pvalue" type="select" label="For volcano plot or heatmap, logarithm transformation of adjusted p-valuewith base 2 or 10">
593839e1f2c3 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 4fe4a0b30469f52c937830d2f3c316f6b9667407" galaxyp parents: 3 diff changeset	588 <option value="2">2</option>
593839e1f2c3 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 4fe4a0b30469f52c937830d2f3c316f6b9667407" galaxyp parents: 3 diff changeset	589 <option value="10" selected="true">10</option>
593839e1f2c3 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 4fe4a0b30469f52c937830d2f3c316f6b9667407" galaxyp parents: 3 diff changeset	590 </param>
593839e1f2c3 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 4fe4a0b30469f52c937830d2f3c316f6b9667407" galaxyp parents: 3 diff changeset	591 <param name="ylimUp" type="float" optional="true" label="For all three plots, upper limit for y-axis." help="Empty (default) for volcano plot/heatmap use maximum of -log2 (adjusted p-value) or -log10 (adjusted p-value), for comparison plot uses maximum of log-fold change + CI. Alternatively, insert specific value of y-axis limit. "/>
593839e1f2c3 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 4fe4a0b30469f52c937830d2f3c316f6b9667407" galaxyp parents: 3 diff changeset	592 <param name="ylimDown" type="float" optional="true" label="For all tree plots, lower limit for y-axis in the log scale" help="Empty (default) for volcano plot/heatmap use minimum of -log2 (adjusted p-value) or -log10 (adjusted p-value), for comparison plot uses minimum of log-fold change - CI. Alternatively, insert specific value of y-axis limit. "/>
593839e1f2c3 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 4fe4a0b30469f52c937830d2f3c316f6b9667407" galaxyp parents: 3 diff changeset	593 <param name="xlimUp" type="float" optional="true" label="For Volcano plot, the limit for x-axis" help="Empty (default) for use maximum for absolute value of log-fold change or 3 as default if maximum for absolute value of log-fold change is less than 3. Alternatively, insert specific value of y-axis limit."/>
593839e1f2c3 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 4fe4a0b30469f52c937830d2f3c316f6b9667407" galaxyp parents: 3 diff changeset	594 <param name="axis_size" type="integer" min="1" value="10" label="Size of axes labels for Residual and QQ Plots"/>
593839e1f2c3 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 4fe4a0b30469f52c937830d2f3c316f6b9667407" galaxyp parents: 3 diff changeset	595 <param name="x_axis_size" type="integer" min="1" value="10" label="Size of x-axis labeling"/>
593839e1f2c3 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 4fe4a0b30469f52c937830d2f3c316f6b9667407" galaxyp parents: 3 diff changeset	596 <param name="y_axis_size" type="integer" min="1" value="10" label="Size of y-axis labeling"/>
593839e1f2c3 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 4fe4a0b30469f52c937830d2f3c316f6b9667407" galaxyp parents: 3 diff changeset	597 <param name="dot_size" type="integer" min="1" value="3" label="Size of dots in residual plots, QQPlots, volcano plot and comparison plot."/>
593839e1f2c3 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 4fe4a0b30469f52c937830d2f3c316f6b9667407" galaxyp parents: 3 diff changeset	598 <param name="text_size" type="integer" min="1" value="4" label="Size of Protein Name label in the graph for Volcano Plot."/>
593839e1f2c3 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 4fe4a0b30469f52c937830d2f3c316f6b9667407" galaxyp parents: 3 diff changeset	599 <param name="text_angle" type="integer" min="0" max="360" value="90" label="Angle of x-axis labels represented each comparison at the bottom of graph incomparison plot."/>
593839e1f2c3 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 4fe4a0b30469f52c937830d2f3c316f6b9667407" galaxyp parents: 3 diff changeset	600 <param name="legend_size" type="integer" min="1" value="7" label="Size of legend for color at the bottom of volcano plot. "/>
593839e1f2c3 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 4fe4a0b30469f52c937830d2f3c316f6b9667407" galaxyp parents: 3 diff changeset	601 <param name="ProteinName" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="true" label="Display protein names in Volcano Plot." help="Yes (default) means protein names, which are significant, are displayed next to the points. No means no protein names are displayed."/>
593839e1f2c3 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 4fe4a0b30469f52c937830d2f3c316f6b9667407" galaxyp parents: 3 diff changeset	602 <param name="colorkey" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="true" label="Show colour key"/>
593839e1f2c3 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 4fe4a0b30469f52c937830d2f3c316f6b9667407" galaxyp parents: 3 diff changeset	603 <param name="numProtein" type="integer" min="1" value="100" max="180" label="Number of proteins which will be presented in each heatmap."/>
593839e1f2c3 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 4fe4a0b30469f52c937830d2f3c316f6b9667407" galaxyp parents: 3 diff changeset	604 <param name="clustering" type="select" label="Determines how to order proteins and comparisons. Hierarchical cluster analysis with Ward method(minimum variance) is performed.">
593839e1f2c3 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 4fe4a0b30469f52c937830d2f3c316f6b9667407" galaxyp parents: 3 diff changeset	605 <help>’protein’ means that protein dendrogram is computed and reordered based on protein means (the order of row is changed). ’comparison’ means comparison dendrogram is computed and reordered based on comparison means (the order of comparison is changed). ’both’ means to reorder both protein and comparison.</help>
593839e1f2c3 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 4fe4a0b30469f52c937830d2f3c316f6b9667407" galaxyp parents: 3 diff changeset	606 <option value="protein" selected="true">protein</option>
593839e1f2c3 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 4fe4a0b30469f52c937830d2f3c316f6b9667407" galaxyp parents: 3 diff changeset	607 <option value="comparison">comparison</option>
593839e1f2c3 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 4fe4a0b30469f52c937830d2f3c316f6b9667407" galaxyp parents: 3 diff changeset	608 <option value="both">both</option>
593839e1f2c3 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 4fe4a0b30469f52c937830d2f3c316f6b9667407" galaxyp parents: 3 diff changeset	609 </param>
593839e1f2c3 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 4fe4a0b30469f52c937830d2f3c316f6b9667407" galaxyp parents: 3 diff changeset	610 <conditional name="which_Comparison">
593839e1f2c3 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 4fe4a0b30469f52c937830d2f3c316f6b9667407" galaxyp parents: 3 diff changeset	611 <param name="select" type="select" label="Select comparisons to draw plots">
593839e1f2c3 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 4fe4a0b30469f52c937830d2f3c316f6b9667407" galaxyp parents: 3 diff changeset	612 <option value="all" selected="true">Generate all plots for each comparison</option>
593839e1f2c3 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 4fe4a0b30469f52c937830d2f3c316f6b9667407" galaxyp parents: 3 diff changeset	613 <option value="list">Comparison names as tabular input</option>
593839e1f2c3 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 4fe4a0b30469f52c937830d2f3c316f6b9667407" galaxyp parents: 3 diff changeset	614 </param>
593839e1f2c3 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 4fe4a0b30469f52c937830d2f3c316f6b9667407" galaxyp parents: 3 diff changeset	615 <when value="all"/>
593839e1f2c3 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 4fe4a0b30469f52c937830d2f3c316f6b9667407" galaxyp parents: 3 diff changeset	616 <when value="list">
593839e1f2c3 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 4fe4a0b30469f52c937830d2f3c316f6b9667407" galaxyp parents: 3 diff changeset	617 <param name="comparison_list" type="data" format="tabular" label="List of comparisons"/>
593839e1f2c3 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 4fe4a0b30469f52c937830d2f3c316f6b9667407" galaxyp parents: 3 diff changeset	618 </when>
593839e1f2c3 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 4fe4a0b30469f52c937830d2f3c316f6b9667407" galaxyp parents: 3 diff changeset	619 </conditional>
593839e1f2c3 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 4fe4a0b30469f52c937830d2f3c316f6b9667407" galaxyp parents: 3 diff changeset	620 </section>
593839e1f2c3 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 4fe4a0b30469f52c937830d2f3c316f6b9667407" galaxyp parents: 3 diff changeset	621 </section>
0 80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	622 </when>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	623 </conditional>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	624 </inputs>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	625 <outputs>
3 8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	626 <data name="log" format="txt" label="${tool.name} on ${on_string}: MSstats log">
4 593839e1f2c3 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 4fe4a0b30469f52c937830d2f3c316f6b9667407" galaxyp parents: 3 diff changeset	627 <filter>'log' in in dp_options['selected_outputs']</filter>
0 80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	628 </data>
3 8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	629 <data name="r_script" format="txt" label="${tool.name} on ${on_string}: Rscript">
4 593839e1f2c3 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 4fe4a0b30469f52c937830d2f3c316f6b9667407" galaxyp parents: 3 diff changeset	630 <filter>'r_script' in dp_options['selected_outputs']</filter>
593839e1f2c3 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 4fe4a0b30469f52c937830d2f3c316f6b9667407" galaxyp parents: 3 diff changeset	631 </data>
593839e1f2c3 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 4fe4a0b30469f52c937830d2f3c316f6b9667407" galaxyp parents: 3 diff changeset	632 <data name="raw_data" format="tabular" label="${tool.name} on ${on_string}: RawData" from_work_dir="raw.tsv">
593839e1f2c3 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 4fe4a0b30469f52c937830d2f3c316f6b9667407" galaxyp parents: 3 diff changeset	633 <filter>'raw_data' in dp_options['selected_outputs']</filter>
0 80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	634 </data>
3 8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	635 <data name="processed_data" format="tabular" label="${tool.name} on ${on_string}: ProcessedData" from_work_dir="ProcessedData.tsv">
4 593839e1f2c3 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 4fe4a0b30469f52c937830d2f3c316f6b9667407" galaxyp parents: 3 diff changeset	636 <filter>'processed_data' in dp_options['selected_outputs']</filter>
593839e1f2c3 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 4fe4a0b30469f52c937830d2f3c316f6b9667407" galaxyp parents: 3 diff changeset	637 <!--actions>
1 3e2606fa85bf "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit fa543ac667f63409bfb2e28fd6c711e74d828a79" galaxyp parents: 0 diff changeset	638 <action name="column_names" type="metadata" default="PROTEIN,PEPTIDE,TRANSITION,FEATURE,LABEL,GROUP_ORIGINAL,SUBJECT_ORIGINAL,RUN,GROUP,SUBJECT,INTENSITY,SUBJECT_NESTED,ABUNDANCE,FRACTION,originalRUN,censored" />
4 593839e1f2c3 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 4fe4a0b30469f52c937830d2f3c316f6b9667407" galaxyp parents: 3 diff changeset	639 </actions-->
0 80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	640 </data>
3 8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	641 <data name="runlevel_data" format="tabular" label="${tool.name} on ${on_string}: RunlevelData" from_work_dir="RunlevelData.tsv">
4 593839e1f2c3 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 4fe4a0b30469f52c937830d2f3c316f6b9667407" galaxyp parents: 3 diff changeset	642 <filter>'runlevel_data' in dp_options['selected_outputs']</filter>
593839e1f2c3 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 4fe4a0b30469f52c937830d2f3c316f6b9667407" galaxyp parents: 3 diff changeset	643 <!--actions>
1 3e2606fa85bf "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit fa543ac667f63409bfb2e28fd6c711e74d828a79" galaxyp parents: 0 diff changeset	644 <action name="column_names" type="metadata" default="RUN,Protein,LogIntensities,NumMeasuredFeature,MissingPercentage,more50missing,NumImputedFeature,originalRUN,GROUP,GROUP_ORIGINAL,SUBJECT_ORIGINAL,SUBJECT_NESTED,SUBJECT" />
4 593839e1f2c3 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 4fe4a0b30469f52c937830d2f3c316f6b9667407" galaxyp parents: 3 diff changeset	645 </actions-->
0 80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	646 </data>
3 8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	647 <data name="QCPlot" format="pdf" label="${tool.name} on ${on_string}: QCPlot" from_work_dir="MSStats_only_QCPlot.pdf">
4 593839e1f2c3 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 4fe4a0b30469f52c937830d2f3c316f6b9667407" galaxyp parents: 3 diff changeset	648 <filter>dp_options['out_plots_opt']['selected_vis_outputs'] and 'QCPlot' in dp_options['out_plots_opt']['selected_vis_outputs']</filter>
0 80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	649 </data>
3 8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	650 <data name="ProfilePlot" format="pdf" label="${tool.name} on ${on_string}: Profile Plot" from_work_dir="MSStats_only_ProfilePlot.pdf">
4 593839e1f2c3 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 4fe4a0b30469f52c937830d2f3c316f6b9667407" galaxyp parents: 3 diff changeset	651 <filter>dp_options['out_plots_opt']['selected_vis_outputs'] and 'ProfilePlot' in dp_options['out_plots_opt']['selected_vis_outputs']</filter>
0 80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	652 </data>
3 8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	653 <data name="profile_wsum_plot" format="pdf" label="${tool.name} on ${on_string}: Profile Plot with Summarization" from_work_dir="MSStats_only_ProfilePlot_wSummarization.pdf">
4 593839e1f2c3 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 4fe4a0b30469f52c937830d2f3c316f6b9667407" galaxyp parents: 3 diff changeset	654 <filter>dp_options['out_plots_opt']['selected_vis_outputs'] and 'profile_wsum_plot' in dp_options['out_plots_opt']['selected_vis_outputs']</filter>
0 80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	655 </data>
3 8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	656 <data name="ConditionPlot" format="pdf" label="${tool.name} on ${on_string}: Condition Plot" from_work_dir="MSStats_only_ConditionPlot.pdf">
4 593839e1f2c3 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 4fe4a0b30469f52c937830d2f3c316f6b9667407" galaxyp parents: 3 diff changeset	657 <filter>dp_options['out_plots_opt']['selected_vis_outputs'] and 'ConditionPlot' in dp_options['out_plots_opt']['selected_vis_outputs']</filter>
0 80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	658 </data>
3 8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	659 <data name="quant_sample_matrix" format="tabular" label="${tool.name} on ${on_string}: Sample Quantification Matrix" from_work_dir="SampleQuantificationMatrix.tsv">
4 593839e1f2c3 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 4fe4a0b30469f52c937830d2f3c316f6b9667407" galaxyp parents: 3 diff changeset	660 <filter>'quant_sample_matrix' in dp_options['selected_outputs']</filter>
0 80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	661 </data>
3 8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	662 <data name="quant_sample_long" format="tabular" label=" ${tool.name} on ${on_string}:Sample Quantification Long" from_work_dir="SampleQuantificationLong.tsv">
4 593839e1f2c3 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 4fe4a0b30469f52c937830d2f3c316f6b9667407" galaxyp parents: 3 diff changeset	663 <filter>'quant_sample_long' in dp_options['selected_outputs']</filter>
593839e1f2c3 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 4fe4a0b30469f52c937830d2f3c316f6b9667407" galaxyp parents: 3 diff changeset	664 <!--actions>
1 3e2606fa85bf "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit fa543ac667f63409bfb2e28fd6c711e74d828a79" galaxyp parents: 0 diff changeset	665 <action name="column_names" type="metadata" default="Protein,Group_Subject,LogIntensity" />
4 593839e1f2c3 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 4fe4a0b30469f52c937830d2f3c316f6b9667407" galaxyp parents: 3 diff changeset	666 </actions-->
0 80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	667 </data>
3 8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	668 <data name="quant_group_matrix" format="tabular" label="${tool.name} on ${on_string}: Group Quantification Matrix" from_work_dir="GroupQuantificationMatrix.tsv">
4 593839e1f2c3 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 4fe4a0b30469f52c937830d2f3c316f6b9667407" galaxyp parents: 3 diff changeset	669 <filter>'quant_group_matrix' in dp_options['selected_outputs']</filter>
0 80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	670 </data>
3 8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	671 <data name="quant_group_long" format="tabular" label="${tool.name} on ${on_string}: Group Quantification Long" from_work_dir="GroupQuantificationLong.tsv">
4 593839e1f2c3 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 4fe4a0b30469f52c937830d2f3c316f6b9667407" galaxyp parents: 3 diff changeset	672 <filter>'quant_group_long' in dp_options['selected_outputs']</filter>
593839e1f2c3 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 4fe4a0b30469f52c937830d2f3c316f6b9667407" galaxyp parents: 3 diff changeset	673 <!--actions>
1 3e2606fa85bf "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit fa543ac667f63409bfb2e28fd6c711e74d828a79" galaxyp parents: 0 diff changeset	674 <action name="column_names" type="metadata" default="Protein,Group,LogIntensity" />
4 593839e1f2c3 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 4fe4a0b30469f52c937830d2f3c316f6b9667407" galaxyp parents: 3 diff changeset	675 </actions-->
0 80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	676 </data>
3 8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	677 <data name="comparison_result" format="tabular" label="${tool.name} on ${on_string}: Comparison Result" from_work_dir="ComparisonResult.tsv">
0 80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	678 <filter> group['group_comparison'] == 'yes' and 'comparison_result' in group['select_outputs']</filter>
4 593839e1f2c3 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 4fe4a0b30469f52c937830d2f3c316f6b9667407" galaxyp parents: 3 diff changeset	679 <!--actions>
1 3e2606fa85bf "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit fa543ac667f63409bfb2e28fd6c711e74d828a79" galaxyp parents: 0 diff changeset	680 <action name="column_names" type="metadata" default="Protein,Label,log2FC,SE,Tvalue,DF,pvalue,adj.pvalue,issue,MissingPercentage,ImputationPercentage" />
4 593839e1f2c3 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 4fe4a0b30469f52c937830d2f3c316f6b9667407" galaxyp parents: 3 diff changeset	681 </actions-->
0 80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	682 </data>
3 8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	683 <data name="fittedmodel" format="txt" label="${tool.name} on ${on_string}: Comparison Fitted Model" from_work_dir="ComparisonFittedModel.txt">
0 80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	684 <filter> group['group_comparison'] == 'yes' and 'fittedmodel' in group['select_outputs']</filter>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	685 </data>
3 8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	686 <data name="model_qc" format="tabular" label="${tool.name} on ${on_string}: Model QC" from_work_dir="ModelQC.tsv">
0 80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	687 <filter> group['group_comparison'] == 'yes' and 'model_qc' in group['select_outputs']</filter>
4 593839e1f2c3 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 4fe4a0b30469f52c937830d2f3c316f6b9667407" galaxyp parents: 3 diff changeset	688 <!--actions>
1 3e2606fa85bf "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit fa543ac667f63409bfb2e28fd6c711e74d828a79" galaxyp parents: 0 diff changeset	689 <action name="column_names" type="metadata" default="RUN,PROTEIN,ABUNDANCE,NumMeasuredFeature,MissingPercentage,more50missing,NumImputedFeature,originalRUN,GROUP,GROUP_ORIGINAL,SUBJECT_ORIGINAL,SUBJECT_NESTED,SUBJECT,residuals,fitted" />
4 593839e1f2c3 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 4fe4a0b30469f52c937830d2f3c316f6b9667407" galaxyp parents: 3 diff changeset	690 </actions-->
0 80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	691 </data>
3 8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	692 <data name="QQPlots" format="pdf" label="${tool.name} on ${on_string}: Model QQ" from_work_dir="MSStats_group_QQPlot.pdf">
4 593839e1f2c3 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 4fe4a0b30469f52c937830d2f3c316f6b9667407" galaxyp parents: 3 diff changeset	693 <filter> group['group_comparison'] == 'yes' and group['comparison_plots_opt']['select_comparison_plots'] and 'QQPlots' in group['comparison_plots_opt']['select_comparison_plots']</filter>
0 80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	694 </data>
3 8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	695 <data name="ResidualPlots" format="pdf" label="${tool.name} on ${on_string}: Residual Plot" from_work_dir="MSStats_group_ResidualPlot.pdf">
4 593839e1f2c3 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 4fe4a0b30469f52c937830d2f3c316f6b9667407" galaxyp parents: 3 diff changeset	696 <filter> group['group_comparison'] == 'yes' and group['comparison_plots_opt']['select_comparison_plots'] and 'ResidualPlots' in group['comparison_plots_opt']['select_comparison_plots']</filter>
0 80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	697 </data>
3 8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	698 <data name="VolcanoPlot" format="pdf" label="${tool.name} on ${on_string}:Volcano Plot" from_work_dir="MSStats_group_VolcanoPlot.pdf">
4 593839e1f2c3 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 4fe4a0b30469f52c937830d2f3c316f6b9667407" galaxyp parents: 3 diff changeset	699 <filter> group['group_comparison'] == 'yes' and group['comparison_plots_opt']['select_comparison_plots'] and 'VolcanoPlot' in group['comparison_plots_opt']['select_comparison_plots']</filter>
0 80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	700 </data>
3 8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	701 <data name="Heatmap" format="pdf" label="${tool.name} on ${on_string}: Heatmap" from_work_dir="MSStats_group_Heatmap.pdf">
4 593839e1f2c3 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 4fe4a0b30469f52c937830d2f3c316f6b9667407" galaxyp parents: 3 diff changeset	702 <filter> group['group_comparison'] == 'yes' and group['comparison_plots_opt']['select_comparison_plots'] and 'Heatmap' in group['comparison_plots_opt']['select_comparison_plots']</filter>
0 80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	703 </data>
3 8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	704 <data name="ComparisonPlot" format="pdf" label="${tool.name} on ${on_string}: Comparison Plot" from_work_dir="MSStats_group_ComparisonPlot.pdf">
4 593839e1f2c3 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 4fe4a0b30469f52c937830d2f3c316f6b9667407" galaxyp parents: 3 diff changeset	705 <filter> group['group_comparison'] == 'yes' and group['comparison_plots_opt']['select_comparison_plots'] and 'ComparisonPlot' in group['comparison_plots_opt']['select_comparison_plots']</filter>
0 80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	706 </data>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	707 </outputs>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	708 <tests>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	709 <test>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	710 <conditional name="input">
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	711 <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	712 <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	713 </conditional>
4 593839e1f2c3 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 4fe4a0b30469f52c937830d2f3c316f6b9667407" galaxyp parents: 3 diff changeset	714 <param name="selected_outputs" value="raw_data,processed_data,quant_sample_matrix,quant_group_long"/>
593839e1f2c3 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 4fe4a0b30469f52c937830d2f3c316f6b9667407" galaxyp parents: 3 diff changeset	715 <param name="selected_vis_outputs" value="ProfilePlot,profile_wsum_plot"/>
0 80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	716 <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	717 <assert_contents>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	718 <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	719 <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	720 <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	721 </assert_contents>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	722 </output>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	723 <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	724 <assert_contents>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	725 <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	726 <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	727 <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	728 </assert_contents>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	729 </output>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	730 <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	731 <assert_contents>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	732 <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	733 <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	734 <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	735 </assert_contents>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	736 </output>
3 8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	737 <output name="ProfilePlot" file="MSstats ProfilePlot.pdf" compare="sim_size"/>
0 80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	738 <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	739 </test>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	740
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	741 <test>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	742 <conditional name="input">
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	743 <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	744 <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	745 </conditional>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	746 <conditional name="group">
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	747 <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	748 <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	749 </conditional>
4 593839e1f2c3 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 4fe4a0b30469f52c937830d2f3c316f6b9667407" galaxyp parents: 3 diff changeset	750 <param name="select_outputs" value="model_qc"/>
593839e1f2c3 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 4fe4a0b30469f52c937830d2f3c316f6b9667407" galaxyp parents: 3 diff changeset	751 <param name="select_comparison_plots" value="ResidualPlots"/>
0 80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	752 <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	753 <assert_contents>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	754 <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	755 <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	756 <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	757 </assert_contents>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	758 </output>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	759 <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	760 <assert_contents>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	761 <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	762 <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	763 <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	764 </assert_contents>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	765 </output>
3 8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	766 <output name="ResidualPlots" file="residual_plot.pdf" compare="sim_size"/>
0 80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	767 </test>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	768
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	769 <test>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	770 <conditional name="input">
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	771 <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	772 <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	773 <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	774 <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	775 </conditional>
4 593839e1f2c3 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 4fe4a0b30469f52c937830d2f3c316f6b9667407" galaxyp parents: 3 diff changeset	776 <param name="selected_outputs" value="processed_data,runlevel_data"/>
593839e1f2c3 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 4fe4a0b30469f52c937830d2f3c316f6b9667407" galaxyp parents: 3 diff changeset	777 <param name="selected_vis_outputs" value="ConditionPlot"/>
0 80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	778 <conditional name="group">
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	779 <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	780 <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	781 </conditional>
4 593839e1f2c3 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 4fe4a0b30469f52c937830d2f3c316f6b9667407" galaxyp parents: 3 diff changeset	782 <param name="select_outputs" value="comparison_result"/>
593839e1f2c3 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 4fe4a0b30469f52c937830d2f3c316f6b9667407" galaxyp parents: 3 diff changeset	783 <param name="select_comparison_plots" value="QQPlots"/>
0 80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	784 <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	785 <assert_contents>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	786 <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	787 <has_n_columns n="16" />
3 8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	788 <has_n_lines n="61" />
0 80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	789 </assert_contents>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	790 </output>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	791 <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	792 <assert_contents>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	793 <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	794 <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	795 <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	796 </assert_contents>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	797 </output>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	798 <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	799 <assert_contents>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	800 <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	801 <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	802 <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	803 </assert_contents>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	804 </output>
3 8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	805 <output name="ConditionPlot" file="condition_plot.pdf" compare="sim_size"/>
8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	806 <output name="QQPlots" file="qq_plot.pdf" compare="sim_size"/>
0 80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	807 </test>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	808
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	809 <test>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	810 <conditional name="input">
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	811 <param name="input_src" value="OpenMS"/>
3 8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	812 <param name="openms_input" ftype="tabular" value="openms_input.tabular"/>
8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	813 </conditional>
4 593839e1f2c3 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 4fe4a0b30469f52c937830d2f3c316f6b9667407" galaxyp parents: 3 diff changeset	814 <param name="selected_outputs" value="processed_data,runlevel_data"/>
593839e1f2c3 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 4fe4a0b30469f52c937830d2f3c316f6b9667407" galaxyp parents: 3 diff changeset	815 <param name="selected_vis_outputs" value="ConditionPlot"/>
3 8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	816 <conditional name="group">
8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	817 <param name="group_comparison" value="yes"/>
8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	818 <param name="comparison_matrix" ftype="tabular" value="openms_comparisonmatrix.tabular"/>
0 80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	819 </conditional>
4 593839e1f2c3 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 4fe4a0b30469f52c937830d2f3c316f6b9667407" galaxyp parents: 3 diff changeset	820 <param name="select_comparison_plots" value="Heatmap"/>
0 80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	821 <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	822 <assert_contents>
3 8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	823 <has_text text="AAAPGIQLVAGEGFQSPLEDR_2_NA_0" />
8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	824 <has_text text="sp\|P09938\|RIR2_YEAST" />
8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	825 <has_n_columns n="16" />
8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	826 <has_n_lines n="121" />
8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	827 </assert_contents>
8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	828 </output>
8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	829 <output name="runlevel_data">
8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	830 <assert_contents>
8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	831 <has_text text="sp\|P09457\|ATPO_YEAST" />
8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	832 <has_n_columns n="13" />
8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	833 <has_n_lines n="76" />
0 80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	834 </assert_contents>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	835 </output>
3 8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	836 <output name="ConditionPlot" file="condition_plot_openms.pdf" compare="sim_size"/>
8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	837 <output name="Heatmap" file="Heatmap_openms.pdf" compare="sim_size"/>
0 80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	838 </test>
3 8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	839 <test>
8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	840 <conditional name="input">
8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	841 <param name="input_src" value="Skyline"/>
8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	842 <param name="skyline_input" ftype="csv" value="skyline_input_first100.csv"/>
8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	843 <param name="annotation" ftype="csv" value="skyline_annotations.csv"/>
8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	844 <param name="removeProtein_with1Peptide" value="TRUE"/>
8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	845 </conditional>
8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	846 <conditional name="summarize">
8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	847 <param name="MBimpute" value="FALSE"/>
8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	848 <param name="censoredInt" value="NULL"/>
8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	849 </conditional>
4 593839e1f2c3 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 4fe4a0b30469f52c937830d2f3c316f6b9667407" galaxyp parents: 3 diff changeset	850 <param name="selected_outputs" value="log,processed_data,quant_sample_long"/>
593839e1f2c3 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 4fe4a0b30469f52c937830d2f3c316f6b9667407" galaxyp parents: 3 diff changeset	851 <param name="selected_vis_outputs" value="ProfilePlot"/>
3 8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	852 <param name="featureName" value="Peptide"/>
8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	853 <param name="width" value="10"/>
8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	854 <param name="height" value="7"/>
8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	855 <conditional name="group">
8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	856 <param name="group_comparison" value="yes"/>
8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	857 <param name="comparison_matrix" ftype="tabular" value="comparison_matrix_skyline.tabular"/>
8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	858 </conditional>
4 593839e1f2c3 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 4fe4a0b30469f52c937830d2f3c316f6b9667407" galaxyp parents: 3 diff changeset	859 <section name="comparison_plots_opt">
593839e1f2c3 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 4fe4a0b30469f52c937830d2f3c316f6b9667407" galaxyp parents: 3 diff changeset	860 <param name="select_outputs" value="comparison_result"/>
593839e1f2c3 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 4fe4a0b30469f52c937830d2f3c316f6b9667407" galaxyp parents: 3 diff changeset	861 <param name="select_comparison_plots" value="VolcanoPlot,ComparisonPlot"/>
593839e1f2c3 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 4fe4a0b30469f52c937830d2f3c316f6b9667407" galaxyp parents: 3 diff changeset	862 <section name="comparison_vis_options">
593839e1f2c3 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 4fe4a0b30469f52c937830d2f3c316f6b9667407" galaxyp parents: 3 diff changeset	863 <param name="FCcutoff" value="2" />
593839e1f2c3 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 4fe4a0b30469f52c937830d2f3c316f6b9667407" galaxyp parents: 3 diff changeset	864 <conditional name="which_Comparison">
593839e1f2c3 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 4fe4a0b30469f52c937830d2f3c316f6b9667407" galaxyp parents: 3 diff changeset	865 <param name="select" value="list"/>
593839e1f2c3 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 4fe4a0b30469f52c937830d2f3c316f6b9667407" galaxyp parents: 3 diff changeset	866 <param name="comparison_list" ftype="tabular" value="comparison_list_skyline.tabular"/>
593839e1f2c3 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 4fe4a0b30469f52c937830d2f3c316f6b9667407" galaxyp parents: 3 diff changeset	867 </conditional>
593839e1f2c3 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 4fe4a0b30469f52c937830d2f3c316f6b9667407" galaxyp parents: 3 diff changeset	868 </section>
593839e1f2c3 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 4fe4a0b30469f52c937830d2f3c316f6b9667407" galaxyp parents: 3 diff changeset	869 </section>
3 8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	870 <output name="quant_sample_long">
8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	871 <assert_contents>
8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	872 <has_text text="P32125" />
8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	873 <has_text text="Condition5_5" />
8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	874 <has_n_columns n="3" />
8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	875 <has_n_lines n="6" />
8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	876 </assert_contents>
8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	877 </output>
8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	878 <output name="log">
8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	879 <assert_contents>
8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	880 <has_text text="ADVGFLC" />
8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	881 <has_text text="1 level of Isotope type labeling in this experiment" />
8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	882 <has_text text="The required input : provided - okay" />
8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	883 </assert_contents>
8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	884 </output>
8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	885 <output name="processed_data">
8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	886 <assert_contents>
8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	887 <has_text text="ADVGFLC[+57]NMLER_2_sum_NA" />
8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	888 <has_text text="319070944" />
8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	889 <has_n_columns n="15" />
8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	890 <has_n_lines n="46" />
8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	891 </assert_contents>
8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	892 </output>
8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	893 <output name="comparison_result">
8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	894 <assert_contents>
8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	895 <has_text text="c1-c4" />
8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	896 <has_text text="log2FC" />
8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	897 <has_n_lines n="4" />
8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	898 </assert_contents>
8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	899 </output>
8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	900 <output name="ProfilePlot" file="Profile_plot_skyline.pdf" compare="sim_size"/>
8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	901 <output name="VolcanoPlot" file="Volcano_plot_skyline.pdf" compare="sim_size"/>
8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	902 <output name="ComparisonPlot" file="Comparison_plot_skyline.pdf" compare="sim_size"/>
8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	903 </test>
0 80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	904
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	905 <test>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	906 <conditional name="input">
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	907 <param name="input_src" value="OpenSWATH"/>
3 8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	908 <param name="openswath_input" ftype="tabular" value="test_swath_input_data.tabular"/>
0 80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	909 <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	910 </conditional>
4 593839e1f2c3 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 4fe4a0b30469f52c937830d2f3c316f6b9667407" galaxyp parents: 3 diff changeset	911 <param name="selected_vis_outputs" value="QCPlot"/>
0 80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	912 <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	913 <assert_contents>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	914 <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	915 <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	916 <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	917 </assert_contents>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	918 </output>
3 8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	919 <output name="QCPlot" file="QC_plot.pdf" compare="sim_size"/>
0 80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	920 </test>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	921
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	922 <test>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	923 <conditional name="input">
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	924 <param name="input_src" value="OpenSWATH"/>
3 8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	925 <param name="openswath_input" ftype="tabular" value="test_swath_input_data.tabular"/>
0 80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	926 <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	927 </conditional>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	928 <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	929 <conditional name="group">
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	930 <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	931 <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	932 </conditional>
4 593839e1f2c3 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 4fe4a0b30469f52c937830d2f3c316f6b9667407" galaxyp parents: 3 diff changeset	933 <param name="select_outputs" value="comparison_result"/>
593839e1f2c3 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 4fe4a0b30469f52c937830d2f3c316f6b9667407" galaxyp parents: 3 diff changeset	934 <param name="select_comparison_plots" value="VolcanoPlot,ResidualPlots"/>
0 80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	935 <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	936 <assert_contents>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	937 <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	938 <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	939 <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	940 </assert_contents>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	941 </output>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	942 <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	943 <assert_contents>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	944 <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	945 <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	946 <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	947 </assert_contents>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	948 </output>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	949 <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	950 <assert_contents>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	951 <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	952 <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	953 <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	954 </assert_contents>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	955 </output>
3 8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	956 <output name="VolcanoPlot" file="volcanoplot.pdf" compare="sim_size"/>
8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	957 <output name="ResidualPlots" file="residualplot.pdf" compare="sim_size"/>
0 80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	958 </test>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	959
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	960 </tests>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	961 <help><![CDATA[
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	962 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	963
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	964 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	965
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	966 -----
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	967
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	968 Input data
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	969
3 8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	970 - Data in tabular or csv format, either in the 10-column MSstats format or the outputs of spectral processing tools such as `MaxQuant <http://coxdocs.org/doku.php?id=maxquant:start/>`_, `OpenSWATH <http://openswath.org/en/latest/>`_
0 80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	971
3 8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	972 - 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:
0 80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	973
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	974 - 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
3 8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	975 - PeptideSequence: Amino acid sequence for each peptide. If the peptide sequences should be distinguished based on post-translational modifications, this column can be renamed to PeptideModifiedSequence.
0 80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	976 - 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	977 - 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	978 - 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	979 - IsotopeLabelType: This column indicates whether this measurement is based on the endogenous peptides (use “L”) or labeled reference peptides (use “H”).
3 8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	980 - Condition: For group comparison experiments, this column indicates groups of interest (such as “Disease” or “Control”). The name of the condition is not allowed to start with a number or contain any special characters. 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.).
0 80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	981 - 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	982 - 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	983 - 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	984 - Example file header:
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	985 ::
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	986
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	987 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	988 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	989 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	990 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	991 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	992 ... ... ... ... ...
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	993
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	994 isotopelabeltype condition bioreplicate run intensity
3 8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	995 L disease ReplA 1 4298.12
8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	996 H disease ReplA 1 1974.59
8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	997 L disease ReplA 1 7183.22
8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	998 H disease ReplA 1 8467.58
0 80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	999 ... ... ... ... ...
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	1000
3 8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	1001 - MaxQuant format: evidence.txt, proteinGroups.txt; plus externally generated annotation file
8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	1002 - OpenSWATH format: pyprophet export file; plus externally generated annotation file
0 80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	1003
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	1004 - 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	1005
2 52ac6fde9a5b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 414edbbd89f9bc83b81289e409c9b688c8c1e40f" galaxyp parents: 1 diff changeset	1006 - 4 columns with exactly these headers: Raw.file, Condition, BioReplicate, Run; additional 5th column only for MaxQuant: IsotopeLabelType
4 593839e1f2c3 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 4fe4a0b30469f52c937830d2f3c316f6b9667407" galaxyp parents: 3 diff changeset	1007 - Example file header:
0 80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	1008
4 593839e1f2c3 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 4fe4a0b30469f52c937830d2f3c316f6b9667407" galaxyp parents: 3 diff changeset	1009 ::
593839e1f2c3 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 4fe4a0b30469f52c937830d2f3c316f6b9667407" galaxyp parents: 3 diff changeset	1010
593839e1f2c3 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 4fe4a0b30469f52c937830d2f3c316f6b9667407" galaxyp parents: 3 diff changeset	1011 Raw.file Condition BioReplicate Run IsotopeLabelType
593839e1f2c3 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 4fe4a0b30469f52c937830d2f3c316f6b9667407" galaxyp parents: 3 diff changeset	1012 ** disease ReplA 1 L
593839e1f2c3 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 4fe4a0b30469f52c937830d2f3c316f6b9667407" galaxyp parents: 3 diff changeset	1013 ** disease ReplA 2 L
593839e1f2c3 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 4fe4a0b30469f52c937830d2f3c316f6b9667407" galaxyp parents: 3 diff changeset	1014 ** disease ReplB 3 L
593839e1f2c3 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 4fe4a0b30469f52c937830d2f3c316f6b9667407" galaxyp parents: 3 diff changeset	1015 ** disease ReplB 4 L
593839e1f2c3 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 4fe4a0b30469f52c937830d2f3c316f6b9667407" galaxyp parents: 3 diff changeset	1016 ... ... ... ... ...
3 8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	1017
4 593839e1f2c3 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 4fe4a0b30469f52c937830d2f3c316f6b9667407" galaxyp parents: 3 diff changeset	1018
593839e1f2c3 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 4fe4a0b30469f52c937830d2f3c316f6b9667407" galaxyp parents: 3 diff changeset	1019 - Raw.file:
593839e1f2c3 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 4fe4a0b30469f52c937830d2f3c316f6b9667407" galaxyp parents: 3 diff changeset	1020
3 8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	1021 - OpenSWATH: File name needs to fit exactly how it is written in OpenSwatch output (e.g. "in/AA12_mzML.mzML")
4 593839e1f2c3 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 4fe4a0b30469f52c937830d2f3c316f6b9667407" galaxyp parents: 3 diff changeset	1022 - MaxQuant: File name needs to fit exactly how it is writtein in the evidence.txt "Raw file" column. (e.g. "file1.raw.thermo")
3 8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	1023 - Condition: The name of the condition is not allowed to start with a number or contain any special characters
8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	1024 - All other columns: see description above for MSstats format columns
0 80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	1025
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	1026 - 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	1027
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	1028 - 1st column: name of comparison
3 8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	1029 - 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.
4 593839e1f2c3 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 4fe4a0b30469f52c937830d2f3c316f6b9667407" galaxyp parents: 3 diff changeset	1030 - First row contains the names of the groups, they must exactly match the condition name used in the annotation file and every condition must be present, even though it will not be used for any comparison such as G4 in the example below. Order of the condition columns is irrelevant.
3 8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	1031 - Each additional row represents one comparison
0 80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	1032 - 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	1033
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	1034 ::
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	1035
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	1036 names groupA groupB
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	1037 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	1038
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	1039
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	1040 - 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	1041
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	1042 ::
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	1043
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	1044 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	1045 G2-G1 -1 1 0 0 0
4 593839e1f2c3 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 4fe4a0b30469f52c937830d2f3c316f6b9667407" galaxyp parents: 3 diff changeset	1046 G3-G5 0 0 1 0 -1
0 80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	1047 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	1048 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	1049
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	1050 Options
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	1051
3 8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	1052 - Data conversion from MaxQuant and OpenSWATH to MSstats format:
8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	1053
8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	1054 - MaxQuant input: Contaminants and reverse and only identified by site from MaxQuant tool are automatically removed during conversion
8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	1055
8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	1056 - Data processing options:
8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	1057
8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	1058 - Log transformation: log2 or log10 transformation of intensities
8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	1059 - Normalization of MS runs: If there are multiple fractionations or injections for one sample, normalization is performed by each fractionation or different m/z range from multiple injections.
0 80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	1060
3 8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	1061 - equalizeMedians: The default option for normalization is equalizeMedians, where all intensities in a run are shifted by a constant, to equalize the median of intensities across runs for label-free experiment. This normalization method is appropriate when we can assume that the majority of proteins do not change across runs. Be cautious when using the equalizeMedians option for a label-free DDA dataset with only a small number of proteins. For label based experiment, equalizeMedians equalizes the median of reference intensities across runs and is generally proper even for a dataset with a small number of proteins.
8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	1062 - globalStandards: If you have a spiked in standard, you may set this option to define the standard with name Standardsoption.
8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	1063 - quantile: The distribution of all the intensities in each run will become the same across runs for label-free experiment. For label-based experiment, the distribution of all the reference intensities will become the same across runs and all the endogenous intensities are shifted by a constant corresponding to reference intensities.
8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	1064 - FALSE: No normalization is performed. If you had your own normalization before MSstats use this option.
8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	1065
8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	1066 - Feature selection
0 80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	1067
3 8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	1068 - all: Use all features in the dataset.
8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	1069 - top3: Use top 3 features which have highest average of log(intensity) across runs.
8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	1070 - topN: Use top N (specify number) features which have highest average of log(intensity) across runs.
8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	1071 - highQuality: Detect and flag uninformative features (as Uninformative in the feature_quality column) and outliers (as TRUE in the is_outliercolumn). These uninformative content may be excluded from run-level summarization by setting the remove features flagged with uninformative feature quality option to TRUE.
8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	1072
8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	1073 - Summarizing intensities per MS run
8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	1074
8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	1075 - TMP: Tukey’s median polish. Robust parameter estimation method with median across rows and columns. Prerequisite for missing value imputation.
4 593839e1f2c3 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 4fe4a0b30469f52c937830d2f3c316f6b9667407" galaxyp parents: 3 diff changeset	1076 - linear: Linear model (lmfunction). Average-based summarization.
593839e1f2c3 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 4fe4a0b30469f52c937830d2f3c316f6b9667407" galaxyp parents: 3 diff changeset	1077
593839e1f2c3 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 4fe4a0b30469f52c937830d2f3c316f6b9667407" galaxyp parents: 3 diff changeset	1078 - Account for heterogeneous variation among intensities from different features: Yes: assumes equal variance among intensities from features. No: means that we cannot assume equal variance among intensities from features, then we will account for heterogeneous variation from different features
3 8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	1079
0 80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	1080 - Missing value imputation:
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	1081
3 8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	1082 - Impute Missing Values: Only possible for Summarization Method TMP. Censored missing values will be determined (by censored intensity; cutoff value for censoring and Maximum quantile for deciding censored missing values") and imputed by Accelerated Failure Time model.
8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	1083
8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	1084 - Remove runs which have more than 50% missing values: Yes or no.
8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	1085 - Censored Intensity: The processing tools report missing values differently. This option is for distinguishwhich value should be considered as missing, and further whether it is censored or at random
8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	1086
8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	1087 - NA - It assumes that all NAs in Intensity column are censored.
8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	1088 - 0 - It assumes that all values between 0 and 1 in Intensity column are censored. If there areNAs inIntensitywith this option, NAs will be considered as random missing.
8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	1089 - NULL - It assumes that all missing values are randomly missing.
8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	1090 - Skyline and OpenSWATH input should use '0'. MaxQuant input should use 'NA'
8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	1091 - Cutoff value for censoring: cutoff for AFT model; only with censored intensity 'NA' or '0'; if NULL it assumes that there is no censored missing and any imputation will not be performed. In case that there are completely missing measurements in a run for a protein, any imputation will not be performed. In addition, the condition, which has no measurement at all in a protein, will be not impute.
0 80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	1092
3 8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	1093 - minimum value for each feature: cutoff for AFT model will be the minimum value for each feature across runs. With this option, those runs with substantial missing measurements will be biased by the cutoff value. In such case, you may remove the runs that have more than 50% missing values from the analysis.
8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	1094 - minimum value for each run: cutoff for AFT model will be the minimum value for each run across features
8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	1095 - smallest between minimum value of corresponding feature and minimum value of corresponding run: cutoff for AFT model will be the smallest value between minimum valueof corresponding feature and minimum value of corresponding run
8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	1096 - Maximum quantile for deciding censored missing values: If you don’t want to apply the threshold of noise intensity in your data, you can use maxQuantileforCensored=NULL.
8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	1097 - Missing value imputation combination with summarization method TMP:
8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	1098
8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	1099 - Summarization method: TMP + censored intensity: 'NULL': It assumes that all intensities are missing at random, therefore no action with missing value imputation: No; or error with missing value imputation: Yes.
8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	1100 - Missing value imputation: Yes + censored intensity:'NA' or '0': AFT model-based imputation using cutoff value for censoring in the AFT model
8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	1101 - Missing value imputation: No + censored intensity:'NA' or '0': censored intensities will be replaced with the value specified in cutoff value for censoring
4 593839e1f2c3 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 4fe4a0b30469f52c937830d2f3c316f6b9667407" galaxyp parents: 3 diff changeset	1102 - Missing value imputation: No + censored intensity: NULL: no imputation
3 8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	1103
8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	1104 - Group comparison: automatic detection of differentially abundant proteins between two conditions, conditions have to be specified with the 'comparison matrix'
8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	1105 - Quantification per sample or group: choose the corresponding output option
8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	1106
8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	1107 - 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.
8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	1108 - 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
8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	1109
0 80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	1110
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	1111 Output options
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	1112
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	1113 - 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	1114
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	1115 - MSstats log - check log file for warnings and information on the analysis steps (txt)
3 8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	1116 - MSstats Rscript - can be used to re-run analysis outside Galaxy or to inspect the executed code (txt)
4 593839e1f2c3 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 4fe4a0b30469f52c937830d2f3c316f6b9667407" galaxyp parents: 3 diff changeset	1117 - MSstats RawData - raw files combined into MSstats format (tabular)
3 8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	1118 - MSstats ProcessedData - transformed, normalized, imputed intensities (tabular)
8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	1119
8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	1120 - Intensity column: includes original intensities values
8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	1121 - Abundance column: contains the log2 transformed and normalized intensities and it will used for run-level summarization
8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	1122 - Censored column: has the decision about censored missing or not, based on censored Intensity and maximum quantile for deciding censored missing values options. Abundances with TRUE value in censored column will be considered as censored missing and imputed when Missing value imputation: Yes.
8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	1123
8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	1124 - MSstats RunlevelData - run and protein level summarized data (tabular)
8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	1125
8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	1126 - LogIntensities: log intensity summarized per run and protein, they will be used for the group comparison and summarized profile plot
8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	1127 - NumMeasuredFeature: shows how many features were used for summarization of the corresponding run and protein
8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	1128 - MissingPercentage: percentage of random and censoredmissing in the corresponding run and protein out of the total number of feature in the corresponding protein.
8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	1129 - more50missing: whether MissingPercentage is greater than 50% or not
8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	1130 - NumImputedFeatures: how many features were imputed in the corresponding run and protein
8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	1131
8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	1132 - MSstats QCPlot - log2 intensity boxplot for all proteins and run on first page, followed by one boxplot per protein (pdf)
8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	1133 - MSstats ProfilePlot - log2 intensity profiles one plot per protein and run (pdf)
8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	1134
8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	1135 - Profile plot helps identify potential sources of variation (both variation of interest and nuisance variation) for each protein: show individual measurements for each peptide (peptide for DDA, transition for SRM orDIA) across runs, grouped per condition. Each peptide has a different color/type layout. Disconnected linesshow that there are missing value (NA).
8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	1136
8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	1137 - MSstats ProfilePlot_wSummarization - log2 intensity profiles one plot per protein and run with run summarization (pdf)
8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	1138
8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	1139 - Run-level summarized data per protein. The same peptides (or transition) in the first plot are presented in grey, with the summarized values overlaid in red.
8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	1140
8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	1141 - MSstats ConditionPlot - log2 intensity range for each protein and condition (pdf)
8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	1142
8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	1143 - Visualizes potential systematic differences in protein intensities between conditions. Dots indicate the mean of log2 intensities for each condition, error bars indicate the confidence interval with 0.95 significant level for each condition. The intervals are for descriptive purposes only.
8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	1144
8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	1145 - Sample Quantification Matrix/Long Table - relative protein abundance in each biological replicate in matrix (rows are proteins, and columns are combinations of biological replicate and group, filled with LogIntensities) or long format (row corresponding to relative protein abundances, and columns are Protein, Group, BioReplicate, LogIntensities) (tabular)
8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	1146
8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	1147 - 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. In presence of completely missing values in a biological replicate, the estimates will be zero.
8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	1148
8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	1149 - Group Quantification Matrix/Long Tableuant_group_matrix - relative protein abundance in each condition in matrix (rows are proteins, and columns are groups) or long format (row corresponding to relative protein abundances, and columns are Protein, Group and LogIntensities) (tabular)
8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	1150
8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	1151 - Outputs the estimates of 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.
8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	1152
8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	1153 - MSstats ComparisonFittedModel (txt)
8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	1154 - MSstats ComparisonResult - summary of statistical results per protein and comparison (tabular)
8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	1155
8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	1156 - Label: name of the comparison (e.g. condition1 - condition2)
8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	1157 - log2FC: log2 fold change for the given comparison name, e.g. condition1-condition2: positive values mean more abundant in condition1, negative values mean more abundant in condition2
8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	1158 - SE: standard error of the log2 fold change
8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	1159 - Tvalue: test statistic of the Student test
8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	1160 - DF: degree of freedom of the Student test
8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	1161 - pvalue: raw p-values
8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	1162 - adj. pvalue: adjusted p-values among all the proteins in the specific comparison
8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	1163 - issue: shows if there is any issue for inference in corresponding protein and comparison,for example,OneConditionMissing or CompleteMissing. If one of condition for compariosn is completely missing, it would flag with OneConditionMissing with adj.pvalue=0 and log2FC=Inf or -Inf even though pvalue=NA. For example, if you want to compare ‘condition1-condition2’, but condition2 has complete missing, log2FC=Inf and adj.pvalue=0. SE,Tvalue, and pvalue will be NA. If you want to compare ‘conditions - condition2’, but condition1 has complete missing, then log2FC=-Inf and adj.pvalue=0. But, please be careful for using this log2FC and adj.pvalue.
8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	1164
8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	1165 - MSstats ModelQC - summary statistics per run and protein (tabular)
8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	1166
8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	1167 - MSstats QQPlot - one QQplot per protein (pdf)
8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	1168
8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	1169 - Normal quantile-quantile plots for each protein, taking as input the results of model fitting and testing in groupComparison. Only large deviations of transition intensities from the straight line are problematic and indicate that the assumption of the normal distribution of the measurement errors may not hold.
8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	1170
8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	1171 - MSstats ResiudalPlot - one residual plot per protein (pdf)
8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	1172
8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	1173 - Residual plot shows variance of the residuals that is associated with the mean feature intensity. Any specific pattern, such as increasing or decreasing by predicted abundance, is problematic and indicates that the assumption of constant variance of the measurement error may not hold.
8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	1174
8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	1175 - MSstats VolcanoPlot - one volcano plot per comparison (pdf)
8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	1176
8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	1177 - Visualizes the outcome of one comparison between conditions for all the proteins, and combine the information on statistical and practical significance. The y-axis displays the FDR-adjusted p-values on the negative log10 scale, representing statistical significance. The horizontal dashed line shows the FDR cutoff. The points above the FDR cutoff line are statistically significant proteins that are differentially abundant across conditions. These points are colored in red and blue for upregulated and downregulated proteins, respectively. The x-axis is the model-based estimate of fold change on log scale and represents practical significance. It is possible to specify a practical significance cutoff based on the estimate of fold change in addition to the statistical significance cutoff. If the fold change cutoff is specified, the points above the horizontal cutoff line but within the vertical cutoff line will be considered as not differentially abundant (and will be colored in black).
8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	1178
8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	1179 - MSstats Heatmap - needs at least 2 comparisons, one heatmap for all proteins and comparisons (pdf)
8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	1180
8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	1181 - Illustrates the patterns of up- and down-regulation of proteins in several comparisons. Columns in the heatmaps are comparison of conditions assigned in contrast matrix, and rows are proteins. The heatmaps display signed FDR-adjusted p-values of the tests, colored in red/blue for significantly up-/down-regulated proteins, while taking into account the specified FDR cutoff and the additional optional fold change cutoff. Brighter colors indicate stronger evidence in favor of differential abundance. Black color represents proteins that are not significantly differentially abundant.
8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	1182
8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	1183 - MSstats ComparisonPlot - log2 intensity range for each protein and comparison (pdf)
8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	1184
8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	1185 - Illustrates model-based estimates of log-fold changes, and the associated uncertainty, in several comparisons of conditions for one protein. X-axis is the comparison of interest. Y-axis is the log fold change. The dots are the model-based estimates of log-fold change, and the error bars are the model-based 95% confidence intervals. For simplicity, the confidence intervals are adjusted for multiple comparisons within protein only, using the Bonferroni approach. For proteins with N comparisons, the individual confidence intervals are at the level of 1-sig/N.
0 80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	1186
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	1187 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	1188
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	1189
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	1190 ]]></help>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	1191 <citations>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	1192 <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	1193 </citations>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	1194 </tool>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	1195

Mercurial > repos > galaxyp > msstats

annotate msstats.xml @ 4:593839e1f2c3 draft