msstats: msstats.xml annotate

annotate msstats.xml @ 6:b7034eff0db1 draft

planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 86de2cd327423c44d042f98108dc93a8f83982d0

author	galaxyp
date	Tue, 31 Jan 2023 18:14:55 +0000
parents	28434abe6c5c
children	de7593c29499

rev	line source
6 b7034eff0db1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 86de2cd327423c44d042f98108dc93a8f83982d0 galaxyp parents: 5 diff changeset	1 <tool id="msstats" name="MSstats" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
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>
6 b7034eff0db1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 86de2cd327423c44d042f98108dc93a8f83982d0 galaxyp parents: 5 diff changeset	4 <token name="@TOOL_VERSION@">4.0.0</token>
b7034eff0db1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 86de2cd327423c44d042f98108dc93a8f83982d0 galaxyp parents: 5 diff changeset	5 <token name="@VERSION_SUFFIX@">1</token>
0 80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	6 <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	7 <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	8 </xml>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	9 <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	10 <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	11 <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	12 <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	13 </param>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	14 </xml>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	15 <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	16 <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	17 <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	18 <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	19 </param>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	20 </xml>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	21 <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	22 <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	23 </xml>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	24
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	25 </macros>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	26 <requirements>
6 b7034eff0db1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 86de2cd327423c44d042f98108dc93a8f83982d0 galaxyp parents: 5 diff changeset	27 <requirement type="package" version="@TOOL_VERSION@">bioconductor-msstats</requirement>
0 80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	28 </requirements>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	29 <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	30 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	31 Rscript '$msstats_script'
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	32 ]]></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=$input.input_options.removeOxidationMpeptides,
5 28434abe6c5c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 0e253b8114e2fe6f4e33edcc5f1a4602073064c3" galaxyp parents: 4 diff changeset	69 removeProtein_with1Peptide=$input.input_options.removeProtein_with1Peptide,
28434abe6c5c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 0e253b8114e2fe6f4e33edcc5f1a4602073064c3" galaxyp parents: 4 diff changeset	70 use_log_file = TRUE,
28434abe6c5c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 0e253b8114e2fe6f4e33edcc5f1a4602073064c3" galaxyp parents: 4 diff changeset	71 append = TRUE,
28434abe6c5c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 0e253b8114e2fe6f4e33edcc5f1a4602073064c3" galaxyp parents: 4 diff changeset	72 log_file_pat = "log.txt")
0 80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	73
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	74 #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	75
3 8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	76 #if $input.openms_input.is_of_type('csv')
8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	77 input <- read.csv("$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	78 #else
3 8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	79 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	80 #end if
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	81
3 8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	82 #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	83 #if $input.annotation.is_of_type('csv')
8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	84 annot <- read.csv("$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	85 #else
8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	86 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	87 #end if
8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	88 #end if
8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	89
8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	90 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	91 #if $input.annotation:
0 80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	92 annotation=annot,
3 8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	93 #end if
0 80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	94 useUniquePeptide=$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	95 summaryforMultipleRows=$input.input_options.summaryforMultipleRows,
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	96 fewMeasurements="$input.input_options.fewMeasurements",
5 28434abe6c5c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 0e253b8114e2fe6f4e33edcc5f1a4602073064c3" galaxyp parents: 4 diff changeset	97 removeProtein_with1Feature=$input.input_options.removeProtein_with1Feature,
28434abe6c5c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 0e253b8114e2fe6f4e33edcc5f1a4602073064c3" galaxyp parents: 4 diff changeset	98 use_log_file = TRUE,
28434abe6c5c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 0e253b8114e2fe6f4e33edcc5f1a4602073064c3" galaxyp parents: 4 diff changeset	99 append = TRUE,
28434abe6c5c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 0e253b8114e2fe6f4e33edcc5f1a4602073064c3" galaxyp parents: 4 diff changeset	100 log_file_pat = "log.txt")
3 8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	101
0 80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	102
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	103 #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	104
3 8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	105 #if $input.openswath_input.is_of_type('csv')
8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	106 input <- read.csv("$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	107 #else
3 8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	108 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	109 #end if
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	110 #if $input.annotation.is_of_type('csv')
3 8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	111 annot <- read.csv("$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	112 #else
3 8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	113 annot <- read.table("$input.annotation", sep="\t", header=TRUE)
0 80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	114 #end if
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	115
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	116 raw <- OpenSWATHtoMSstatsFormat(input,
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	117 annotation=annot,
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	118 filter_with_mscore=$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	119 mscore_cutoff=$input.input_options.mscore_cutoff,
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	120 useUniquePeptide=$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	121 fewMeasurements="$input.input_options.fewMeasurements",
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	122 removeProtein_with1Feature=$input.input_options.removeProtein_with1Feature,
5 28434abe6c5c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 0e253b8114e2fe6f4e33edcc5f1a4602073064c3" galaxyp parents: 4 diff changeset	123 summaryforMultipleRows=$input.input_options.summaryforMultipleRows,
28434abe6c5c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 0e253b8114e2fe6f4e33edcc5f1a4602073064c3" galaxyp parents: 4 diff changeset	124 use_log_file = TRUE,
28434abe6c5c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 0e253b8114e2fe6f4e33edcc5f1a4602073064c3" galaxyp parents: 4 diff changeset	125 append = TRUE,
28434abe6c5c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 0e253b8114e2fe6f4e33edcc5f1a4602073064c3" galaxyp parents: 4 diff changeset	126 log_file_pat = "log.txt")
28434abe6c5c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 0e253b8114e2fe6f4e33edcc5f1a4602073064c3" galaxyp parents: 4 diff changeset	127
3 8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	128 #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	129
8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	130 #if $input.skyline_input.is_of_type('csv')
8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	131 input <- read.csv("$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	132 #else
8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	133 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	134 #end if
8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	135
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 #if $input.annotation.is_of_type('csv')
8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	138 annot <- read.csv("$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	139 #else
8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	140 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	141 #end if
8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	142 #end if
8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	143
8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	144 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	145 #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	146 annotation = annot,
8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	147 #end if
8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	148 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	149 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	150 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	151 useUniquePeptide = $input.input_options.useUniquePeptide,
8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	152 fewMeasurements="$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	153 removeOxidationMpeptides = $input.input_options.removeOxidationMpeptides,
5 28434abe6c5c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 0e253b8114e2fe6f4e33edcc5f1a4602073064c3" galaxyp parents: 4 diff changeset	154 removeProtein_with1Feature = $input.input_options.removeProtein_with1Feature,
28434abe6c5c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 0e253b8114e2fe6f4e33edcc5f1a4602073064c3" galaxyp parents: 4 diff changeset	155 use_log_file = TRUE,
28434abe6c5c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 0e253b8114e2fe6f4e33edcc5f1a4602073064c3" galaxyp parents: 4 diff changeset	156 append = TRUE,
28434abe6c5c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 0e253b8114e2fe6f4e33edcc5f1a4602073064c3" galaxyp parents: 4 diff changeset	157 log_file_pat = "log.txt")
3 8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	158
0 80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	159 #end if
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	160
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	161 processed_data <- dataProcess(raw,
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	162 logTrans=$dp_options.logTrans,
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	163 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	164 #if $dp_options.norm.normalization == 'globalStandards'
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	165 nameStandards=c($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	166 #end if
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	167 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	168 #if $dp_options.features.featureSubset == 'topN'
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	169 n_top_feature=$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	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 $dp_options.features.featureSubset == 'highQuality'
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	172 remove_uninformative_feature_outlier=$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	173 #end if
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	174 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	175 #if $dp_options.summarize.summaryMethod == 'TMP'
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	176 MBimpute=$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	177 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	178 #end if
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	179 #if $dp_options.summarize.summaryMethod == 'linear'
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	180 equalFeatureVar=$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	181 #end if
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	182 #if $dp_options.censoredInt == 'NULL'
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	183 censoredInt=NULL,
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	184 #else
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	185 censoredInt="$dp_options.censoredInt",
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	186 #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	187 #if $dp_options.maxQuantileforCensored == ''
5 28434abe6c5c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 0e253b8114e2fe6f4e33edcc5f1a4602073064c3" galaxyp parents: 4 diff changeset	188 maxQuantileforCensored = NULL,
4 593839e1f2c3 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 4fe4a0b30469f52c937830d2f3c316f6b9667407" galaxyp parents: 3 diff changeset	189 #else
5 28434abe6c5c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 0e253b8114e2fe6f4e33edcc5f1a4602073064c3" galaxyp parents: 4 diff changeset	190 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	191 #end if
5 28434abe6c5c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 0e253b8114e2fe6f4e33edcc5f1a4602073064c3" galaxyp parents: 4 diff changeset	192 use_log_file = TRUE,
28434abe6c5c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 0e253b8114e2fe6f4e33edcc5f1a4602073064c3" galaxyp parents: 4 diff changeset	193 append = TRUE,
28434abe6c5c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 0e253b8114e2fe6f4e33edcc5f1a4602073064c3" galaxyp parents: 4 diff changeset	194 log_file_pat = "log.txt")
28434abe6c5c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 0e253b8114e2fe6f4e33edcc5f1a4602073064c3" galaxyp parents: 4 diff changeset	195
4 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 #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	198 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	199 #end if
593839e1f2c3 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 4fe4a0b30469f52c937830d2f3c316f6b9667407" galaxyp parents: 3 diff changeset	200
5 28434abe6c5c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 0e253b8114e2fe6f4e33edcc5f1a4602073064c3" galaxyp parents: 4 diff changeset	201 #if 'featurelevel_data' in $dp_options.selected_outputs
28434abe6c5c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 0e253b8114e2fe6f4e33edcc5f1a4602073064c3" galaxyp parents: 4 diff changeset	202 write.table(processed_data\$FeatureLevelData, "featurelevelData.tsv", sep = "\t", quote = F, row.names = F, dec = ".")
0 80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	203 #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	204
5 28434abe6c5c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 0e253b8114e2fe6f4e33edcc5f1a4602073064c3" galaxyp parents: 4 diff changeset	205 #if 'proteinlevel_data' in $dp_options.selected_outputs
28434abe6c5c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 0e253b8114e2fe6f4e33edcc5f1a4602073064c3" galaxyp parents: 4 diff changeset	206 write.table(processed_data\$ProteinLevelData, "proteinlevelData.tsv", sep = "\t", quote = F, row.names = F, dec = ".")
0 80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	207 #end if
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	208
4 593839e1f2c3 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 4fe4a0b30469f52c937830d2f3c316f6b9667407" galaxyp parents: 3 diff changeset	209 #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	210
593839e1f2c3 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 4fe4a0b30469f52c937830d2f3c316f6b9667407" galaxyp parents: 3 diff changeset	211
3 8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	212 #if $plot_type[-4:] == "Plot"
0 80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	213
3 8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	214 dataProcessPlots(data = processed_data,
8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	215 type = '$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	216 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	217 #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	218 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	219 #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	220 #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	221 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	222 #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	223 scale = $dp_options.out_plots_opt.proc_plots_advanced.scale,
593839e1f2c3 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 4fe4a0b30469f52c937830d2f3c316f6b9667407" galaxyp parents: 3 diff changeset	224 interval = "$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	225 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	226 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	227 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	228 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	229 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	230 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	231 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	232 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	233 height = $dp_options.out_plots_opt.height,
5 28434abe6c5c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 0e253b8114e2fe6f4e33edcc5f1a4602073064c3" galaxyp parents: 4 diff changeset	234 #if $dp_options.out_plots_opt.which_Protein.select == 'list'
28434abe6c5c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 0e253b8114e2fe6f4e33edcc5f1a4602073064c3" galaxyp parents: 4 diff changeset	235 which.Protein = unlist(read.table("$dp_options.out_plots_opt.which_Protein.protein_list", sep = "\n", header = FALSE), use.names = FALSE),
28434abe6c5c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 0e253b8114e2fe6f4e33edcc5f1a4602073064c3" galaxyp parents: 4 diff changeset	236 #elif $dp_options.out_plots_opt.which_Protein.select == 'allonly'
28434abe6c5c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 0e253b8114e2fe6f4e33edcc5f1a4602073064c3" galaxyp parents: 4 diff changeset	237 #if $plot_type == "QCPlot"
28434abe6c5c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 0e253b8114e2fe6f4e33edcc5f1a4602073064c3" galaxyp parents: 4 diff changeset	238 which.Protein = "allonly",
28434abe6c5c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 0e253b8114e2fe6f4e33edcc5f1a4602073064c3" galaxyp parents: 4 diff changeset	239 #else
28434abe6c5c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 0e253b8114e2fe6f4e33edcc5f1a4602073064c3" galaxyp parents: 4 diff changeset	240 which.Protein = "all",
28434abe6c5c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 0e253b8114e2fe6f4e33edcc5f1a4602073064c3" galaxyp parents: 4 diff changeset	241 #end if
3 8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	242 #else
5 28434abe6c5c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 0e253b8114e2fe6f4e33edcc5f1a4602073064c3" galaxyp parents: 4 diff changeset	243 which.Protein = "all",
3 8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	244 #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	245 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	246 address="MSStats_only_")
8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	247 #end if
8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	248 #end for
0 80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	249
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	250 ## Quantifiaction
4 593839e1f2c3 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 4fe4a0b30469f52c937830d2f3c316f6b9667407" galaxyp parents: 3 diff changeset	251 #if 'quant_sample_matrix' in $dp_options.selected_outputs
5 28434abe6c5c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 0e253b8114e2fe6f4e33edcc5f1a4602073064c3" galaxyp parents: 4 diff changeset	252 sampleQuantMatrix <- quantification(processed_data, type="Sample", use_log_file = TRUE, append = TRUE, log_file_pat = "log.txt")
0 80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	253 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	254 #end if
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	255
4 593839e1f2c3 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 4fe4a0b30469f52c937830d2f3c316f6b9667407" galaxyp parents: 3 diff changeset	256 #if 'quant_sample_long' in $dp_options.selected_outputs
5 28434abe6c5c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 0e253b8114e2fe6f4e33edcc5f1a4602073064c3" galaxyp parents: 4 diff changeset	257 sampleQuantLong <- quantification(processed_data, type="Sample", format="long", use_log_file = TRUE, append = TRUE, log_file_pat = "log.txt")
0 80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	258 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	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
4 593839e1f2c3 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 4fe4a0b30469f52c937830d2f3c316f6b9667407" galaxyp parents: 3 diff changeset	261 #if 'quant_group_matrix' in $dp_options.selected_outputs
5 28434abe6c5c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 0e253b8114e2fe6f4e33edcc5f1a4602073064c3" galaxyp parents: 4 diff changeset	262 groupQuantMatrix <- quantification(processed_data, type="Group", use_log_file = TRUE, append = TRUE, log_file_pat = "log.txt")
0 80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	263 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	264 #end if
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	265
4 593839e1f2c3 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 4fe4a0b30469f52c937830d2f3c316f6b9667407" galaxyp parents: 3 diff changeset	266 #if 'quant_group_long' in $dp_options.selected_outputs
5 28434abe6c5c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 0e253b8114e2fe6f4e33edcc5f1a4602073064c3" galaxyp parents: 4 diff changeset	267 groupQuantLong <- quantification(processed_data, type="Group", format="long", use_log_file = TRUE, append = TRUE, log_file_pat = "log.txt")
0 80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	268 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	269 #end if
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	270
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	271 ## Group Comparison
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	272 #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	273 \# Group Comparison
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	274 #if $group.comparison_matrix.is_of_type('csv')
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	275 comp_matrix <- read.csv("$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	276 #else
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	277 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	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 ## 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	281 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	282 row.names(comparison) <- as.character(comp_matrix[,1])
5 28434abe6c5c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 0e253b8114e2fe6f4e33edcc5f1a4602073064c3" galaxyp parents: 4 diff changeset	283
0 80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	284 ## order of conditions has to be the same as they appear in the levels function
5 28434abe6c5c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 0e253b8114e2fe6f4e33edcc5f1a4602073064c3" galaxyp parents: 4 diff changeset	285 comparison <- as.matrix(comparison[levels(processed_data\$FeatureLevelData\$GROUP)])
0 80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	286
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	287 ## perform group comparison
5 28434abe6c5c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 0e253b8114e2fe6f4e33edcc5f1a4602073064c3" galaxyp parents: 4 diff changeset	288 comparisons <- groupComparison(contrast.matrix = comparison, data = processed_data, use_log_file = TRUE, append = TRUE, log_file_pat = "log.txt")
0 80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	289
5 28434abe6c5c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 0e253b8114e2fe6f4e33edcc5f1a4602073064c3" galaxyp parents: 4 diff changeset	290 #if 'fittedmodel' in $group.select_outputs
28434abe6c5c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 0e253b8114e2fe6f4e33edcc5f1a4602073064c3" galaxyp parents: 4 diff changeset	291 capture.output(print(comparisons\$FittedModel), file="ComparisonFittedModel.txt")
28434abe6c5c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 0e253b8114e2fe6f4e33edcc5f1a4602073064c3" galaxyp parents: 4 diff changeset	292 #end if
0 80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	293
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	294
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	295 #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	296 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	297 #end if
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	298
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	299 #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	300 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	301 #end if
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	302
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	303 ## Visualizations:
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	304
4 593839e1f2c3 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 4fe4a0b30469f52c937830d2f3c316f6b9667407" galaxyp parents: 3 diff changeset	305 #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	306
3 8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	307
8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	308 #if $plot_type == "QQPlots" or $plot_type == "ResidualPlots"
0 80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	309
3 8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	310 modelBasedQCPlots(data = comparisons,
8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	311 type = "$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	312 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	313 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	314 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	315 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	316 #if $group.comparison_plots_opt.which_Protein.select != 'list'
593839e1f2c3 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 4fe4a0b30469f52c937830d2f3c316f6b9667407" galaxyp parents: 3 diff changeset	317 which.Protein = "$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	318 #else
4 593839e1f2c3 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 4fe4a0b30469f52c937830d2f3c316f6b9667407" galaxyp parents: 3 diff changeset	319 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	320 #end if
8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	321 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	322
8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	323
8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	324 #elif $plot_type == "VolcanoPlot" or $plot_type == "Heatmap" or $plot_type == "ComparisonPlot"
0 80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	325
3 8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	326 groupComparisonPlots(data = comparisons\$ComparisonResult,
8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	327 type = "$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	328 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	329 #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	330 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	331 #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	332 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	333 #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	334 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	335 #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	336 #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	337 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	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 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	340 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	341 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	342 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	343 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	344 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	345 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	346 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	347 numProtein = $group.comparison_plots_opt.comparison_vis_options.numProtein,
593839e1f2c3 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 4fe4a0b30469f52c937830d2f3c316f6b9667407" galaxyp parents: 3 diff changeset	348 clustering = "$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	349 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	350 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	351 #if $group.comparison_plots_opt.which_Protein.select != 'list'
593839e1f2c3 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 4fe4a0b30469f52c937830d2f3c316f6b9667407" galaxyp parents: 3 diff changeset	352 which.Protein = "$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	353 #else
4 593839e1f2c3 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 4fe4a0b30469f52c937830d2f3c316f6b9667407" galaxyp parents: 3 diff changeset	354 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	355 #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	356 #if $group.comparison_plots_opt.comparison_vis_options.which_Comparison.select != 'list'
593839e1f2c3 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 4fe4a0b30469f52c937830d2f3c316f6b9667407" galaxyp parents: 3 diff changeset	357 which.Comparison = "$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	358 #else
4 593839e1f2c3 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 4fe4a0b30469f52c937830d2f3c316f6b9667407" galaxyp parents: 3 diff changeset	359 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	360 #end if
8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	361 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	362
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	363
3 8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	364 #end if
8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	365 #end for
0 80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	366
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	367 #end if
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	368 ]]></configfile>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	369 </configfiles>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	370 <inputs>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	371 <conditional name="input">
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	372 <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	373 <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	374 <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	375 <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	376 <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	377 <!--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	378 <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	379 </param>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	380 <when value="MSstats">
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	381 <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	382 </when>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	383 <when value="MaxQuant">
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	384 <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	385 <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	386 <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	387
0 80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	388 <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	389 <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	390 <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	391 </param>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	392 <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	393 <expand macro="useUniquePeptide"/>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	394 <expand macro="summaryforMultipleRows"/>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	395 <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	396 <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	397 <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	398 <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	399 </section>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	400 </when>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	401 <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	402 <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	403 <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	404 <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	405 <expand macro="useUniquePeptide"/>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	406 <expand macro="summaryforMultipleRows"/>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	407 <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	408 <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	409 </section>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	410 </when>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	411 <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	412 <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	413 <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	414 <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	415 <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	416 <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	417 <expand macro="useUniquePeptide"/>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	418 <expand macro="fewMeasurements"/>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	419 <expand macro="summaryforMultipleRows"/>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	420 <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	421 </section>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	422 </when>
3 8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	423 <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	424 <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	425 <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	426 <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	427 <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	428 <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	429 <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	430 <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	431 <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	432 <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	433 <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	434 <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	435 </section>
8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	436 </when>
8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	437 </conditional>
8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	438
4 593839e1f2c3 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 4fe4a0b30469f52c937830d2f3c316f6b9667407" galaxyp parents: 3 diff changeset	439 <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	440 <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	441 <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	442 <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	443 <option value="raw_data" selected="true">MSstats RawData</option>
5 28434abe6c5c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 0e253b8114e2fe6f4e33edcc5f1a4602073064c3" galaxyp parents: 4 diff changeset	444 <option value="featurelevel_data" selected="true">MSstats FeatureLevelData</option>
28434abe6c5c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 0e253b8114e2fe6f4e33edcc5f1a4602073064c3" galaxyp parents: 4 diff changeset	445 <option value="proteinlevel_data" selected="false">MSstats ProteinLevelData</option>
4 593839e1f2c3 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 4fe4a0b30469f52c937830d2f3c316f6b9667407" galaxyp parents: 3 diff changeset	446 <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	447 <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	448 <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	449 <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	450 </param>
3 8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	451 <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	452 <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	453 <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	454 </param>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	455 <conditional name="norm">
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	456 <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	457 <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	458 <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	459 <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	460 <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	461 </param>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	462 <when value="equalizeMedians"/>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	463 <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	464 <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	465 <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	466 <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	467 <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	468 </param>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	469 </when>
3 8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	470 <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	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="features">
3 8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	473 <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	474 <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	475 <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	476 <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	477 <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	478 </param>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	479 <when value="all"/>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	480 <when value="top3"/>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	481 <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	482 <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	483 </when>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	484 <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	485 <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	486 </when>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	487 </conditional>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	488 <conditional name="summarize">
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	489 <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	490 <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	491 <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	492 </param>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	493 <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	494 <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	495 <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	496 </when>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	497 <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	498 <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	499 </when>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	500 </conditional>
3 8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	501 <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	502 <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	503 <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	504 <option value="0">0 - Use zero intensities '0' as censored intensity</option>
5 28434abe6c5c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 0e253b8114e2fe6f4e33edcc5f1a4602073064c3" galaxyp parents: 4 diff changeset	505 <!--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	506 </param>
4 593839e1f2c3 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 4fe4a0b30469f52c937830d2f3c316f6b9667407" galaxyp parents: 3 diff changeset	507 <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	508
593839e1f2c3 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 4fe4a0b30469f52c937830d2f3c316f6b9667407" galaxyp parents: 3 diff changeset	509
593839e1f2c3 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 4fe4a0b30469f52c937830d2f3c316f6b9667407" galaxyp parents: 3 diff changeset	510 <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	511 <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	512 <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	513 <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	514 <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	515 <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	516 </param>
3 8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	517 <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	518 <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	519 <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	520 <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	521 <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	522 </param>
8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	523 <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	524 <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	525 <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	526 <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	527 </when>
8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	528 </conditional>
4 593839e1f2c3 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 4fe4a0b30469f52c937830d2f3c316f6b9667407" galaxyp parents: 3 diff changeset	529 <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	530 <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	531
593839e1f2c3 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 4fe4a0b30469f52c937830d2f3c316f6b9667407" galaxyp parents: 3 diff changeset	532 <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	533 <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	534 <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	535 <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	536 <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	537 </param>
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="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	539 <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	540
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="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	542 <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	543 <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	544 <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	545 </param>
593839e1f2c3 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 4fe4a0b30469f52c937830d2f3c316f6b9667407" galaxyp parents: 3 diff changeset	546 <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	547 <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	548 <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	549 <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	550 <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	551 <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	552 <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	553
593839e1f2c3 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 4fe4a0b30469f52c937830d2f3c316f6b9667407" galaxyp parents: 3 diff changeset	554 <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	555 </section>
593839e1f2c3 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 4fe4a0b30469f52c937830d2f3c316f6b9667407" galaxyp parents: 3 diff changeset	556 </section>
593839e1f2c3 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 4fe4a0b30469f52c937830d2f3c316f6b9667407" galaxyp parents: 3 diff changeset	557 </section>
593839e1f2c3 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 4fe4a0b30469f52c937830d2f3c316f6b9667407" galaxyp parents: 3 diff changeset	558
0 80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	559 <conditional name="group">
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	560 <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	561 <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	562 <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	563 </param>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	564 <when value="no"/>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	565 <when value="yes">
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	566 <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	567 <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	568 <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	569 <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	570 <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	571 </param>
593839e1f2c3 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 4fe4a0b30469f52c937830d2f3c316f6b9667407" galaxyp parents: 3 diff changeset	572
593839e1f2c3 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 4fe4a0b30469f52c937830d2f3c316f6b9667407" galaxyp parents: 3 diff changeset	573 <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	574 <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	575 <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	576 <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	577 <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	578 <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	579 <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	580 </param>
4 593839e1f2c3 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 4fe4a0b30469f52c937830d2f3c316f6b9667407" galaxyp parents: 3 diff changeset	581 <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	582 <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	583 <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	584 <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	585 <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	586 <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	587 </param>
593839e1f2c3 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 4fe4a0b30469f52c937830d2f3c316f6b9667407" galaxyp parents: 3 diff changeset	588 <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	589 <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	590 <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	591 </when>
593839e1f2c3 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 4fe4a0b30469f52c937830d2f3c316f6b9667407" galaxyp parents: 3 diff changeset	592 </conditional>
593839e1f2c3 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 4fe4a0b30469f52c937830d2f3c316f6b9667407" galaxyp parents: 3 diff changeset	593
593839e1f2c3 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 4fe4a0b30469f52c937830d2f3c316f6b9667407" galaxyp parents: 3 diff changeset	594 <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	595
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="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	597 <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	598 <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	599 <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	600 <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	601 </param>
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="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	603 <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	604 <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	605 <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	606 <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	607 <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	608 <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	609 <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	610 <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	611 <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	612 <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	613 <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	614 <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	615 <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	616 <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	617 <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	618 <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	619 <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	620 </param>
593839e1f2c3 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 4fe4a0b30469f52c937830d2f3c316f6b9667407" galaxyp parents: 3 diff changeset	621 <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	622 <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	623 <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	624 <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	625 </param>
593839e1f2c3 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 4fe4a0b30469f52c937830d2f3c316f6b9667407" galaxyp parents: 3 diff changeset	626 <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	627 <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	628 <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	629 </when>
593839e1f2c3 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 4fe4a0b30469f52c937830d2f3c316f6b9667407" galaxyp parents: 3 diff changeset	630 </conditional>
593839e1f2c3 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 4fe4a0b30469f52c937830d2f3c316f6b9667407" galaxyp parents: 3 diff changeset	631 </section>
593839e1f2c3 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 4fe4a0b30469f52c937830d2f3c316f6b9667407" galaxyp parents: 3 diff changeset	632 </section>
0 80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	633 </when>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	634 </conditional>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	635 </inputs>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	636 <outputs>
5 28434abe6c5c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 0e253b8114e2fe6f4e33edcc5f1a4602073064c3" galaxyp parents: 4 diff changeset	637 <data name="log" format="txt" label="${tool.name} on ${on_string}: log" from_work_dir="log.txt">
28434abe6c5c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 0e253b8114e2fe6f4e33edcc5f1a4602073064c3" galaxyp parents: 4 diff changeset	638 <filter>'log' in dp_options['selected_outputs']</filter>
0 80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	639 </data>
3 8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	640 <data name="r_script" format="txt" label="${tool.name} on ${on_string}: Rscript">
4 593839e1f2c3 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 4fe4a0b30469f52c937830d2f3c316f6b9667407" galaxyp parents: 3 diff changeset	641 <filter>'r_script' in dp_options['selected_outputs']</filter>
593839e1f2c3 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 4fe4a0b30469f52c937830d2f3c316f6b9667407" galaxyp parents: 3 diff changeset	642 </data>
593839e1f2c3 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 4fe4a0b30469f52c937830d2f3c316f6b9667407" galaxyp parents: 3 diff changeset	643 <data name="raw_data" format="tabular" label="${tool.name} on ${on_string}: RawData" from_work_dir="raw.tsv">
593839e1f2c3 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 4fe4a0b30469f52c937830d2f3c316f6b9667407" galaxyp parents: 3 diff changeset	644 <filter>'raw_data' in dp_options['selected_outputs']</filter>
0 80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	645 </data>
5 28434abe6c5c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 0e253b8114e2fe6f4e33edcc5f1a4602073064c3" galaxyp parents: 4 diff changeset	646 <data name="featurelevel_data" format="tabular" label="${tool.name} on ${on_string}: FeatureLevelData" from_work_dir="featurelevelData.tsv">
28434abe6c5c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 0e253b8114e2fe6f4e33edcc5f1a4602073064c3" galaxyp parents: 4 diff changeset	647 <filter>'featurelevel_data' in dp_options['selected_outputs']</filter>
4 593839e1f2c3 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 4fe4a0b30469f52c937830d2f3c316f6b9667407" galaxyp parents: 3 diff changeset	648 <!--actions>
1 3e2606fa85bf "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit fa543ac667f63409bfb2e28fd6c711e74d828a79" galaxyp parents: 0 diff changeset	649 <action name="column_names" type="metadata" default="PROTEIN,PEPTIDE,TRANSITION,FEATURE,LABEL,GROUP_ORIGINAL,SUBJECT_ORIGINAL,RUN,GROUP,SUBJECT,INTENSITY,SUBJECT_NESTED,ABUNDANCE,FRACTION,originalRUN,censored" />
4 593839e1f2c3 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 4fe4a0b30469f52c937830d2f3c316f6b9667407" galaxyp parents: 3 diff changeset	650 </actions-->
0 80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	651 </data>
5 28434abe6c5c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 0e253b8114e2fe6f4e33edcc5f1a4602073064c3" galaxyp parents: 4 diff changeset	652 <data name="proteinlevel_data" format="tabular" label="${tool.name} on ${on_string}: ProteinLevelData" from_work_dir="proteinlevelData.tsv">
28434abe6c5c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 0e253b8114e2fe6f4e33edcc5f1a4602073064c3" galaxyp parents: 4 diff changeset	653 <filter>'proteinlevel_data' in dp_options['selected_outputs']</filter>
4 593839e1f2c3 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 4fe4a0b30469f52c937830d2f3c316f6b9667407" galaxyp parents: 3 diff changeset	654 <!--actions>
1 3e2606fa85bf "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit fa543ac667f63409bfb2e28fd6c711e74d828a79" galaxyp parents: 0 diff changeset	655 <action name="column_names" type="metadata" default="RUN,Protein,LogIntensities,NumMeasuredFeature,MissingPercentage,more50missing,NumImputedFeature,originalRUN,GROUP,GROUP_ORIGINAL,SUBJECT_ORIGINAL,SUBJECT_NESTED,SUBJECT" />
4 593839e1f2c3 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 4fe4a0b30469f52c937830d2f3c316f6b9667407" galaxyp parents: 3 diff changeset	656 </actions-->
0 80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	657 </data>
3 8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	658 <data name="QCPlot" format="pdf" label="${tool.name} on ${on_string}: QCPlot" from_work_dir="MSStats_only_QCPlot.pdf">
4 593839e1f2c3 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 4fe4a0b30469f52c937830d2f3c316f6b9667407" galaxyp parents: 3 diff changeset	659 <filter>dp_options['out_plots_opt']['selected_vis_outputs'] and 'QCPlot' in dp_options['out_plots_opt']['selected_vis_outputs']</filter>
0 80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	660 </data>
3 8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	661 <data name="ProfilePlot" format="pdf" label="${tool.name} on ${on_string}: Profile Plot" from_work_dir="MSStats_only_ProfilePlot.pdf">
4 593839e1f2c3 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 4fe4a0b30469f52c937830d2f3c316f6b9667407" galaxyp parents: 3 diff changeset	662 <filter>dp_options['out_plots_opt']['selected_vis_outputs'] and 'ProfilePlot' in dp_options['out_plots_opt']['selected_vis_outputs']</filter>
0 80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	663 </data>
3 8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	664 <data name="profile_wsum_plot" format="pdf" label="${tool.name} on ${on_string}: Profile Plot with Summarization" from_work_dir="MSStats_only_ProfilePlot_wSummarization.pdf">
4 593839e1f2c3 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 4fe4a0b30469f52c937830d2f3c316f6b9667407" galaxyp parents: 3 diff changeset	665 <filter>dp_options['out_plots_opt']['selected_vis_outputs'] and 'profile_wsum_plot' in dp_options['out_plots_opt']['selected_vis_outputs']</filter>
0 80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	666 </data>
3 8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	667 <data name="ConditionPlot" format="pdf" label="${tool.name} on ${on_string}: Condition Plot" from_work_dir="MSStats_only_ConditionPlot.pdf">
4 593839e1f2c3 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 4fe4a0b30469f52c937830d2f3c316f6b9667407" galaxyp parents: 3 diff changeset	668 <filter>dp_options['out_plots_opt']['selected_vis_outputs'] and 'ConditionPlot' in dp_options['out_plots_opt']['selected_vis_outputs']</filter>
0 80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	669 </data>
3 8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	670 <data name="quant_sample_matrix" format="tabular" label="${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	671 <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	672 </data>
3 8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	673 <data name="quant_sample_long" format="tabular" label=" ${tool.name} on ${on_string}:Sample Quantification Long" from_work_dir="SampleQuantificationLong.tsv">
4 593839e1f2c3 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 4fe4a0b30469f52c937830d2f3c316f6b9667407" galaxyp parents: 3 diff changeset	674 <filter>'quant_sample_long' in dp_options['selected_outputs']</filter>
593839e1f2c3 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 4fe4a0b30469f52c937830d2f3c316f6b9667407" galaxyp parents: 3 diff changeset	675 <!--actions>
1 3e2606fa85bf "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit fa543ac667f63409bfb2e28fd6c711e74d828a79" galaxyp parents: 0 diff changeset	676 <action name="column_names" type="metadata" default="Protein,Group_Subject,LogIntensity" />
4 593839e1f2c3 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 4fe4a0b30469f52c937830d2f3c316f6b9667407" galaxyp parents: 3 diff changeset	677 </actions-->
0 80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	678 </data>
3 8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	679 <data name="quant_group_matrix" format="tabular" label="${tool.name} on ${on_string}: Group Quantification Matrix" from_work_dir="GroupQuantificationMatrix.tsv">
4 593839e1f2c3 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 4fe4a0b30469f52c937830d2f3c316f6b9667407" galaxyp parents: 3 diff changeset	680 <filter>'quant_group_matrix' in dp_options['selected_outputs']</filter>
0 80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	681 </data>
3 8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	682 <data name="quant_group_long" format="tabular" label="${tool.name} on ${on_string}: Group Quantification Long" from_work_dir="GroupQuantificationLong.tsv">
4 593839e1f2c3 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 4fe4a0b30469f52c937830d2f3c316f6b9667407" galaxyp parents: 3 diff changeset	683 <filter>'quant_group_long' in dp_options['selected_outputs']</filter>
593839e1f2c3 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 4fe4a0b30469f52c937830d2f3c316f6b9667407" galaxyp parents: 3 diff changeset	684 <!--actions>
1 3e2606fa85bf "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit fa543ac667f63409bfb2e28fd6c711e74d828a79" galaxyp parents: 0 diff changeset	685 <action name="column_names" type="metadata" default="Protein,Group,LogIntensity" />
4 593839e1f2c3 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 4fe4a0b30469f52c937830d2f3c316f6b9667407" galaxyp parents: 3 diff changeset	686 </actions-->
0 80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	687 </data>
3 8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	688 <data name="comparison_result" format="tabular" label="${tool.name} on ${on_string}: Comparison Result" from_work_dir="ComparisonResult.tsv">
0 80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	689 <filter> group['group_comparison'] == 'yes' and 'comparison_result' in group['select_outputs']</filter>
4 593839e1f2c3 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 4fe4a0b30469f52c937830d2f3c316f6b9667407" galaxyp parents: 3 diff changeset	690 <!--actions>
1 3e2606fa85bf "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit fa543ac667f63409bfb2e28fd6c711e74d828a79" galaxyp parents: 0 diff changeset	691 <action name="column_names" type="metadata" default="Protein,Label,log2FC,SE,Tvalue,DF,pvalue,adj.pvalue,issue,MissingPercentage,ImputationPercentage" />
4 593839e1f2c3 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 4fe4a0b30469f52c937830d2f3c316f6b9667407" galaxyp parents: 3 diff changeset	692 </actions-->
0 80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	693 </data>
3 8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	694 <data name="fittedmodel" format="txt" label="${tool.name} on ${on_string}: Comparison Fitted Model" from_work_dir="ComparisonFittedModel.txt">
0 80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	695 <filter> group['group_comparison'] == 'yes' and 'fittedmodel' in group['select_outputs']</filter>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	696 </data>
3 8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	697 <data name="model_qc" format="tabular" label="${tool.name} on ${on_string}: Model QC" from_work_dir="ModelQC.tsv">
0 80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	698 <filter> group['group_comparison'] == 'yes' and 'model_qc' in group['select_outputs']</filter>
4 593839e1f2c3 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 4fe4a0b30469f52c937830d2f3c316f6b9667407" galaxyp parents: 3 diff changeset	699 <!--actions>
1 3e2606fa85bf "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit fa543ac667f63409bfb2e28fd6c711e74d828a79" galaxyp parents: 0 diff changeset	700 <action name="column_names" type="metadata" default="RUN,PROTEIN,ABUNDANCE,NumMeasuredFeature,MissingPercentage,more50missing,NumImputedFeature,originalRUN,GROUP,GROUP_ORIGINAL,SUBJECT_ORIGINAL,SUBJECT_NESTED,SUBJECT,residuals,fitted" />
4 593839e1f2c3 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 4fe4a0b30469f52c937830d2f3c316f6b9667407" galaxyp parents: 3 diff changeset	701 </actions-->
0 80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	702 </data>
3 8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	703 <data name="QQPlots" format="pdf" label="${tool.name} on ${on_string}: Model QQ" from_work_dir="MSStats_group_QQPlot.pdf">
4 593839e1f2c3 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 4fe4a0b30469f52c937830d2f3c316f6b9667407" galaxyp parents: 3 diff changeset	704 <filter> group['group_comparison'] == 'yes' and group['comparison_plots_opt']['select_comparison_plots'] and 'QQPlots' in group['comparison_plots_opt']['select_comparison_plots']</filter>
0 80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	705 </data>
3 8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	706 <data name="ResidualPlots" format="pdf" label="${tool.name} on ${on_string}: Residual Plot" from_work_dir="MSStats_group_ResidualPlot.pdf">
4 593839e1f2c3 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 4fe4a0b30469f52c937830d2f3c316f6b9667407" galaxyp parents: 3 diff changeset	707 <filter> group['group_comparison'] == 'yes' and group['comparison_plots_opt']['select_comparison_plots'] and 'ResidualPlots' in group['comparison_plots_opt']['select_comparison_plots']</filter>
0 80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	708 </data>
3 8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	709 <data name="VolcanoPlot" format="pdf" label="${tool.name} on ${on_string}:Volcano Plot" from_work_dir="MSStats_group_VolcanoPlot.pdf">
4 593839e1f2c3 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 4fe4a0b30469f52c937830d2f3c316f6b9667407" galaxyp parents: 3 diff changeset	710 <filter> group['group_comparison'] == 'yes' and group['comparison_plots_opt']['select_comparison_plots'] and 'VolcanoPlot' in group['comparison_plots_opt']['select_comparison_plots']</filter>
0 80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	711 </data>
3 8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	712 <data name="Heatmap" format="pdf" label="${tool.name} on ${on_string}: Heatmap" from_work_dir="MSStats_group_Heatmap.pdf">
4 593839e1f2c3 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 4fe4a0b30469f52c937830d2f3c316f6b9667407" galaxyp parents: 3 diff changeset	713 <filter> group['group_comparison'] == 'yes' and group['comparison_plots_opt']['select_comparison_plots'] and 'Heatmap' in group['comparison_plots_opt']['select_comparison_plots']</filter>
0 80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	714 </data>
3 8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	715 <data name="ComparisonPlot" format="pdf" label="${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	716 <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	717 </data>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	718 </outputs>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	719 <tests>
5 28434abe6c5c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 0e253b8114e2fe6f4e33edcc5f1a4602073064c3" galaxyp parents: 4 diff changeset	720 <test expect_num_outputs="6">
0 80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	721 <conditional name="input">
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	722 <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	723 <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	724 </conditional>
5 28434abe6c5c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 0e253b8114e2fe6f4e33edcc5f1a4602073064c3" galaxyp parents: 4 diff changeset	725 <param name="selected_outputs" value="raw_data,featurelevel_data,quant_sample_matrix,quant_group_long"/>
4 593839e1f2c3 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 4fe4a0b30469f52c937830d2f3c316f6b9667407" galaxyp parents: 3 diff changeset	726 <param name="selected_vis_outputs" value="ProfilePlot,profile_wsum_plot"/>
5 28434abe6c5c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 0e253b8114e2fe6f4e33edcc5f1a4602073064c3" galaxyp parents: 4 diff changeset	727 <output name="featurelevel_data">
0 80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	728 <assert_contents>
5 28434abe6c5c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 0e253b8114e2fe6f4e33edcc5f1a4602073064c3" galaxyp parents: 4 diff changeset	729 <has_text text="-.PHSHPALTPEQK_347_NA_347_NA" />
28434abe6c5c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 0e253b8114e2fe6f4e33edcc5f1a4602073064c3" galaxyp parents: 4 diff changeset	730 <has_n_columns n="15" />
0 80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	731 <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	732 </assert_contents>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	733 </output>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	734 <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	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 <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	737 <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	738 <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	739 </assert_contents>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	740 </output>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	741 <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	742 <assert_contents>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	743 <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	744 <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	745 <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	746 </assert_contents>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	747 </output>
3 8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	748 <output name="ProfilePlot" file="MSstats ProfilePlot.pdf" compare="sim_size"/>
5 28434abe6c5c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 0e253b8114e2fe6f4e33edcc5f1a4602073064c3" galaxyp parents: 4 diff changeset	749 <output name="profile_wsum_plot" file="profile_wsum_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	750 </test>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	751
5 28434abe6c5c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 0e253b8114e2fe6f4e33edcc5f1a4602073064c3" galaxyp parents: 4 diff changeset	752 <test expect_num_outputs="6">
0 80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	753 <conditional name="input">
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	754 <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	755 <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	756 </conditional>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	757 <conditional name="group">
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	758 <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	759 <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	760 </conditional>
4 593839e1f2c3 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 4fe4a0b30469f52c937830d2f3c316f6b9667407" galaxyp parents: 3 diff changeset	761 <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	762 <param name="select_comparison_plots" value="ResidualPlots"/>
5 28434abe6c5c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 0e253b8114e2fe6f4e33edcc5f1a4602073064c3" galaxyp parents: 4 diff changeset	763 <output name="featurelevel_data">
0 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 <has_text text="D.GPLTGTYR" />
5 28434abe6c5c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 0e253b8114e2fe6f4e33edcc5f1a4602073064c3" galaxyp parents: 4 diff changeset	766 <has_n_columns n="15" />
0 80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	767 <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	768 </assert_contents>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	769 </output>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	770 <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	771 <assert_contents>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	772 <has_text text="MissingPercentage" />
5 28434abe6c5c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 0e253b8114e2fe6f4e33edcc5f1a4602073064c3" galaxyp parents: 4 diff changeset	773 <has_n_columns n="13" />
0 80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	774 <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	775 </assert_contents>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	776 </output>
3 8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	777 <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	778 </test>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	779
5 28434abe6c5c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 0e253b8114e2fe6f4e33edcc5f1a4602073064c3" galaxyp parents: 4 diff changeset	780 <test expect_num_outputs="5">
0 80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	781 <conditional name="input">
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	782 <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	783 <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	784 <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	785 <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	786 </conditional>
5 28434abe6c5c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 0e253b8114e2fe6f4e33edcc5f1a4602073064c3" galaxyp parents: 4 diff changeset	787 <param name="selected_outputs" value="featurelevel_data,proteinlevel_data"/>
4 593839e1f2c3 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 4fe4a0b30469f52c937830d2f3c316f6b9667407" galaxyp parents: 3 diff changeset	788 <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	789 <conditional name="group">
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	790 <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	791 <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	792 </conditional>
4 593839e1f2c3 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 4fe4a0b30469f52c937830d2f3c316f6b9667407" galaxyp parents: 3 diff changeset	793 <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	794 <param name="select_comparison_plots" value="QQPlots"/>
5 28434abe6c5c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 0e253b8114e2fe6f4e33edcc5f1a4602073064c3" galaxyp parents: 4 diff changeset	795 <output name="featurelevel_data">
0 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 <has_text text="SPILVATAVAAR" />
5 28434abe6c5c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 0e253b8114e2fe6f4e33edcc5f1a4602073064c3" galaxyp parents: 4 diff changeset	798 <has_n_columns n="15" />
3 8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	799 <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	800 </assert_contents>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	801 </output>
5 28434abe6c5c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 0e253b8114e2fe6f4e33edcc5f1a4602073064c3" galaxyp parents: 4 diff changeset	802 <output name="proteinlevel_data">
0 80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	803 <assert_contents>
5 28434abe6c5c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 0e253b8114e2fe6f4e33edcc5f1a4602073064c3" galaxyp parents: 4 diff changeset	804 <has_text text="qx017084rawthermo" />
28434abe6c5c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 0e253b8114e2fe6f4e33edcc5f1a4602073064c3" galaxyp parents: 4 diff changeset	805 <has_text text="sp\|O75340\|PDCD6_HUMANProgrammedcelldeathprotein6OS=HomosapiensOX=9606GN=PDCD6PE=1SV=1" />
28434abe6c5c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 0e253b8114e2fe6f4e33edcc5f1a4602073064c3" galaxyp parents: 4 diff changeset	806 <has_n_columns n="11" />
0 80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	807 <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	808 </assert_contents>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	809 </output>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	810 <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	811 <assert_contents>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	812 <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	813 <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	814 <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	815 </assert_contents>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	816 </output>
3 8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	817 <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	818 <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	819 </test>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	820
5 28434abe6c5c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 0e253b8114e2fe6f4e33edcc5f1a4602073064c3" galaxyp parents: 4 diff changeset	821 <test expect_num_outputs="5">
0 80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	822 <conditional name="input">
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	823 <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	824 <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	825 </conditional>
5 28434abe6c5c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 0e253b8114e2fe6f4e33edcc5f1a4602073064c3" galaxyp parents: 4 diff changeset	826 <param name="selected_outputs" value="featurelevel_data,proteinlevel_data"/>
4 593839e1f2c3 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 4fe4a0b30469f52c937830d2f3c316f6b9667407" galaxyp parents: 3 diff changeset	827 <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	828 <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	829 <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	830 <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	831 </conditional>
4 593839e1f2c3 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 4fe4a0b30469f52c937830d2f3c316f6b9667407" galaxyp parents: 3 diff changeset	832 <param name="select_comparison_plots" value="Heatmap"/>
5 28434abe6c5c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 0e253b8114e2fe6f4e33edcc5f1a4602073064c3" galaxyp parents: 4 diff changeset	833 <output name="featurelevel_data">
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>
3 8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	835 <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	836 <has_text text="sp\|P09938\|RIR2_YEAST" />
5 28434abe6c5c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 0e253b8114e2fe6f4e33edcc5f1a4602073064c3" galaxyp parents: 4 diff changeset	837 <has_n_columns n="15" />
3 8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	838 <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	839 </assert_contents>
8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	840 </output>
5 28434abe6c5c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 0e253b8114e2fe6f4e33edcc5f1a4602073064c3" galaxyp parents: 4 diff changeset	841 <output name="proteinlevel_data">
3 8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	842 <assert_contents>
8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	843 <has_text text="sp\|P09457\|ATPO_YEAST" />
5 28434abe6c5c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 0e253b8114e2fe6f4e33edcc5f1a4602073064c3" galaxyp parents: 4 diff changeset	844 <has_n_columns n="11" />
3 8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	845 <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	846 </assert_contents>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	847 </output>
3 8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	848 <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	849 <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	850 </test>
5 28434abe6c5c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 0e253b8114e2fe6f4e33edcc5f1a4602073064c3" galaxyp parents: 4 diff changeset	851
28434abe6c5c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 0e253b8114e2fe6f4e33edcc5f1a4602073064c3" galaxyp parents: 4 diff changeset	852 <test expect_num_outputs="7">
3 8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	853 <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	854 <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	855 <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	856 <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	857 <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	858 </conditional>
8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	859 <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	860 <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	861 </conditional>
5 28434abe6c5c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 0e253b8114e2fe6f4e33edcc5f1a4602073064c3" galaxyp parents: 4 diff changeset	862 <param name="censoredInt" value="NA"/>
28434abe6c5c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 0e253b8114e2fe6f4e33edcc5f1a4602073064c3" galaxyp parents: 4 diff changeset	863 <param name="selected_outputs" value="log,featurelevel_data,quant_sample_long"/>
4 593839e1f2c3 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 4fe4a0b30469f52c937830d2f3c316f6b9667407" galaxyp parents: 3 diff changeset	864 <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	865 <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	866 <param name="height" value="7"/>
5 28434abe6c5c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 0e253b8114e2fe6f4e33edcc5f1a4602073064c3" galaxyp parents: 4 diff changeset	867 <param name="featureName" value="Peptide"/>
3 8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	868 <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	869 <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	870 <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	871 </conditional>
4 593839e1f2c3 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 4fe4a0b30469f52c937830d2f3c316f6b9667407" galaxyp parents: 3 diff changeset	872 <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	873 <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	874 <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	875 <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	876 <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	877 <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	878 <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	879 <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	880 </conditional>
593839e1f2c3 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 4fe4a0b30469f52c937830d2f3c316f6b9667407" galaxyp parents: 3 diff changeset	881 </section>
593839e1f2c3 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 4fe4a0b30469f52c937830d2f3c316f6b9667407" galaxyp parents: 3 diff changeset	882 </section>
3 8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	883 <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	884 <assert_contents>
8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	885 <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	886 <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	887 <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	888 <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	889 </assert_contents>
8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	890 </output>
8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	891 <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	892 <assert_contents>
5 28434abe6c5c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 0e253b8114e2fe6f4e33edcc5f1a4602073064c3" galaxyp parents: 4 diff changeset	893 <has_text text="3-3" />
28434abe6c5c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 0e253b8114e2fe6f4e33edcc5f1a4602073064c3" galaxyp parents: 4 diff changeset	894 <has_text text="summaryforMultipleRows: sum" />
28434abe6c5c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 0e253b8114e2fe6f4e33edcc5f1a4602073064c3" galaxyp parents: 4 diff changeset	895 <has_text text="Shared peptides are removed" />
3 8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	896 </assert_contents>
8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	897 </output>
5 28434abe6c5c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 0e253b8114e2fe6f4e33edcc5f1a4602073064c3" galaxyp parents: 4 diff changeset	898 <output name="featurelevel_data">
3 8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	899 <assert_contents>
5 28434abe6c5c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 0e253b8114e2fe6f4e33edcc5f1a4602073064c3" galaxyp parents: 4 diff changeset	900 <has_text text="ADVGFLC[+57]NMLER_2" />
3 8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	901 <has_text text="319070944" />
5 28434abe6c5c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 0e253b8114e2fe6f4e33edcc5f1a4602073064c3" galaxyp parents: 4 diff changeset	902 <has_n_columns n="14" />
3 8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	903 <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	904 </assert_contents>
8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	905 </output>
8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	906 <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	907 <assert_contents>
8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	908 <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	909 <has_text text="log2FC" />
5 28434abe6c5c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 0e253b8114e2fe6f4e33edcc5f1a4602073064c3" galaxyp parents: 4 diff changeset	910 <has_n_columns n="11" />
3 8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	911 <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	912 </assert_contents>
8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	913 </output>
8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	914 <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	915 <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	916 <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	917 </test>
5 28434abe6c5c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 0e253b8114e2fe6f4e33edcc5f1a4602073064c3" galaxyp parents: 4 diff changeset	918
28434abe6c5c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 0e253b8114e2fe6f4e33edcc5f1a4602073064c3" galaxyp parents: 4 diff changeset	919 <test expect_num_outputs="3">
28434abe6c5c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 0e253b8114e2fe6f4e33edcc5f1a4602073064c3" galaxyp parents: 4 diff changeset	920 <conditional name="input">
28434abe6c5c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 0e253b8114e2fe6f4e33edcc5f1a4602073064c3" galaxyp parents: 4 diff changeset	921 <param name="input_src" value="Skyline"/>
28434abe6c5c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 0e253b8114e2fe6f4e33edcc5f1a4602073064c3" galaxyp parents: 4 diff changeset	922 <param name="skyline_input" ftype="csv" value="skyline_input_first100.csv"/>
28434abe6c5c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 0e253b8114e2fe6f4e33edcc5f1a4602073064c3" galaxyp parents: 4 diff changeset	923 <param name="annotation" ftype="csv" value="skyline_annotations.csv"/>
28434abe6c5c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 0e253b8114e2fe6f4e33edcc5f1a4602073064c3" galaxyp parents: 4 diff changeset	924 <param name="removeProtein_with1Peptide" value="TRUE"/>
28434abe6c5c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 0e253b8114e2fe6f4e33edcc5f1a4602073064c3" galaxyp parents: 4 diff changeset	925 </conditional>
28434abe6c5c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 0e253b8114e2fe6f4e33edcc5f1a4602073064c3" galaxyp parents: 4 diff changeset	926 <conditional name="summarize">
28434abe6c5c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 0e253b8114e2fe6f4e33edcc5f1a4602073064c3" galaxyp parents: 4 diff changeset	927 <param name="MBimpute" value="TRUE"/>
28434abe6c5c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 0e253b8114e2fe6f4e33edcc5f1a4602073064c3" galaxyp parents: 4 diff changeset	928 <param name="featureSubset" value="highQuality"/>
28434abe6c5c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 0e253b8114e2fe6f4e33edcc5f1a4602073064c3" galaxyp parents: 4 diff changeset	929 <param name="remove_uninformative_feature_outlier" value="TRUE"/>
28434abe6c5c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 0e253b8114e2fe6f4e33edcc5f1a4602073064c3" galaxyp parents: 4 diff changeset	930 </conditional>
28434abe6c5c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 0e253b8114e2fe6f4e33edcc5f1a4602073064c3" galaxyp parents: 4 diff changeset	931 <param name="censoredInt" value="0"/>
28434abe6c5c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 0e253b8114e2fe6f4e33edcc5f1a4602073064c3" galaxyp parents: 4 diff changeset	932 <param name="selected_outputs" value="log,featurelevel_data,quant_sample_matrix"/>
28434abe6c5c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 0e253b8114e2fe6f4e33edcc5f1a4602073064c3" galaxyp parents: 4 diff changeset	933 <output name="quant_sample_matrix">
28434abe6c5c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 0e253b8114e2fe6f4e33edcc5f1a4602073064c3" galaxyp parents: 4 diff changeset	934 <assert_contents>
28434abe6c5c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 0e253b8114e2fe6f4e33edcc5f1a4602073064c3" galaxyp parents: 4 diff changeset	935 <has_text text="P32125" />
28434abe6c5c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 0e253b8114e2fe6f4e33edcc5f1a4602073064c3" galaxyp parents: 4 diff changeset	936 <has_text text="Condition5_5" />
28434abe6c5c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 0e253b8114e2fe6f4e33edcc5f1a4602073064c3" galaxyp parents: 4 diff changeset	937 <has_n_columns n="6" />
28434abe6c5c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 0e253b8114e2fe6f4e33edcc5f1a4602073064c3" galaxyp parents: 4 diff changeset	938 <has_n_lines n="2" />
28434abe6c5c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 0e253b8114e2fe6f4e33edcc5f1a4602073064c3" galaxyp parents: 4 diff changeset	939 </assert_contents>
28434abe6c5c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 0e253b8114e2fe6f4e33edcc5f1a4602073064c3" galaxyp parents: 4 diff changeset	940 </output>
28434abe6c5c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 0e253b8114e2fe6f4e33edcc5f1a4602073064c3" galaxyp parents: 4 diff changeset	941 <output name="log">
28434abe6c5c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 0e253b8114e2fe6f4e33edcc5f1a4602073064c3" galaxyp parents: 4 diff changeset	942 <assert_contents>
28434abe6c5c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 0e253b8114e2fe6f4e33edcc5f1a4602073064c3" galaxyp parents: 4 diff changeset	943 <has_text text="3-3" />
28434abe6c5c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 0e253b8114e2fe6f4e33edcc5f1a4602073064c3" galaxyp parents: 4 diff changeset	944 <has_text text="summaryforMultipleRows: sum" />
28434abe6c5c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 0e253b8114e2fe6f4e33edcc5f1a4602073064c3" galaxyp parents: 4 diff changeset	945 <has_text text="Shared peptides are removed" />
28434abe6c5c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 0e253b8114e2fe6f4e33edcc5f1a4602073064c3" galaxyp parents: 4 diff changeset	946 </assert_contents>
28434abe6c5c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 0e253b8114e2fe6f4e33edcc5f1a4602073064c3" galaxyp parents: 4 diff changeset	947 </output>
28434abe6c5c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 0e253b8114e2fe6f4e33edcc5f1a4602073064c3" galaxyp parents: 4 diff changeset	948 <output name="featurelevel_data">
28434abe6c5c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 0e253b8114e2fe6f4e33edcc5f1a4602073064c3" galaxyp parents: 4 diff changeset	949 <assert_contents>
28434abe6c5c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 0e253b8114e2fe6f4e33edcc5f1a4602073064c3" galaxyp parents: 4 diff changeset	950 <has_text text="AFAEAMANNSFNADEK_2" />
28434abe6c5c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 0e253b8114e2fe6f4e33edcc5f1a4602073064c3" galaxyp parents: 4 diff changeset	951 <has_text text="114949068" />
28434abe6c5c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 0e253b8114e2fe6f4e33edcc5f1a4602073064c3" galaxyp parents: 4 diff changeset	952 <has_n_columns n="15" />
28434abe6c5c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 0e253b8114e2fe6f4e33edcc5f1a4602073064c3" galaxyp parents: 4 diff changeset	953 <has_n_lines n="46" />
28434abe6c5c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 0e253b8114e2fe6f4e33edcc5f1a4602073064c3" galaxyp parents: 4 diff changeset	954 </assert_contents>
28434abe6c5c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 0e253b8114e2fe6f4e33edcc5f1a4602073064c3" galaxyp parents: 4 diff changeset	955 </output>
28434abe6c5c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 0e253b8114e2fe6f4e33edcc5f1a4602073064c3" galaxyp parents: 4 diff changeset	956 </test>
0 80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	957
5 28434abe6c5c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 0e253b8114e2fe6f4e33edcc5f1a4602073064c3" galaxyp parents: 4 diff changeset	958 <test expect_num_outputs="5">
0 80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	959 <conditional name="input">
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	960 <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	961 <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	962 <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	963 </conditional>
4 593839e1f2c3 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 4fe4a0b30469f52c937830d2f3c316f6b9667407" galaxyp parents: 3 diff changeset	964 <param name="selected_vis_outputs" value="QCPlot"/>
5 28434abe6c5c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 0e253b8114e2fe6f4e33edcc5f1a4602073064c3" galaxyp parents: 4 diff changeset	965 <output name="featurelevel_data">
0 80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	966 <assert_contents>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	967 <has_text text="GETLGLIGFGR" />
5 28434abe6c5c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 0e253b8114e2fe6f4e33edcc5f1a4602073064c3" galaxyp parents: 4 diff changeset	968 <has_n_columns n="15" />
0 80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	969 <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	970 </assert_contents>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	971 </output>
3 8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	972 <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	973 </test>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	974
5 28434abe6c5c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 0e253b8114e2fe6f4e33edcc5f1a4602073064c3" galaxyp parents: 4 diff changeset	975 <test expect_num_outputs="6">
0 80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	976 <conditional name="input">
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	977 <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	978 <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	979 <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	980 </conditional>
5 28434abe6c5c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 0e253b8114e2fe6f4e33edcc5f1a4602073064c3" galaxyp parents: 4 diff changeset	981 <param name="selected_outputs" value="r_script,featurelevel_data,quant_sample_long"/>
0 80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	982 <conditional name="group">
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	983 <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	984 <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	985 </conditional>
4 593839e1f2c3 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 4fe4a0b30469f52c937830d2f3c316f6b9667407" galaxyp parents: 3 diff changeset	986 <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	987 <param name="select_comparison_plots" value="VolcanoPlot,ResidualPlots"/>
5 28434abe6c5c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 0e253b8114e2fe6f4e33edcc5f1a4602073064c3" galaxyp parents: 4 diff changeset	988 <output name="featurelevel_data">
0 80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	989 <assert_contents>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	990 <has_text text="GETLGLIGFGR" />
5 28434abe6c5c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 0e253b8114e2fe6f4e33edcc5f1a4602073064c3" galaxyp parents: 4 diff changeset	991 <has_n_columns n="15" />
0 80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	992 <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	993 </assert_contents>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	994 </output>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	995 <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	996 <assert_contents>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	997 <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	998 <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	999 <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	1000 </assert_contents>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	1001 </output>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	1002 <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	1003 <assert_contents>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	1004 <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	1005 <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	1006 <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	1007 </assert_contents>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	1008 </output>
3 8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	1009 <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	1010 <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	1011 </test>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	1012
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	1013 </tests>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	1014 <help><![CDATA[
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	1015 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	1016
6 b7034eff0db1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 86de2cd327423c44d042f98108dc93a8f83982d0 galaxyp parents: 5 diff changeset	1017 The MSstats Galaxy tool (version @TOOL_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.
0 80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	1018
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	1019 -----
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	1020
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	1021 Input data
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	1022
3 8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	1023 - 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	1024
3 8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	1025 - 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	1026
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	1027 - 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	1028 - 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	1029 - 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	1030 - 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	1031 - 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	1032 - 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	1033 - 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	1034 - 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	1035 - 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	1036 - 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	1037 - Example file header:
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 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	1041 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	1042 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	1043 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	1044 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	1045 ... ... ... ... ...
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	1046
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	1047 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	1048 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	1049 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	1050 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	1051 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	1052 ... ... ... ... ...
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	1053
3 8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	1054 - 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	1055 - 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	1056
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	1057 - 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	1058
2 52ac6fde9a5b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 414edbbd89f9bc83b81289e409c9b688c8c1e40f" galaxyp parents: 1 diff changeset	1059 - 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	1060 - 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	1061
4 593839e1f2c3 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 4fe4a0b30469f52c937830d2f3c316f6b9667407" galaxyp parents: 3 diff changeset	1062 ::
593839e1f2c3 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 4fe4a0b30469f52c937830d2f3c316f6b9667407" galaxyp parents: 3 diff changeset	1063
593839e1f2c3 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 4fe4a0b30469f52c937830d2f3c316f6b9667407" galaxyp parents: 3 diff changeset	1064 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	1065 ** 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	1066 ** 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	1067 ** 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	1068 ** 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	1069 ... ... ... ... ...
3 8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	1070
4 593839e1f2c3 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 4fe4a0b30469f52c937830d2f3c316f6b9667407" galaxyp parents: 3 diff changeset	1071
593839e1f2c3 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 4fe4a0b30469f52c937830d2f3c316f6b9667407" galaxyp parents: 3 diff changeset	1072 - Raw.file:
593839e1f2c3 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 4fe4a0b30469f52c937830d2f3c316f6b9667407" galaxyp parents: 3 diff changeset	1073
3 8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	1074 - 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	1075 - 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	1076 - 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	1077 - 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	1078
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	1079 - 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	1080
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	1081 - 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	1082 - 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	1083 - 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	1084 - 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	1085 - 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	1086
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	1087 ::
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	1088
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	1089 names groupA groupB
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	1090 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	1091
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	1092
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	1093 - 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	1094
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	1095 ::
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	1096
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	1097 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	1098 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	1099 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	1100 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	1101 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	1102
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	1103 Options
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	1104
3 8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	1105 - 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	1106
8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	1107 - 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	1108
8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	1109 - 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	1110
8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	1111 - 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	1112 - 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	1113
3 8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	1114 - 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	1115 - 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	1116 - 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	1117 - 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	1118
8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	1119 - Feature selection
0 80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	1120
3 8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	1121 - 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	1122 - 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	1123 - 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	1124 - 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	1125
8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	1126 - 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	1127
8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	1128 - 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	1129 - 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	1130
593839e1f2c3 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 4fe4a0b30469f52c937830d2f3c316f6b9667407" galaxyp parents: 3 diff changeset	1131 - 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	1132
0 80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	1133 - Missing value imputation:
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	1134
5 28434abe6c5c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 0e253b8114e2fe6f4e33edcc5f1a4602073064c3" galaxyp parents: 4 diff changeset	1135 - Impute Missing Values: Only possible for Summarization Method TMP. Censored missing values will be determined and imputed by Accelerated Failure Time model.
3 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 - 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	1138 - 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	1139
8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	1140 - 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	1141 - 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	1142 - 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	1143
8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	1144 - 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	1145 - 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	1146
8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	1147 - 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	1148 - 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	1149
0 80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	1150
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	1151 Output options
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	1152
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	1153 - 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	1154
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	1155 - 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	1156 - 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	1157 - MSstats RawData - raw files combined into MSstats format (tabular)
5 28434abe6c5c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 0e253b8114e2fe6f4e33edcc5f1a4602073064c3" galaxyp parents: 4 diff changeset	1158 - MSstats FeatureLevelData - transformed, normalized, imputed intensities (tabular)
3 8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	1159
8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	1160 - 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	1161 - 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	1162 - 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	1163
5 28434abe6c5c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 0e253b8114e2fe6f4e33edcc5f1a4602073064c3" galaxyp parents: 4 diff changeset	1164 - MSstats ProteinLevelData - run and protein level summarized data (tabular)
3 8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	1165
8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	1166 - 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	1167 - 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	1168 - 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	1169 - 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	1170 - 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	1171
8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	1172 - 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	1173 - 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	1174
8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	1175 - 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	1176
8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	1177 - 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	1178
8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	1179 - 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	1180
8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	1181 - 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	1182
8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	1183 - 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	1184
8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	1185 - 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	1186
8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	1187 - 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	1188
8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	1189 - 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	1190
8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	1191 - 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	1192
8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	1193 - 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	1194 - 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	1195
8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	1196 - 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	1197 - 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	1198 - 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	1199 - 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	1200 - 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	1201 - 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	1202 - 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	1203 - 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	1204
8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	1205 - 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	1206
8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	1207 - 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	1208
8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	1209 - 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	1210
8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	1211 - 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	1212
8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	1213 - 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	1214
8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	1215 - 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	1216
8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	1217 - 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	1218
8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	1219 - 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	1220
8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	1221 - 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	1222
8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	1223 - 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	1224
8212e342e482 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit ad490a2f231f5ee1b6db160c117181e693ea1079" galaxyp parents: 2 diff changeset	1225 - 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	1226
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	1227 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	1228
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	1229
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	1230 ]]></help>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	1231 <citations>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	1232 <citation type="doi">10.1093/bioinformatics/btu305</citation>
6 b7034eff0db1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 86de2cd327423c44d042f98108dc93a8f83982d0 galaxyp parents: 5 diff changeset	1233 <citation type="doi">10.1021/acs.jproteome.2c00051</citation>
0 80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	1234 </citations>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	1235 </tool>
80b40b9ab835 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit d2341b64b690d975bc6e29c81f7d13b66c0c5b7f" galaxyp parents: diff changeset	1236

Mercurial > repos > galaxyp > msstats

annotate msstats.xml @ 6:b7034eff0db1 draft