Mercurial > repos > iuc > edger
annotate edger.xml @ 13:0cb907a2a810 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 95a36f5b0bd139f161d131b4c2c9c36940e749c6
| author | iuc |
|---|---|
| date | Wed, 27 Sep 2023 19:53:04 +0000 |
| parents | a8305cf0c951 |
| children | 070900306913 |
| rev | line source |
|---|---|
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df0c8d0a5992
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 38cf93fd693c810b4150c5d8aa3763aebc988b07"
iuc
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1 <tool id="edger" name="edgeR" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@"> |
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9bdff28ae1b1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
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2 <description> |
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9bdff28ae1b1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
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3 Perform differential expression of count data |
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9bdff28ae1b1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
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4 </description> |
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df0c8d0a5992
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 38cf93fd693c810b4150c5d8aa3763aebc988b07"
iuc
parents:
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5 <macros> |
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f2843df56434
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 23907b040426238b00ca0644a643c3ff0b3451b9"
iuc
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6 <token name="@TOOL_VERSION@">3.36.0</token> |
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13
0cb907a2a810
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 95a36f5b0bd139f161d131b4c2c9c36940e749c6
iuc
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7 <token name="@VERSION_SUFFIX@">2</token> |
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df0c8d0a5992
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 38cf93fd693c810b4150c5d8aa3763aebc988b07"
iuc
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8 </macros> |
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8
3d89af8a44f0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc"
iuc
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9 <edam_topics> |
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3d89af8a44f0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc"
iuc
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10 <edam_topic>topic_3308</edam_topic> |
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3d89af8a44f0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc"
iuc
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11 </edam_topics> |
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3d89af8a44f0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc"
iuc
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12 <edam_operations> |
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3d89af8a44f0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc"
iuc
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13 <edam_operation>operation_3563</edam_operation> |
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3d89af8a44f0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc"
iuc
parents:
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14 <edam_operation>operation_3223</edam_operation> |
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3d89af8a44f0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc"
iuc
parents:
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15 </edam_operations> |
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12
a8305cf0c951
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4955aeed800ea8e45057b7e8578dc878a07f9cfc
iuc
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16 <xrefs> |
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a8305cf0c951
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4955aeed800ea8e45057b7e8578dc878a07f9cfc
iuc
parents:
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17 <xref type="bio.tools">edger</xref> |
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a8305cf0c951
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4955aeed800ea8e45057b7e8578dc878a07f9cfc
iuc
parents:
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18 <xref type="bioconductor">edger</xref> |
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a8305cf0c951
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4955aeed800ea8e45057b7e8578dc878a07f9cfc
iuc
parents:
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19 </xrefs> |
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9bdff28ae1b1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
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20 <requirements> |
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df0c8d0a5992
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 38cf93fd693c810b4150c5d8aa3763aebc988b07"
iuc
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21 <requirement type="package" version="@TOOL_VERSION@">bioconductor-edger</requirement> |
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f2843df56434
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 23907b040426238b00ca0644a643c3ff0b3451b9"
iuc
parents:
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22 <requirement type="package" version="3.50.0">bioconductor-limma</requirement> |
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4730985c816f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 230fc767e2e402ee460440afab0e348f2ccab179
iuc
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23 <requirement type="package" version="0.2.20">r-rjson</requirement> |
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3d89af8a44f0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc"
iuc
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24 <requirement type="package" version="1.20.3">r-getopt</requirement> |
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3d89af8a44f0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc"
iuc
parents:
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25 <requirement type="package" version="1.4.36">r-statmod</requirement> |
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9bdff28ae1b1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
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26 <!-- required for alpha function used with plotMD --> |
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3d89af8a44f0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc"
iuc
parents:
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27 <requirement type="package" version="1.1.1">r-scales</requirement> |
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9bdff28ae1b1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
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28 </requirements> |
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9bdff28ae1b1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
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29 <version_command><![CDATA[ |
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2
a1634a9c2ee1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 910ffba48cb5f981aad1e00b77056bbbec7f9617
iuc
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30 echo $(R --version | grep version | grep -v GNU)", edgeR version" $(R --vanilla --slave -e "library(edgeR); cat(sessionInfo()\$otherPkgs\$edgeR\$Version)" 2> /dev/null | grep -v -i "WARNING: ")", limma version" $(R --vanilla --slave -e "library(limma); cat(sessionInfo()\$otherPkgs\$limma\$Version)" 2> /dev/null | grep -v -i "WARNING: ")", scales version" $(R --vanilla --slave -e "library(scales); cat(sessionInfo()\$otherPkgs\$scales\$Version)" 2> /dev/null | grep -v -i "WARNING: ")", rjson version" $(R --vanilla --slave -e "library(rjson); cat(sessionInfo()\$otherPkgs\$rjson\$Version)" 2> /dev/null | grep -v -i "WARNING: ")", getopt version" $(R --vanilla --slave -e "library(getopt); cat(sessionInfo()\$otherPkgs\$getopt\$Version)" 2> /dev/null | grep -v -i "WARNING: ") |
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9bdff28ae1b1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
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31 ]]></version_command> |
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9bdff28ae1b1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
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32 <command detect_errors="exit_code"><![CDATA[ |
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9bdff28ae1b1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
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33 #import json |
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9bdff28ae1b1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
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34 Rscript '$__tool_directory__/edger.R' |
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9bdff28ae1b1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
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35 |
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9bdff28ae1b1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
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36 -R '$outReport' |
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9bdff28ae1b1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
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37 -o '$outReport.files_path' |
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9bdff28ae1b1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
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38 |
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9bdff28ae1b1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
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39 #if $input.format=="files": |
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9bdff28ae1b1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
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40 |
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9bdff28ae1b1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
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41 ## Adapted from DESeq2 wrapper |
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9bdff28ae1b1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
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42 #set $temp_factor_names = list() |
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9bdff28ae1b1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
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43 #for $fact in $input.rep_factor: |
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9bdff28ae1b1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
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44 #set $temp_factor = list() |
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9bdff28ae1b1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
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45 #for $g in $fact.rep_group: |
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9bdff28ae1b1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
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46 #set $count_files = list() |
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9bdff28ae1b1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
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47 #for $file in $g.countsFile: |
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9bdff28ae1b1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
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48 $count_files.append(str($file)) |
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9bdff28ae1b1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
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49 #end for |
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9bdff28ae1b1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
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50 $temp_factor.append( {str($g.groupName): $count_files} ) |
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9bdff28ae1b1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
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51 #end for |
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9bdff28ae1b1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
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52 |
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9bdff28ae1b1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
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53 $temp_factor.reverse() |
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9bdff28ae1b1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
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54 $temp_factor_names.append([str($fact.factorName), $temp_factor]) |
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9bdff28ae1b1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
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55 #end for |
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9bdff28ae1b1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
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56 -j '#echo json.dumps(temp_factor_names)#' |
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9bdff28ae1b1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
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57 |
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9bdff28ae1b1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
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58 #elif $input.format=="matrix": |
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9bdff28ae1b1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
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59 -m '$input.counts' |
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9bdff28ae1b1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
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60 #if $input.fact.ffile=='yes': |
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9bdff28ae1b1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
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61 -f '$input.fact.finfo' |
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9bdff28ae1b1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
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62 #else: |
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9bdff28ae1b1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
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63 -i '${ '|'.join( ['%s::%s' % ($x.factorName, $x.groupNames) for x in $input.fact.rep_factor] ) }' |
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9bdff28ae1b1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
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64 #end if |
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9bdff28ae1b1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
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65 #end if |
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9bdff28ae1b1
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66 |
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9bdff28ae1b1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
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67 #if $anno.annoOpt=='yes': |
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9bdff28ae1b1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
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68 -a '$anno.geneanno' |
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9bdff28ae1b1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
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69 #end if |
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9bdff28ae1b1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
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70 |
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9bdff28ae1b1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
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71 -C '${ ','.join( ['%s' % $x.contrast for x in $rep_contrast] ) }' |
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9bdff28ae1b1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
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72 |
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9bdff28ae1b1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
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73 #if $f.filt.filt_select == 'yes': |
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9bdff28ae1b1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
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74 #if $f.filt.cformat.format_select == 'cpm': |
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9bdff28ae1b1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
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75 -c '$f.filt.cformat.cpmReq' |
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9bdff28ae1b1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
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76 -s '$f.filt.cformat.cpmSampleReq' |
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77 #elif $f.filt.cformat.format_select == 'counts': |
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78 -z '$f.filt.cformat.cntReq' |
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79 #if $f.filt.cformat.samples.count_select == 'total': |
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80 -y |
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81 #elif $f.filt.cformat.samples.count_select == 'sample': |
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82 -s '$f.filt.cformat.samples.cntSampleReq' |
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83 #end if |
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84 #end if |
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85 #end if |
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86 |
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87 #if $out.normCounts: |
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88 -x |
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89 #end if |
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90 #if $out.rdaOption: |
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91 -r |
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92 #end if |
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93 |
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94 -l '$adv.lfc' |
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95 -p '$adv.pVal' |
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96 -d '$adv.pAdjust' |
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97 -n '$adv.normalisationOption' |
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98 #if $adv.robOption: |
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99 -b |
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100 #end if |
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101 #if $adv.lrtOption: |
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102 -t |
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103 #end if |
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104 |
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105 && |
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106 mkdir ./output_dir |
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107 |
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108 && |
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109 cp '$outReport.files_path'/*.tsv output_dir/ |
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2
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110 |
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111 #if $out.rscript: |
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112 && cp '$__tool_directory__/edger.R' '$rscript' |
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113 #end if |
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0
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114 ]]></command> |
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115 <inputs> |
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116 <!-- Counts and Factors --> |
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117 <conditional name="input"> |
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12
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118 <param name="format" type="select" label="Count Files or Matrix?" help="You can choose to input either separate count files (one per sample) or a single count matrix"> |
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0
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119 <option value="files">Separate Count Files</option> |
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120 <option value="matrix">Single Count Matrix</option> |
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121 </param> |
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122 <when value="files"> |
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123 <repeat name="rep_factor" title="Factor" min="1"> |
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6
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124 <param name="factorName" type="text" label="Name" help="Name of experiment factor of interest (e.g. Genotype). One factor must be entered and there must be two or more groups per factor. Optional additional factors (e.g. Batch) can be entered using the Insert Factor button below, see Help section for more information. NOTE: Please only use letters, numbers or underscores, and the first character of each factor must be a letter"> |
|
12
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125 <sanitizer> |
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126 <valid initial="string.letters,string.digits"> |
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127 <add value="_"/> |
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128 </valid> |
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129 </sanitizer> |
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0
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130 </param> |
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131 <repeat name="rep_group" title="Group" min="2" default="2"> |
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12
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132 <param name="groupName" type="text" label="Name" help="Name of group that the counts files belong to (e.g. WT or Mut). NOTE: Please only use letters, numbers or underscores (case sensitive), and the first character of each group must be a letter"> |
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133 <sanitizer> |
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134 <valid initial="string.letters,string.digits"> |
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135 <add value="_"/> |
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136 </valid> |
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137 </sanitizer> |
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0
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138 </param> |
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3
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139 <param name="countsFile" type="data" format="tabular" multiple="true" label="Counts files"/> |
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0
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140 </repeat> |
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141 </repeat> |
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142 </when> |
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143 <when value="matrix"> |
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144 <param name="counts" type="data" format="tabular" label="Count Matrix"/> |
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145 <conditional name="fact"> |
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12
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146 <param name="ffile" type="select" label="Input factor information from file?" help="You can choose to input the factor and group information for the samples from a file or manually enter below. NOTE: Please only use letters, numbers or underscores (case sensitive), and the first character of each sample, factor and group must be a letter"> |
|
0
9bdff28ae1b1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
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147 <option value="no">No</option> |
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148 <option value="yes">Yes</option> |
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149 </param> |
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150 <when value="yes"> |
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151 <param name="finfo" type="data" format="tabular" label="Factor File"/> |
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152 </when> |
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12
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153 <when value="no"> |
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0
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154 <repeat name="rep_factor" title="Factor" min="1"> |
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12
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155 <param name="factorName" type="text" label="Factor Name" help="Name of experiment factor of interest (e.g. Genotype). One factor must be entered and there must be two or more groups per factor. Additional factors (e.g. Batch) can be entered using the Insert Factor button below, see Help section below. NOTE: Please only use letters, numbers or underscores, and the first character of each factor must be a letter"> |
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156 <validator type="empty_field"/> |
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157 <validator type="regex" message="Please only use letters, numbers or underscores">^[\w]+$</validator> |
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158 </param> |
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159 <param name="groupNames" type="text" label="Groups" help="Enter the group names for the samples separated with commas e.g. WT,WT,WT,Mut,Mut,Mut. The order of the names must match the order of the samples in the columns of the count matrix. NOTE: Please only use letters, numbers or underscores (case sensitive), and the first character of each group must be a letter"> |
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160 <validator type="empty_field"/> |
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161 <validator type="regex" message="Please only use letters, numbers or underscores, and separate levels by commas">^[\w,]+$</validator> |
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162 </param> |
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163 </repeat> |
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164 </when> |
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165 </conditional> |
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166 </when> |
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167 </conditional> |
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168 <!-- Gene Annotations --> |
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169 <conditional name="anno"> |
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170 <param name="annoOpt" type="select" label="Use Gene Annotations?" help="If you provide an annotation file, annotations will be added to the table(s) of differential expression results to provide descriptions for each gene. See Help section below."> |
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171 <option value="no">No</option> |
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172 <option value="yes">Yes</option> |
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173 </param> |
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174 <when value="yes"> |
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175 <param name="geneanno" type="data" format="tabular" label="Gene Annotations"/> |
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176 </when> |
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12
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177 <when value="no"/> |
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178 </conditional> |
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179 <!-- Contrasts --> |
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180 <repeat name="rep_contrast" title="Contrast" min="1" default="1"> |
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181 <param name="contrast" type="text" label="Contrast of Interest" help="Names of two groups to compare separated by a hyphen e.g. Mut-WT. If the order is Mut-WT the fold changes in the results will be up/down in Mut relative to WT. If you have more than one contrast enter each separately using the Insert Contrast button below. For differences between contrasts use e.g. (MT.t1-MT.t0)-(WT.t1-WT.t0). For more info, see Chapter 8 in the limma User's guide: https://www.bioconductor.org/packages/release/bioc/vignettes/limma/inst/doc/usersguide.pdf or https://bioconductor.org/packages/release/bioc/vignettes/edgeR/inst/doc/edgeRUsersGuide.pdf page 36 for nested comparisons."> |
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182 <validator type="empty_field"/> |
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7
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183 <validator type="regex" message="Please only use letters, numbers, parentheses or underscores">^[\w\-()]+$</validator> |
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184 </param> |
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185 </repeat> |
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186 <!-- Filter Options --> |
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187 <section name="f" expanded="false" title="Filter Low Counts"> |
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188 <conditional name="filt"> |
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189 <param name="filt_select" type="select" label="Filter lowly expressed genes?" help="Treat genes with very low expression as unexpressed and filter out. See the Filter Low Counts section below for more information. Default: No"> |
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190 <option value="no" selected="true">No</option> |
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191 <option value="yes">Yes</option> |
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192 </param> |
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193 <when value="yes"> |
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194 <conditional name="cformat"> |
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195 <param name="format_select" type="select" label="Filter on CPM or Count values?" help="It is slightly better to base the filtering on count-per-million (CPM) rather than the raw count values so as to avoid favoring genes expressed in samples sequenced to a higher depth. "> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
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196 <option value="cpm">CPM</option> |
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197 <option value="counts">Counts</option> |
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198 </param> |
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199 <when value="cpm"> |
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200 <param name="cpmReq" type="float" value="1" min="0" label="Minimum CPM" help="Treat genes with CPM below this value as unexpressed and filter out. See the Filter Low Counts section below for more information."/> |
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201 <param name="cpmSampleReq" type="integer" value="0" min="0" label="Minimum Samples" help="Filter out all genes that do not meet the Minimum CPM in at least this many samples. See the Filter Low Counts section below for more information."/> |
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202 </when> |
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203 <when value="counts"> |
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204 <param name="cntReq" type="integer" value="0" min="0" label="Minimum Count" help="Filter out all genes that do not meet this minimum count. You can choose below to apply this filter to the total count for all samples or specify the number of samples under Minimum Samples. See the Filter Low Counts section below for more information."/> |
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205 <conditional name="samples"> |
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206 <param name="count_select" type="select" label="Filter on Total Count or per Sample Count values?"> |
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207 <option value="total">Total</option> |
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208 <option value="sample">Sample</option> |
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209 </param> |
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10
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210 <when value="total"/> |
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211 <when value="sample"> |
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212 <param name="cntSampleReq" type="integer" value="0" min="0" label="Minimum Samples" help="Filter out all genes that do not meet the Minimum Count in at least this many samples. See the Filter Low Counts section below for more information."/> |
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213 </when> |
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214 </conditional> |
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215 </when> |
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216 </conditional> |
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217 </when> |
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218 <when value="no"/> |
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219 </conditional> |
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220 </section> |
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221 <!-- Output Options --> |
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222 <section name="out" expanded="false" title="Output Options"> |
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223 <param name="normCounts" type="boolean" truevalue="1" falsevalue="0" checked="false" label="Output Normalised Counts Table?" help="Output a file containing the normalised counts, these are in log2 counts per million (logCPM). Default: No"> |
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224 </param> |
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225 <param name="rscript" type="boolean" truevalue="True" falsevalue="False" checked="False" label="Output Rscript?" help="If this option is set to Yes, the Rscript used will be provided as a text file in the output. Default: No"/> |
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226 <param name="rdaOption" type="boolean" truevalue="1" falsevalue="0" checked="false" label="Output RData file?" help="Output all the data used by R to construct the plots and tables, can be loaded into R. A link to the RData file will be provided in the HTML report. Default: No"> |
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0
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227 </param> |
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228 </section> |
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229 <!-- Advanced Options --> |
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230 <section name="adv" expanded="false" title="Advanced Options"> |
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231 <param name="lfc" type="float" value="0" min="0" label="Minimum Log2 Fold Change" help="Genes above this threshold and below the p-value threshold are considered significant and highlighted in the MD plot. Default: 0."/> |
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232 <param name="pVal" type="float" value="0.05" min="0" max="1" label="P-Value Adjusted Threshold" help="Genes below this threshold are considered significant and highlighted in the MD plot. If either BH(1995) or BY(2001) are selected then this value is a false-discovery-rate control. If Holm(1979) is selected then this is an adjusted p-value for family-wise error rate. Default: 0.05."/> |
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233 <param name="pAdjust" type="select" label="P-Value Adjustment Method" help="Default: BH"> |
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234 <option value="BH" selected="true">Benjamini and Hochberg (1995)</option> |
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235 <option value="BY">Benjamini and Yekutieli (2001)</option> |
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236 <option value="holm">Holm (1979)</option> |
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237 <option value="none">None</option> |
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238 </param> |
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239 <param name="normalisationOption" type="select" label="Normalisation Method" help="Default: TMM"> |
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240 <option value="TMM" selected="true">TMM</option> |
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241 <option value="RLE">RLE</option> |
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242 <option value="upperquartile">Upperquartile</option> |
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243 <option value="none">None (Don't normalise)</option> |
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244 </param> |
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245 <param name="robOption" type="boolean" truevalue="1" falsevalue="0" checked="true" label="Use Robust Settings?" help="Using robust settings is usually recommended to protect against outlier genes. Default: Yes"/> |
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246 <param name="lrtOption" type="boolean" truevalue="1" falsevalue="0" checked="false" label="Use Likelihood Ratio Test?" help="Use likelihood ratio test instead of quasi-likelihood F-test. Default: No"/> |
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247 </section> |
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248 </inputs> |
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249 <outputs> |
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250 <data name="outReport" format="html" label="${tool.name} on ${on_string}: Report"/> |
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251 <collection name="outTables" type="list" label="${tool.name} on ${on_string}: Tables"> |
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252 <discover_datasets pattern="(?P<name>.+)\.tsv$" format="tabular" directory="output_dir" visible="false"/> |
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253 </collection> |
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254 <data name="rscript" format="txt" label="${tool.name} on ${on_string}: Rscript"> |
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255 <filter>out['rscript']</filter> |
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256 </data> |
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257 </outputs> |
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258 <tests> |
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259 <!-- Ensure report is output --> |
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260 <test expect_num_outputs="2"> |
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261 <param name="format" value="matrix"/> |
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262 <param name="counts" value="matrix.txt"/> |
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263 <repeat name="rep_factor"> |
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264 <param name="factorName" value="Genotype"/> |
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265 <param name="groupNames" value="Mut,Mut,Mut,WT,WT,WT"/> |
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266 </repeat> |
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267 <repeat name="rep_contrast"> |
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268 <param name="contrast" value="Mut-WT"/> |
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269 </repeat> |
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270 <repeat name="rep_contrast"> |
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271 <param name="contrast" value="WT-Mut"/> |
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272 </repeat> |
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273 <param name="normalisationOption" value="TMM"/> |
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274 <output_collection name="outTables" count="2"> |
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275 <element name="edgeR_Mut-WT" ftype="tabular"> |
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276 <assert_contents> |
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277 <has_text_matching expression="GeneID.*logFC.*logCPM.*F.*PValue.*FDR"/> |
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278 <has_text_matching expression="11304.*0.4582"/> |
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279 </assert_contents> |
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280 </element> |
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281 <element name="edgeR_WT-Mut" ftype="tabular"> |
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282 <assert_contents> |
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283 <has_text_matching expression="GeneID.*logFC.*logCPM.*F.*PValue.*FDR"/> |
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284 <has_text_matching expression="11304.*-0.4582"/> |
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285 </assert_contents> |
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286 </element> |
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287 </output_collection> |
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288 <output name="outReport"> |
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289 <assert_contents> |
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290 <has_text text="edgeR Analysis Output"/> |
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291 <has_text text="quasi-likelihood"/> |
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292 <not_has_text text="likelihood ratio"/> |
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293 <not_has_text text="RData"/> |
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294 </assert_contents> |
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295 </output> |
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296 </test> |
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297 <!-- Complex contrasts constructions --> |
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298 <test expect_num_outputs="2"> |
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299 <param name="format" value="matrix"/> |
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300 <param name="counts" value="matrix-complex.txt"/> |
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301 <repeat name="rep_factor"> |
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302 <param name="factorName" value="Genotype"/> |
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303 <param name="groupNames" value="MutA,MutA,MutA,MutB,MutB,MutB,WTA,WTA,WTA,WTB,WTB,WTB"/> |
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304 </repeat> |
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305 <repeat name="rep_contrast"> |
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12
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306 <param name="contrast" value="(MutA-MutB)-(WTA-WTB)"/> |
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7
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307 </repeat> |
|
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308 <param name="normalisationOption" value="TMM"/> |
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7
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309 <output_collection name="outTables" count="1"> |
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12
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310 <element name="edgeR_(MutA-MutB)-(WTA-WTB)" ftype="tabular"> |
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7
334ce9b1bac5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 106b877ec24a2422c0c13e37bf275c7441108b36
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311 <assert_contents> |
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12
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312 <has_text_matching expression="GeneID.*logFC.*logCPM.*F.*PValue.*FDR"/> |
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a8305cf0c951
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313 <has_text_matching expression="11304.*15.53"/> |
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a8305cf0c951
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4955aeed800ea8e45057b7e8578dc878a07f9cfc
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314 </assert_contents> |
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315 </element> |
|
7
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 106b877ec24a2422c0c13e37bf275c7441108b36
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316 </output_collection> |
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12
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317 <output name="outReport"> |
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7
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 106b877ec24a2422c0c13e37bf275c7441108b36
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318 <assert_contents> |
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12
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319 <has_text text="edgeR Analysis Output"/> |
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320 <has_text text="quasi-likelihood"/> |
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a8305cf0c951
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4955aeed800ea8e45057b7e8578dc878a07f9cfc
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321 <not_has_text text="likelihood ratio"/> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4955aeed800ea8e45057b7e8578dc878a07f9cfc
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322 <not_has_text text="RData"/> |
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334ce9b1bac5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 106b877ec24a2422c0c13e37bf275c7441108b36
iuc
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323 </assert_contents> |
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334ce9b1bac5
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324 </output> |
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325 </test> |
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326 <!-- Ensure annotation file input works --> |
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327 <test expect_num_outputs="2"> |
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328 <param name="format" value="matrix"/> |
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a8305cf0c951
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4955aeed800ea8e45057b7e8578dc878a07f9cfc
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329 <param name="annoOpt" value="yes"/> |
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330 <param name="geneanno" value="anno.txt"/> |
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a8305cf0c951
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4955aeed800ea8e45057b7e8578dc878a07f9cfc
iuc
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331 <param name="counts" value="matrix.txt"/> |
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0
9bdff28ae1b1
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332 <repeat name="rep_factor"> |
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9bdff28ae1b1
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333 <param name="factorName" value="Genotype"/> |
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12
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334 <param name="groupNames" value="Mut,Mut,Mut,WT,WT,WT"/> |
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0
9bdff28ae1b1
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335 </repeat> |
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9bdff28ae1b1
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336 <repeat name="rep_contrast"> |
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12
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337 <param name="contrast" value="Mut-WT"/> |
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0
9bdff28ae1b1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
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338 </repeat> |
|
12
a8305cf0c951
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339 <param name="normalisationOption" value="TMM"/> |
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0
9bdff28ae1b1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
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340 <output_collection name="outTables" count="1"> |
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12
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341 <element name="edgeR_Mut-WT" ftype="tabular"> |
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2
a1634a9c2ee1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 910ffba48cb5f981aad1e00b77056bbbec7f9617
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342 <assert_contents> |
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12
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343 <has_text_matching expression="EntrezID.*Symbol.*logFC.*logCPM.*F.*PValue.*FDR"/> |
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a8305cf0c951
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344 <has_text_matching expression="11304.*Abca4.*0.4582"/> |
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a8305cf0c951
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345 </assert_contents> |
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346 </element> |
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0
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347 </output_collection> |
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348 </test> |
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2
a1634a9c2ee1
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349 <!-- Ensure RScript and RData file can be output --> |
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12
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350 <test expect_num_outputs="3"> |
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351 <param name="format" value="matrix"/> |
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2
a1634a9c2ee1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 910ffba48cb5f981aad1e00b77056bbbec7f9617
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352 <param name="rscript" value="True"/> |
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12
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353 <param name="rdaOption" value="true"/> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4955aeed800ea8e45057b7e8578dc878a07f9cfc
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354 <param name="counts" value="matrix.txt"/> |
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0
9bdff28ae1b1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
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355 <repeat name="rep_factor"> |
|
9bdff28ae1b1
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356 <param name="factorName" value="Genotype"/> |
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12
a8305cf0c951
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4955aeed800ea8e45057b7e8578dc878a07f9cfc
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357 <param name="groupNames" value="Mut,Mut,Mut,WT,WT,WT"/> |
|
0
9bdff28ae1b1
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358 </repeat> |
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9bdff28ae1b1
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359 <repeat name="rep_contrast"> |
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12
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360 <param name="contrast" value="Mut-WT"/> |
|
0
9bdff28ae1b1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
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361 </repeat> |
|
12
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4955aeed800ea8e45057b7e8578dc878a07f9cfc
iuc
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362 <param name="normalisationOption" value="TMM"/> |
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a8305cf0c951
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4955aeed800ea8e45057b7e8578dc878a07f9cfc
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363 <output name="outReport"> |
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0
9bdff28ae1b1
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364 <assert_contents> |
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12
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365 <has_text text="RData"/> |
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0
9bdff28ae1b1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
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366 </assert_contents> |
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9bdff28ae1b1
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367 </output> |
|
4
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368 <output name="rscript"> |
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4730985c816f
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369 <assert_contents> |
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12
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370 <has_text_matching expression="Task run time"/> |
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4
4730985c816f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 230fc767e2e402ee460440afab0e348f2ccab179
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371 </assert_contents> |
|
4730985c816f
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372 </output> |
|
0
9bdff28ae1b1
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373 </test> |
|
9bdff28ae1b1
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374 <!-- Ensure secondary factors work --> |
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12
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375 <test expect_num_outputs="2"> |
|
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iuc
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376 <param name="format" value="matrix"/> |
|
a8305cf0c951
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4955aeed800ea8e45057b7e8578dc878a07f9cfc
iuc
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377 <param name="counts" value="matrix.txt"/> |
|
0
9bdff28ae1b1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
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changeset
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378 <repeat name="rep_factor"> |
|
9bdff28ae1b1
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iuc
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379 <param name="factorName" value="Genotype"/> |
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12
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4955aeed800ea8e45057b7e8578dc878a07f9cfc
iuc
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380 <param name="groupNames" value="Mut,Mut,Mut,WT,WT,WT"/> |
|
0
9bdff28ae1b1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
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381 </repeat> |
|
9bdff28ae1b1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
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changeset
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382 <repeat name="rep_factor"> |
|
9bdff28ae1b1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
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383 <param name="factorName" value="Batch"/> |
|
9bdff28ae1b1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
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384 <param name="groupNames" value="b1,b2,b3,b1,b2,b3"/> |
|
9bdff28ae1b1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
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385 </repeat> |
|
9bdff28ae1b1
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iuc
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changeset
|
386 <repeat name="rep_contrast"> |
|
12
a8305cf0c951
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4955aeed800ea8e45057b7e8578dc878a07f9cfc
iuc
parents:
11
diff
changeset
|
387 <param name="contrast" value="Mut-WT"/> |
|
0
9bdff28ae1b1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff
changeset
|
388 </repeat> |
|
12
a8305cf0c951
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4955aeed800ea8e45057b7e8578dc878a07f9cfc
iuc
parents:
11
diff
changeset
|
389 <param name="normalisationOption" value="TMM"/> |
|
a8305cf0c951
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4955aeed800ea8e45057b7e8578dc878a07f9cfc
iuc
parents:
11
diff
changeset
|
390 <output_collection name="outTables" count="1"> |
|
a8305cf0c951
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4955aeed800ea8e45057b7e8578dc878a07f9cfc
iuc
parents:
11
diff
changeset
|
391 <element name="edgeR_Mut-WT" ftype="tabular"> |
|
2
a1634a9c2ee1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 910ffba48cb5f981aad1e00b77056bbbec7f9617
iuc
parents:
1
diff
changeset
|
392 <assert_contents> |
|
12
a8305cf0c951
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4955aeed800ea8e45057b7e8578dc878a07f9cfc
iuc
parents:
11
diff
changeset
|
393 <has_text_matching expression="GeneID.*logFC.*logCPM.*F.*PValue.*FDR"/> |
|
a8305cf0c951
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4955aeed800ea8e45057b7e8578dc878a07f9cfc
iuc
parents:
11
diff
changeset
|
394 <has_text_matching expression="11304.*0.4584"/> |
|
a8305cf0c951
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4955aeed800ea8e45057b7e8578dc878a07f9cfc
iuc
parents:
11
diff
changeset
|
395 </assert_contents> |
|
a8305cf0c951
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4955aeed800ea8e45057b7e8578dc878a07f9cfc
iuc
parents:
11
diff
changeset
|
396 </element> |
|
0
9bdff28ae1b1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff
changeset
|
397 </output_collection> |
|
9bdff28ae1b1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff
changeset
|
398 </test> |
|
4
4730985c816f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 230fc767e2e402ee460440afab0e348f2ccab179
iuc
parents:
3
diff
changeset
|
399 <!-- Ensure factors file with unordered samples works --> |
|
12
a8305cf0c951
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4955aeed800ea8e45057b7e8578dc878a07f9cfc
iuc
parents:
11
diff
changeset
|
400 <test expect_num_outputs="2"> |
|
a8305cf0c951
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4955aeed800ea8e45057b7e8578dc878a07f9cfc
iuc
parents:
11
diff
changeset
|
401 <param name="format" value="matrix"/> |
|
a8305cf0c951
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4955aeed800ea8e45057b7e8578dc878a07f9cfc
iuc
parents:
11
diff
changeset
|
402 <param name="ffile" value="yes"/> |
|
a8305cf0c951
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4955aeed800ea8e45057b7e8578dc878a07f9cfc
iuc
parents:
11
diff
changeset
|
403 <param name="finfo" value="factorinfo.txt"/> |
|
a8305cf0c951
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4955aeed800ea8e45057b7e8578dc878a07f9cfc
iuc
parents:
11
diff
changeset
|
404 <param name="counts" value="matrix.txt"/> |
|
0
9bdff28ae1b1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff
changeset
|
405 <repeat name="rep_contrast"> |
|
12
a8305cf0c951
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4955aeed800ea8e45057b7e8578dc878a07f9cfc
iuc
parents:
11
diff
changeset
|
406 <param name="contrast" value="Mut-WT"/> |
|
0
9bdff28ae1b1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff
changeset
|
407 </repeat> |
|
12
a8305cf0c951
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4955aeed800ea8e45057b7e8578dc878a07f9cfc
iuc
parents:
11
diff
changeset
|
408 <param name="normalisationOption" value="TMM"/> |
|
0
9bdff28ae1b1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff
changeset
|
409 <output_collection name="outTables" count="1"> |
|
12
a8305cf0c951
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4955aeed800ea8e45057b7e8578dc878a07f9cfc
iuc
parents:
11
diff
changeset
|
410 <element name="edgeR_Mut-WT" ftype="tabular"> |
|
2
a1634a9c2ee1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 910ffba48cb5f981aad1e00b77056bbbec7f9617
iuc
parents:
1
diff
changeset
|
411 <assert_contents> |
|
12
a8305cf0c951
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4955aeed800ea8e45057b7e8578dc878a07f9cfc
iuc
parents:
11
diff
changeset
|
412 <has_text_matching expression="GeneID.*logFC.*logCPM.*F.*PValue.*FDR"/> |
|
a8305cf0c951
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4955aeed800ea8e45057b7e8578dc878a07f9cfc
iuc
parents:
11
diff
changeset
|
413 <has_text_matching expression="11304.*0.4584"/> |
|
a8305cf0c951
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4955aeed800ea8e45057b7e8578dc878a07f9cfc
iuc
parents:
11
diff
changeset
|
414 </assert_contents> |
|
a8305cf0c951
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4955aeed800ea8e45057b7e8578dc878a07f9cfc
iuc
parents:
11
diff
changeset
|
415 </element> |
|
0
9bdff28ae1b1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff
changeset
|
416 </output_collection> |
|
9bdff28ae1b1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff
changeset
|
417 </test> |
|
9bdff28ae1b1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff
changeset
|
418 <!-- Ensure normalised counts file output works--> |
|
12
a8305cf0c951
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4955aeed800ea8e45057b7e8578dc878a07f9cfc
iuc
parents:
11
diff
changeset
|
419 <test expect_num_outputs="2"> |
|
a8305cf0c951
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4955aeed800ea8e45057b7e8578dc878a07f9cfc
iuc
parents:
11
diff
changeset
|
420 <param name="format" value="matrix"/> |
|
a8305cf0c951
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4955aeed800ea8e45057b7e8578dc878a07f9cfc
iuc
parents:
11
diff
changeset
|
421 <param name="normCounts" value="true"/> |
|
a8305cf0c951
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4955aeed800ea8e45057b7e8578dc878a07f9cfc
iuc
parents:
11
diff
changeset
|
422 <param name="counts" value="matrix.txt"/> |
|
0
9bdff28ae1b1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff
changeset
|
423 <repeat name="rep_factor"> |
|
9bdff28ae1b1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff
changeset
|
424 <param name="factorName" value="Genotype"/> |
|
12
a8305cf0c951
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4955aeed800ea8e45057b7e8578dc878a07f9cfc
iuc
parents:
11
diff
changeset
|
425 <param name="groupNames" value="Mut,Mut,Mut,WT,WT,WT"/> |
|
0
9bdff28ae1b1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff
changeset
|
426 </repeat> |
|
9bdff28ae1b1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff
changeset
|
427 <repeat name="rep_contrast"> |
|
12
a8305cf0c951
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4955aeed800ea8e45057b7e8578dc878a07f9cfc
iuc
parents:
11
diff
changeset
|
428 <param name="contrast" value="Mut-WT"/> |
|
0
9bdff28ae1b1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff
changeset
|
429 </repeat> |
|
12
a8305cf0c951
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4955aeed800ea8e45057b7e8578dc878a07f9cfc
iuc
parents:
11
diff
changeset
|
430 <param name="normalisationOption" value="TMM"/> |
|
0
9bdff28ae1b1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff
changeset
|
431 <output_collection name="outTables" count="2"> |
|
12
a8305cf0c951
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4955aeed800ea8e45057b7e8578dc878a07f9cfc
iuc
parents:
11
diff
changeset
|
432 <element name="edgeR_Mut-WT" ftype="tabular"> |
|
2
a1634a9c2ee1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 910ffba48cb5f981aad1e00b77056bbbec7f9617
iuc
parents:
1
diff
changeset
|
433 <assert_contents> |
|
12
a8305cf0c951
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4955aeed800ea8e45057b7e8578dc878a07f9cfc
iuc
parents:
11
diff
changeset
|
434 <has_text_matching expression="GeneID.*logFC.*logCPM.*F.*PValue.*FDR"/> |
|
a8305cf0c951
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4955aeed800ea8e45057b7e8578dc878a07f9cfc
iuc
parents:
11
diff
changeset
|
435 <has_text_matching expression="11304.*0.4582"/> |
|
a8305cf0c951
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4955aeed800ea8e45057b7e8578dc878a07f9cfc
iuc
parents:
11
diff
changeset
|
436 </assert_contents> |
|
a8305cf0c951
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4955aeed800ea8e45057b7e8578dc878a07f9cfc
iuc
parents:
11
diff
changeset
|
437 </element> |
|
a8305cf0c951
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4955aeed800ea8e45057b7e8578dc878a07f9cfc
iuc
parents:
11
diff
changeset
|
438 <element name="edgeR_normcounts" ftype="tabular"> |
|
2
a1634a9c2ee1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 910ffba48cb5f981aad1e00b77056bbbec7f9617
iuc
parents:
1
diff
changeset
|
439 <assert_contents> |
|
12
a8305cf0c951
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4955aeed800ea8e45057b7e8578dc878a07f9cfc
iuc
parents:
11
diff
changeset
|
440 <has_text_matching expression="GeneID.*Mut1.*Mut2.*Mut3.*WT1.*WT2.*WT3"/> |
|
a8305cf0c951
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4955aeed800ea8e45057b7e8578dc878a07f9cfc
iuc
parents:
11
diff
changeset
|
441 <has_text_matching expression="11304.*15.75"/> |
|
a8305cf0c951
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4955aeed800ea8e45057b7e8578dc878a07f9cfc
iuc
parents:
11
diff
changeset
|
442 </assert_contents> |
|
a8305cf0c951
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4955aeed800ea8e45057b7e8578dc878a07f9cfc
iuc
parents:
11
diff
changeset
|
443 </element> |
|
0
9bdff28ae1b1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff
changeset
|
444 </output_collection> |
|
9bdff28ae1b1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff
changeset
|
445 </test> |
|
9bdff28ae1b1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff
changeset
|
446 <!-- Ensure likelihood ratio option works --> |
|
12
a8305cf0c951
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4955aeed800ea8e45057b7e8578dc878a07f9cfc
iuc
parents:
11
diff
changeset
|
447 <test expect_num_outputs="2"> |
|
a8305cf0c951
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4955aeed800ea8e45057b7e8578dc878a07f9cfc
iuc
parents:
11
diff
changeset
|
448 <param name="format" value="matrix"/> |
|
a8305cf0c951
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4955aeed800ea8e45057b7e8578dc878a07f9cfc
iuc
parents:
11
diff
changeset
|
449 <param name="counts" value="matrix.txt"/> |
|
0
9bdff28ae1b1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff
changeset
|
450 <repeat name="rep_factor"> |
|
9bdff28ae1b1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff
changeset
|
451 <param name="factorName" value="Genotype"/> |
|
12
a8305cf0c951
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4955aeed800ea8e45057b7e8578dc878a07f9cfc
iuc
parents:
11
diff
changeset
|
452 <param name="groupNames" value="Mut,Mut,Mut,WT,WT,WT"/> |
|
0
9bdff28ae1b1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff
changeset
|
453 </repeat> |
|
9bdff28ae1b1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff
changeset
|
454 <repeat name="rep_contrast"> |
|
12
a8305cf0c951
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4955aeed800ea8e45057b7e8578dc878a07f9cfc
iuc
parents:
11
diff
changeset
|
455 <param name="contrast" value="Mut-WT"/> |
|
0
9bdff28ae1b1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff
changeset
|
456 </repeat> |
|
12
a8305cf0c951
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4955aeed800ea8e45057b7e8578dc878a07f9cfc
iuc
parents:
11
diff
changeset
|
457 <param name="normalisationOption" value="TMM"/> |
|
a8305cf0c951
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4955aeed800ea8e45057b7e8578dc878a07f9cfc
iuc
parents:
11
diff
changeset
|
458 <param name="lrtOption" value="true"/> |
|
a8305cf0c951
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4955aeed800ea8e45057b7e8578dc878a07f9cfc
iuc
parents:
11
diff
changeset
|
459 <output name="outReport"> |
|
0
9bdff28ae1b1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff
changeset
|
460 <assert_contents> |
|
12
a8305cf0c951
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4955aeed800ea8e45057b7e8578dc878a07f9cfc
iuc
parents:
11
diff
changeset
|
461 <has_text text="likelihood ratio"/> |
|
a8305cf0c951
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4955aeed800ea8e45057b7e8578dc878a07f9cfc
iuc
parents:
11
diff
changeset
|
462 <not_has_text text="quasi-likelihood"/> |
|
0
9bdff28ae1b1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff
changeset
|
463 </assert_contents> |
|
9bdff28ae1b1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff
changeset
|
464 </output> |
|
9bdff28ae1b1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff
changeset
|
465 </test> |
|
9bdff28ae1b1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff
changeset
|
466 <!-- Ensure multiple counts files input works --> |
|
12
a8305cf0c951
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4955aeed800ea8e45057b7e8578dc878a07f9cfc
iuc
parents:
11
diff
changeset
|
467 <test expect_num_outputs="2"> |
|
a8305cf0c951
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4955aeed800ea8e45057b7e8578dc878a07f9cfc
iuc
parents:
11
diff
changeset
|
468 <param name="format" value="files"/> |
|
0
9bdff28ae1b1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff
changeset
|
469 <repeat name="rep_factor"> |
|
9bdff28ae1b1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff
changeset
|
470 <param name="factorName" value="Genotype"/> |
|
9bdff28ae1b1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff
changeset
|
471 <repeat name="rep_group"> |
|
9bdff28ae1b1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff
changeset
|
472 <param name="groupName" value="WT"/> |
|
9bdff28ae1b1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff
changeset
|
473 <param name="countsFile" value="WT1.counts,WT2.counts,WT3.counts"/> |
|
9bdff28ae1b1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff
changeset
|
474 </repeat> |
|
9bdff28ae1b1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff
changeset
|
475 <repeat name="rep_group"> |
|
9bdff28ae1b1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff
changeset
|
476 <param name="groupName" value="Mut"/> |
|
9bdff28ae1b1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff
changeset
|
477 <param name="countsFile" value="Mut1.counts,Mut2.counts,Mut3.counts"/> |
|
9bdff28ae1b1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff
changeset
|
478 </repeat> |
|
9bdff28ae1b1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff
changeset
|
479 </repeat> |
|
9bdff28ae1b1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff
changeset
|
480 <repeat name="rep_factor"> |
|
9bdff28ae1b1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff
changeset
|
481 <param name="factorName" value="Batch"/> |
|
9bdff28ae1b1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff
changeset
|
482 <repeat name="rep_group"> |
|
9bdff28ae1b1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff
changeset
|
483 <param name="groupName" value="b1"/> |
|
9bdff28ae1b1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff
changeset
|
484 <param name="countsFile" value="WT1.counts,Mut1.counts"/> |
|
9bdff28ae1b1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff
changeset
|
485 </repeat> |
|
9bdff28ae1b1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff
changeset
|
486 <repeat name="rep_group"> |
|
9bdff28ae1b1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff
changeset
|
487 <param name="groupName" value="b2"/> |
|
9bdff28ae1b1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff
changeset
|
488 <param name="countsFile" value="WT2.counts,Mut2.counts"/> |
|
9bdff28ae1b1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff
changeset
|
489 </repeat> |
|
9bdff28ae1b1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff
changeset
|
490 <repeat name="rep_group"> |
|
9bdff28ae1b1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff
changeset
|
491 <param name="groupName" value="b3"/> |
|
9bdff28ae1b1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff
changeset
|
492 <param name="countsFile" value="WT3.counts,Mut3.counts"/> |
|
9bdff28ae1b1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff
changeset
|
493 </repeat> |
|
9bdff28ae1b1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff
changeset
|
494 </repeat> |
|
12
a8305cf0c951
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4955aeed800ea8e45057b7e8578dc878a07f9cfc
iuc
parents:
11
diff
changeset
|
495 <param name="annoOpt" value="yes"/> |
|
a8305cf0c951
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4955aeed800ea8e45057b7e8578dc878a07f9cfc
iuc
parents:
11
diff
changeset
|
496 <param name="geneanno" value="anno.txt"/> |
|
0
9bdff28ae1b1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff
changeset
|
497 <repeat name="rep_contrast"> |
|
12
a8305cf0c951
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4955aeed800ea8e45057b7e8578dc878a07f9cfc
iuc
parents:
11
diff
changeset
|
498 <param name="contrast" value="Mut-WT"/> |
|
0
9bdff28ae1b1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff
changeset
|
499 </repeat> |
|
9bdff28ae1b1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff
changeset
|
500 <repeat name="rep_contrast"> |
|
12
a8305cf0c951
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4955aeed800ea8e45057b7e8578dc878a07f9cfc
iuc
parents:
11
diff
changeset
|
501 <param name="contrast" value="WT-Mut"/> |
|
0
9bdff28ae1b1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff
changeset
|
502 </repeat> |
|
12
a8305cf0c951
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4955aeed800ea8e45057b7e8578dc878a07f9cfc
iuc
parents:
11
diff
changeset
|
503 <param name="normCounts" value="true"/> |
|
0
9bdff28ae1b1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff
changeset
|
504 <output_collection name="outTables" count="3"> |
|
12
a8305cf0c951
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4955aeed800ea8e45057b7e8578dc878a07f9cfc
iuc
parents:
11
diff
changeset
|
505 <element name="edgeR_Mut-WT" ftype="tabular"> |
|
2
a1634a9c2ee1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 910ffba48cb5f981aad1e00b77056bbbec7f9617
iuc
parents:
1
diff
changeset
|
506 <assert_contents> |
|
12
a8305cf0c951
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4955aeed800ea8e45057b7e8578dc878a07f9cfc
iuc
parents:
11
diff
changeset
|
507 <has_text_matching expression="EntrezID.*Symbol.*logFC.*logCPM.*F.*PValue.*FDR"/> |
|
a8305cf0c951
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4955aeed800ea8e45057b7e8578dc878a07f9cfc
iuc
parents:
11
diff
changeset
|
508 <has_text_matching expression="11304.*Abca4.*0.4584"/> |
|
a8305cf0c951
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4955aeed800ea8e45057b7e8578dc878a07f9cfc
iuc
parents:
11
diff
changeset
|
509 </assert_contents> |
|
a8305cf0c951
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4955aeed800ea8e45057b7e8578dc878a07f9cfc
iuc
parents:
11
diff
changeset
|
510 </element> |
|
a8305cf0c951
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4955aeed800ea8e45057b7e8578dc878a07f9cfc
iuc
parents:
11
diff
changeset
|
511 <element name="edgeR_WT-Mut" ftype="tabular"> |
|
2
a1634a9c2ee1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 910ffba48cb5f981aad1e00b77056bbbec7f9617
iuc
parents:
1
diff
changeset
|
512 <assert_contents> |
|
12
a8305cf0c951
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4955aeed800ea8e45057b7e8578dc878a07f9cfc
iuc
parents:
11
diff
changeset
|
513 <has_text_matching expression="logFC.*logCPM.*F.*PValue.*FDR"/> |
|
a8305cf0c951
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4955aeed800ea8e45057b7e8578dc878a07f9cfc
iuc
parents:
11
diff
changeset
|
514 <has_text_matching expression="11304.*Abca4.*-0.4584"/> |
|
a8305cf0c951
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4955aeed800ea8e45057b7e8578dc878a07f9cfc
iuc
parents:
11
diff
changeset
|
515 </assert_contents> |
|
a8305cf0c951
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4955aeed800ea8e45057b7e8578dc878a07f9cfc
iuc
parents:
11
diff
changeset
|
516 </element> |
|
a8305cf0c951
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4955aeed800ea8e45057b7e8578dc878a07f9cfc
iuc
parents:
11
diff
changeset
|
517 <element name="edgeR_normcounts" ftype="tabular"> |
|
2
a1634a9c2ee1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 910ffba48cb5f981aad1e00b77056bbbec7f9617
iuc
parents:
1
diff
changeset
|
518 <assert_contents> |
|
12
a8305cf0c951
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4955aeed800ea8e45057b7e8578dc878a07f9cfc
iuc
parents:
11
diff
changeset
|
519 <has_text_matching expression="Mut1.*Mut2.*Mut3.*WT1.*WT2.*WT3"/> |
|
a8305cf0c951
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4955aeed800ea8e45057b7e8578dc878a07f9cfc
iuc
parents:
11
diff
changeset
|
520 <has_text_matching expression="11304.*Abca4.*15.75"/> |
|
a8305cf0c951
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4955aeed800ea8e45057b7e8578dc878a07f9cfc
iuc
parents:
11
diff
changeset
|
521 </assert_contents> |
|
a8305cf0c951
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4955aeed800ea8e45057b7e8578dc878a07f9cfc
iuc
parents:
11
diff
changeset
|
522 </element> |
|
0
9bdff28ae1b1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff
changeset
|
523 </output_collection> |
|
9bdff28ae1b1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff
changeset
|
524 </test> |
|
9bdff28ae1b1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff
changeset
|
525 <!-- Ensure filtering on CPM in Mnimum Samples works --> |
|
12
a8305cf0c951
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4955aeed800ea8e45057b7e8578dc878a07f9cfc
iuc
parents:
11
diff
changeset
|
526 <test expect_num_outputs="2"> |
|
a8305cf0c951
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4955aeed800ea8e45057b7e8578dc878a07f9cfc
iuc
parents:
11
diff
changeset
|
527 <param name="format" value="matrix"/> |
|
a8305cf0c951
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4955aeed800ea8e45057b7e8578dc878a07f9cfc
iuc
parents:
11
diff
changeset
|
528 <param name="counts" value="matrix.txt"/> |
|
0
9bdff28ae1b1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff
changeset
|
529 <repeat name="rep_factor"> |
|
9bdff28ae1b1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff
changeset
|
530 <param name="factorName" value="Genotype"/> |
|
12
a8305cf0c951
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4955aeed800ea8e45057b7e8578dc878a07f9cfc
iuc
parents:
11
diff
changeset
|
531 <param name="groupNames" value="Mut,Mut,Mut,WT,WT,WT"/> |
|
0
9bdff28ae1b1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff
changeset
|
532 </repeat> |
|
9bdff28ae1b1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff
changeset
|
533 <repeat name="rep_contrast"> |
|
12
a8305cf0c951
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4955aeed800ea8e45057b7e8578dc878a07f9cfc
iuc
parents:
11
diff
changeset
|
534 <param name="contrast" value="Mut-WT"/> |
|
0
9bdff28ae1b1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff
changeset
|
535 </repeat> |
|
12
a8305cf0c951
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4955aeed800ea8e45057b7e8578dc878a07f9cfc
iuc
parents:
11
diff
changeset
|
536 <param name="normalisationOption" value="TMM"/> |
|
a8305cf0c951
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4955aeed800ea8e45057b7e8578dc878a07f9cfc
iuc
parents:
11
diff
changeset
|
537 <param name="filt_select" value="yes"/> |
|
a8305cf0c951
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4955aeed800ea8e45057b7e8578dc878a07f9cfc
iuc
parents:
11
diff
changeset
|
538 <param name="format_select" value="cpm"/> |
|
0
9bdff28ae1b1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff
changeset
|
539 <!-- real cpmReq values would be a lot lower |
|
9bdff28ae1b1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff
changeset
|
540 this is just for this tiny test dataset --> |
|
12
a8305cf0c951
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4955aeed800ea8e45057b7e8578dc878a07f9cfc
iuc
parents:
11
diff
changeset
|
541 <param name="cpmReq" value="1000"/> |
|
a8305cf0c951
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4955aeed800ea8e45057b7e8578dc878a07f9cfc
iuc
parents:
11
diff
changeset
|
542 <param name="cpmSampleReq" value="3"/> |
|
a8305cf0c951
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4955aeed800ea8e45057b7e8578dc878a07f9cfc
iuc
parents:
11
diff
changeset
|
543 <output name="outReport"> |
|
0
9bdff28ae1b1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff
changeset
|
544 <assert_contents> |
|
12
a8305cf0c951
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4955aeed800ea8e45057b7e8578dc878a07f9cfc
iuc
parents:
11
diff
changeset
|
545 <has_text text="CPM in at least"/> |
|
a8305cf0c951
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4955aeed800ea8e45057b7e8578dc878a07f9cfc
iuc
parents:
11
diff
changeset
|
546 <not_has_text text="after summing counts for all samples"/> |
|
a8305cf0c951
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4955aeed800ea8e45057b7e8578dc878a07f9cfc
iuc
parents:
11
diff
changeset
|
547 <not_has_text text="counts in at least"/> |
|
0
9bdff28ae1b1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff
changeset
|
548 </assert_contents> |
|
9bdff28ae1b1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff
changeset
|
549 </output> |
|
12
a8305cf0c951
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4955aeed800ea8e45057b7e8578dc878a07f9cfc
iuc
parents:
11
diff
changeset
|
550 <output_collection name="outTables" count="1"> |
|
a8305cf0c951
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4955aeed800ea8e45057b7e8578dc878a07f9cfc
iuc
parents:
11
diff
changeset
|
551 <element name="edgeR_Mut-WT" ftype="tabular"> |
|
2
a1634a9c2ee1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 910ffba48cb5f981aad1e00b77056bbbec7f9617
iuc
parents:
1
diff
changeset
|
552 <assert_contents> |
|
12
a8305cf0c951
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4955aeed800ea8e45057b7e8578dc878a07f9cfc
iuc
parents:
11
diff
changeset
|
553 <has_text_matching expression="GeneID.*logFC.*logCPM.*F.*PValue.*FDR"/> |
|
a8305cf0c951
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4955aeed800ea8e45057b7e8578dc878a07f9cfc
iuc
parents:
11
diff
changeset
|
554 <has_text_matching expression="11304.*0.4568"/> |
|
a8305cf0c951
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4955aeed800ea8e45057b7e8578dc878a07f9cfc
iuc
parents:
11
diff
changeset
|
555 <not_has_text text="-0.0682"/> |
|
a8305cf0c951
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4955aeed800ea8e45057b7e8578dc878a07f9cfc
iuc
parents:
11
diff
changeset
|
556 </assert_contents> |
|
a8305cf0c951
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4955aeed800ea8e45057b7e8578dc878a07f9cfc
iuc
parents:
11
diff
changeset
|
557 </element> |
|
0
9bdff28ae1b1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff
changeset
|
558 </output_collection> |
|
9bdff28ae1b1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff
changeset
|
559 </test> |
|
9bdff28ae1b1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff
changeset
|
560 <!-- Ensure filtering on Count in Minmum Samples works --> |
|
12
a8305cf0c951
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4955aeed800ea8e45057b7e8578dc878a07f9cfc
iuc
parents:
11
diff
changeset
|
561 <test expect_num_outputs="2"> |
|
a8305cf0c951
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4955aeed800ea8e45057b7e8578dc878a07f9cfc
iuc
parents:
11
diff
changeset
|
562 <param name="format" value="matrix"/> |
|
a8305cf0c951
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4955aeed800ea8e45057b7e8578dc878a07f9cfc
iuc
parents:
11
diff
changeset
|
563 <param name="counts" value="matrix.txt"/> |
|
0
9bdff28ae1b1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff
changeset
|
564 <repeat name="rep_factor"> |
|
9bdff28ae1b1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff
changeset
|
565 <param name="factorName" value="Genotype"/> |
|
12
a8305cf0c951
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4955aeed800ea8e45057b7e8578dc878a07f9cfc
iuc
parents:
11
diff
changeset
|
566 <param name="groupNames" value="Mut,Mut,Mut,WT,WT,WT"/> |
|
0
9bdff28ae1b1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff
changeset
|
567 </repeat> |
|
9bdff28ae1b1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff
changeset
|
568 <repeat name="rep_contrast"> |
|
12
a8305cf0c951
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4955aeed800ea8e45057b7e8578dc878a07f9cfc
iuc
parents:
11
diff
changeset
|
569 <param name="contrast" value="Mut-WT"/> |
|
0
9bdff28ae1b1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff
changeset
|
570 </repeat> |
|
12
a8305cf0c951
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4955aeed800ea8e45057b7e8578dc878a07f9cfc
iuc
parents:
11
diff
changeset
|
571 <param name="normalisationOption" value="TMM"/> |
|
a8305cf0c951
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4955aeed800ea8e45057b7e8578dc878a07f9cfc
iuc
parents:
11
diff
changeset
|
572 <param name="filt_select" value="yes"/> |
|
a8305cf0c951
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4955aeed800ea8e45057b7e8578dc878a07f9cfc
iuc
parents:
11
diff
changeset
|
573 <param name="format_select" value="counts"/> |
|
a8305cf0c951
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4955aeed800ea8e45057b7e8578dc878a07f9cfc
iuc
parents:
11
diff
changeset
|
574 <param name="cntReq" value="10"/> |
|
a8305cf0c951
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4955aeed800ea8e45057b7e8578dc878a07f9cfc
iuc
parents:
11
diff
changeset
|
575 <param name="count_select" value="sample"/> |
|
a8305cf0c951
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4955aeed800ea8e45057b7e8578dc878a07f9cfc
iuc
parents:
11
diff
changeset
|
576 <param name="cntSampleReq" value="3"/> |
|
a8305cf0c951
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4955aeed800ea8e45057b7e8578dc878a07f9cfc
iuc
parents:
11
diff
changeset
|
577 <output name="outReport"> |
|
0
9bdff28ae1b1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff
changeset
|
578 <assert_contents> |
|
12
a8305cf0c951
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4955aeed800ea8e45057b7e8578dc878a07f9cfc
iuc
parents:
11
diff
changeset
|
579 <has_text text="counts in at least"/> |
|
a8305cf0c951
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4955aeed800ea8e45057b7e8578dc878a07f9cfc
iuc
parents:
11
diff
changeset
|
580 <not_has_text text="after summing counts for all samples"/> |
|
a8305cf0c951
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4955aeed800ea8e45057b7e8578dc878a07f9cfc
iuc
parents:
11
diff
changeset
|
581 <not_has_text text="CPM in at least"/> |
|
0
9bdff28ae1b1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff
changeset
|
582 </assert_contents> |
|
9bdff28ae1b1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff
changeset
|
583 </output> |
|
12
a8305cf0c951
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4955aeed800ea8e45057b7e8578dc878a07f9cfc
iuc
parents:
11
diff
changeset
|
584 <output_collection name="outTables" count="1"> |
|
a8305cf0c951
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4955aeed800ea8e45057b7e8578dc878a07f9cfc
iuc
parents:
11
diff
changeset
|
585 <element name="edgeR_Mut-WT" ftype="tabular"> |
|
2
a1634a9c2ee1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 910ffba48cb5f981aad1e00b77056bbbec7f9617
iuc
parents:
1
diff
changeset
|
586 <assert_contents> |
|
12
a8305cf0c951
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4955aeed800ea8e45057b7e8578dc878a07f9cfc
iuc
parents:
11
diff
changeset
|
587 <has_text_matching expression="GeneID.*logFC.*logCPM.*F.*PValue.*FDR"/> |
|
a8305cf0c951
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4955aeed800ea8e45057b7e8578dc878a07f9cfc
iuc
parents:
11
diff
changeset
|
588 <has_text_matching expression="11304.*0.4568"/> |
|
a8305cf0c951
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4955aeed800ea8e45057b7e8578dc878a07f9cfc
iuc
parents:
11
diff
changeset
|
589 <not_has_text text="-0.0682"/> |
|
a8305cf0c951
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4955aeed800ea8e45057b7e8578dc878a07f9cfc
iuc
parents:
11
diff
changeset
|
590 </assert_contents> |
|
a8305cf0c951
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4955aeed800ea8e45057b7e8578dc878a07f9cfc
iuc
parents:
11
diff
changeset
|
591 </element> |
|
0
9bdff28ae1b1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff
changeset
|
592 </output_collection> |
|
9bdff28ae1b1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff
changeset
|
593 </test> |
|
9bdff28ae1b1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff
changeset
|
594 <!-- Ensure filtering on Total Count works --> |
|
12
a8305cf0c951
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4955aeed800ea8e45057b7e8578dc878a07f9cfc
iuc
parents:
11
diff
changeset
|
595 <test expect_num_outputs="2"> |
|
a8305cf0c951
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4955aeed800ea8e45057b7e8578dc878a07f9cfc
iuc
parents:
11
diff
changeset
|
596 <param name="format" value="matrix"/> |
|
a8305cf0c951
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4955aeed800ea8e45057b7e8578dc878a07f9cfc
iuc
parents:
11
diff
changeset
|
597 <param name="counts" value="matrix.txt"/> |
|
0
9bdff28ae1b1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff
changeset
|
598 <repeat name="rep_factor"> |
|
9bdff28ae1b1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff
changeset
|
599 <param name="factorName" value="Genotype"/> |
|
12
a8305cf0c951
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4955aeed800ea8e45057b7e8578dc878a07f9cfc
iuc
parents:
11
diff
changeset
|
600 <param name="groupNames" value="Mut,Mut,Mut,WT,WT,WT"/> |
|
0
9bdff28ae1b1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff
changeset
|
601 </repeat> |
|
9bdff28ae1b1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff
changeset
|
602 <repeat name="rep_contrast"> |
|
12
a8305cf0c951
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4955aeed800ea8e45057b7e8578dc878a07f9cfc
iuc
parents:
11
diff
changeset
|
603 <param name="contrast" value="Mut-WT"/> |
|
0
9bdff28ae1b1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff
changeset
|
604 </repeat> |
|
12
a8305cf0c951
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4955aeed800ea8e45057b7e8578dc878a07f9cfc
iuc
parents:
11
diff
changeset
|
605 <param name="normalisationOption" value="TMM"/> |
|
a8305cf0c951
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4955aeed800ea8e45057b7e8578dc878a07f9cfc
iuc
parents:
11
diff
changeset
|
606 <param name="filt_select" value="yes"/> |
|
a8305cf0c951
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4955aeed800ea8e45057b7e8578dc878a07f9cfc
iuc
parents:
11
diff
changeset
|
607 <param name="format_select" value="counts"/> |
|
0
9bdff28ae1b1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff
changeset
|
608 <!-- real cntReq values would be a lot lower |
|
9bdff28ae1b1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff
changeset
|
609 this is just for this tiny test dataset --> |
|
12
a8305cf0c951
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4955aeed800ea8e45057b7e8578dc878a07f9cfc
iuc
parents:
11
diff
changeset
|
610 <param name="cntReq" value="1000"/> |
|
a8305cf0c951
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4955aeed800ea8e45057b7e8578dc878a07f9cfc
iuc
parents:
11
diff
changeset
|
611 <param name="count_select" value="total"/> |
|
a8305cf0c951
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4955aeed800ea8e45057b7e8578dc878a07f9cfc
iuc
parents:
11
diff
changeset
|
612 <output name="outReport"> |
|
0
9bdff28ae1b1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff
changeset
|
613 <assert_contents> |
|
12
a8305cf0c951
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4955aeed800ea8e45057b7e8578dc878a07f9cfc
iuc
parents:
11
diff
changeset
|
614 <has_text text="after summing counts for all samples"/> |
|
a8305cf0c951
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4955aeed800ea8e45057b7e8578dc878a07f9cfc
iuc
parents:
11
diff
changeset
|
615 <not_has_text text="counts in at least"/> |
|
a8305cf0c951
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4955aeed800ea8e45057b7e8578dc878a07f9cfc
iuc
parents:
11
diff
changeset
|
616 <not_has_text text="CPM in at least"/> |
|
0
9bdff28ae1b1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff
changeset
|
617 </assert_contents> |
|
9bdff28ae1b1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff
changeset
|
618 </output> |
|
12
a8305cf0c951
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4955aeed800ea8e45057b7e8578dc878a07f9cfc
iuc
parents:
11
diff
changeset
|
619 <output_collection name="outTables" count="1"> |
|
a8305cf0c951
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4955aeed800ea8e45057b7e8578dc878a07f9cfc
iuc
parents:
11
diff
changeset
|
620 <element name="edgeR_Mut-WT" ftype="tabular"> |
|
2
a1634a9c2ee1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 910ffba48cb5f981aad1e00b77056bbbec7f9617
iuc
parents:
1
diff
changeset
|
621 <assert_contents> |
|
12
a8305cf0c951
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4955aeed800ea8e45057b7e8578dc878a07f9cfc
iuc
parents:
11
diff
changeset
|
622 <has_text_matching expression="GeneID.*logFC.*logCPM.*F.*PValue.*FDR"/> |
|
a8305cf0c951
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4955aeed800ea8e45057b7e8578dc878a07f9cfc
iuc
parents:
11
diff
changeset
|
623 <has_text_matching expression="11304.*0.4568"/> |
|
a8305cf0c951
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4955aeed800ea8e45057b7e8578dc878a07f9cfc
iuc
parents:
11
diff
changeset
|
624 <not_has_text text="-0.0682"/> |
|
a8305cf0c951
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4955aeed800ea8e45057b7e8578dc878a07f9cfc
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625 </assert_contents> |
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a8305cf0c951
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4955aeed800ea8e45057b7e8578dc878a07f9cfc
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626 </element> |
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0
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
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627 </output_collection> |
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9bdff28ae1b1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
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628 </test> |
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9bdff28ae1b1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
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629 </tests> |
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9bdff28ae1b1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
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630 <help><![CDATA[ |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
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631 .. class:: infomark |
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9bdff28ae1b1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
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632 |
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9bdff28ae1b1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
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633 **What it does** |
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9bdff28ae1b1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
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634 |
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9bdff28ae1b1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
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parents:
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changeset
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635 Given a counts matrix, or a set of counts files, for example from **featureCounts**, and optional information about the genes, this tool |
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9bdff28ae1b1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
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changeset
|
636 produces plots and tables useful in the analysis of differential gene expression. |
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9bdff28ae1b1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
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637 |
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9bdff28ae1b1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
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638 This tool uses the `edgeR`_ quasi-likelihood pipeline (edgeR-quasi) for differential expression analysis. This statistical methodology uses negative binomial generalized linear models, but with F-tests instead of likelihood ratio tests. This method provides stricter error rate control than other negative binomial based pipelines, including the traditional edgeR pipelines or DESeq2. While the limma pipelines are recommended for large-scale datasets, because of their speed and flexibility, the edgeR-quasi pipeline gives better performance in low-count situations. For the data analyzed in this `edgeR workflow article`_ ,the edgeR-quasi, limma-voom and limma-trend pipelines are all equally suitable and give similar results. |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
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639 |
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9bdff28ae1b1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
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640 .. _edgeR: http://www.bioconductor.org/packages/release/bioc/html/edgeR.html |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
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641 .. _edgeR workflow article: https://f1000research.com/articles/5-1438 |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
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642 |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
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643 ----- |
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9bdff28ae1b1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
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644 |
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9bdff28ae1b1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
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645 **Inputs** |
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9bdff28ae1b1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
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646 |
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9bdff28ae1b1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
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647 **Counts Data:** |
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9bdff28ae1b1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
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648 |
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6
555659de7321
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 21f0bc6c64129122212a6d182fdf3e360617e629
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649 The counts data can either be input as separate counts files (one sample per file) or a single count matrix (one sample per column). The rows correspond to genes, and columns correspond to the counts for the samples. Values must be tab separated, with the first row containing the sample/column labels and the first column containing the row/gene labels. The sample labels must start with a letter. Gene identifiers can be of any type but must be unique and not repeated within a counts file. |
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650 |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
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651 Example - **Separate Count Files**: |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
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652 |
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9bdff28ae1b1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
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653 ========== ======= |
|
9bdff28ae1b1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
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654 **GeneID** **WT1** |
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9bdff28ae1b1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
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655 ---------- ------- |
|
9bdff28ae1b1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
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changeset
|
656 11287 1699 |
|
9bdff28ae1b1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
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changeset
|
657 11298 1905 |
|
9bdff28ae1b1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
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658 11302 6 |
|
9bdff28ae1b1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
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changeset
|
659 11303 2099 |
|
9bdff28ae1b1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
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660 11304 356 |
|
9bdff28ae1b1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
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661 11305 2528 |
|
9bdff28ae1b1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
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662 ========== ======= |
|
9bdff28ae1b1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
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663 |
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9bdff28ae1b1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
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664 Example - **Single Count Matrix**: |
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9bdff28ae1b1
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665 |
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9bdff28ae1b1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
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666 ========== ======= ======= ======= ======== ======== ======== |
|
9bdff28ae1b1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
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667 **GeneID** **WT1** **WT2** **WT3** **Mut1** **Mut2** **Mut3** |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
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668 ---------- ------- ------- ------- -------- -------- -------- |
|
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
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669 11287 1699 1528 1601 1463 1441 1495 |
|
9bdff28ae1b1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
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670 11298 1905 1744 1834 1345 1291 1346 |
|
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
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671 11302 6 8 7 5 6 5 |
|
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
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672 11303 2099 1974 2100 1574 1519 1654 |
|
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673 11304 356 312 337 361 397 346 |
|
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674 11305 2528 2438 2493 1762 1942 2027 |
|
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
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675 ========== ======= ======= ======= ======== ======== ======== |
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9bdff28ae1b1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
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676 |
|
9bdff28ae1b1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
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677 |
|
9bdff28ae1b1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
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678 **Gene Annotations:** |
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9bdff28ae1b1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
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679 Optional input for gene annotations, this can contain more |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
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680 information about the genes than just an ID number. The annotations will |
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3
d79ed3ec25fe
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit e646be741e315df9332b5206cec1e47c11370ff1
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681 be available in the differential expression results table and the optional normalised counts table. The file must contain a header row and have the gene IDs in the first column. The number of rows should match that of the counts files, add NA for any gene IDs with no annotation. The Galaxy tool **annotateMyIDs** can be used to obtain annotations for human, mouse, fly and zebrafish. |
|
0
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682 |
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683 Example: |
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684 |
|
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685 ========== ========== =================================================== |
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9bdff28ae1b1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
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686 **GeneID** **Symbol** **GeneName** |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
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687 ---------- ---------- --------------------------------------------------- |
|
3
d79ed3ec25fe
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit e646be741e315df9332b5206cec1e47c11370ff1
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688 11287 Pzp pregnancy zone protein |
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d79ed3ec25fe
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit e646be741e315df9332b5206cec1e47c11370ff1
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689 11298 Aanat arylalkylamine N-acetyltransferase |
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d79ed3ec25fe
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit e646be741e315df9332b5206cec1e47c11370ff1
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690 11302 Aatk apoptosis-associated tyrosine kinase |
|
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit e646be741e315df9332b5206cec1e47c11370ff1
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691 11303 Abca1 ATP-binding cassette, sub-family A (ABC1), member 1 |
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d79ed3ec25fe
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit e646be741e315df9332b5206cec1e47c11370ff1
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692 11304 Abca4 ATP-binding cassette, sub-family A (ABC1), member 4 |
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d79ed3ec25fe
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit e646be741e315df9332b5206cec1e47c11370ff1
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693 11305 Abca2 ATP-binding cassette, sub-family A (ABC1), member 2 |
|
0
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694 ========== ========== =================================================== |
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695 |
|
4
4730985c816f
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696 **Factor Information:** |
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697 Enter factor names and groups in the tool form, or provide a tab-separated file that has the names of the samples in the first column and one header row. The sample names must be the same as the names in the columns of the count matrix. The second column should contain the primary factor levels (e.g. WT, Mut) with optional additional columns for any secondary factors. |
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698 |
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699 Example: |
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700 |
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701 ========== ============ ========= |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 230fc767e2e402ee460440afab0e348f2ccab179
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702 **Sample** **Genotype** **Batch** |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 230fc767e2e402ee460440afab0e348f2ccab179
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703 ---------- ------------ --------- |
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4730985c816f
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704 WT1 WT b1 |
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4730985c816f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 230fc767e2e402ee460440afab0e348f2ccab179
iuc
parents:
3
diff
changeset
|
705 WT2 WT b2 |
|
4730985c816f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 230fc767e2e402ee460440afab0e348f2ccab179
iuc
parents:
3
diff
changeset
|
706 WT3 WT b3 |
|
4730985c816f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 230fc767e2e402ee460440afab0e348f2ccab179
iuc
parents:
3
diff
changeset
|
707 Mut1 Mut b1 |
|
4730985c816f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 230fc767e2e402ee460440afab0e348f2ccab179
iuc
parents:
3
diff
changeset
|
708 Mut2 Mut b2 |
|
4730985c816f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 230fc767e2e402ee460440afab0e348f2ccab179
iuc
parents:
3
diff
changeset
|
709 Mut3 Mut b3 |
|
4730985c816f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 230fc767e2e402ee460440afab0e348f2ccab179
iuc
parents:
3
diff
changeset
|
710 ========== ============ ========= |
|
4730985c816f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 230fc767e2e402ee460440afab0e348f2ccab179
iuc
parents:
3
diff
changeset
|
711 |
|
6
555659de7321
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 21f0bc6c64129122212a6d182fdf3e360617e629
iuc
parents:
5
diff
changeset
|
712 *Factor Name:* The name of the experimental factor being investigated e.g. Genotype, Treatment. One factor must be entered, the name should start with a letter and spaces must not be used. Optionally, additional factors can be included, these are variables that might influence your experiment e.g. Batch, Gender, Subject. If additional factors are entered, an additive linear model will be used. |
|
4
4730985c816f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 230fc767e2e402ee460440afab0e348f2ccab179
iuc
parents:
3
diff
changeset
|
713 |
|
6
555659de7321
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 21f0bc6c64129122212a6d182fdf3e360617e629
iuc
parents:
5
diff
changeset
|
714 *Groups:* The names of the groups for the factor. The names should start with a letter, and only contain letters, numbers and underscores, other characters such as spaces and hyphens must not be used. If entered into the tool form above, the order must be the same as the samples (to which the groups correspond) are listed in the columns of the counts matrix, with the values separated by commas. |
|
4
4730985c816f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 230fc767e2e402ee460440afab0e348f2ccab179
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parents:
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diff
changeset
|
715 |
|
0
9bdff28ae1b1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff
changeset
|
716 **Contrasts of Interest:** |
|
9bdff28ae1b1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff
changeset
|
717 The contrasts you wish to make between levels. |
|
9bdff28ae1b1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff
changeset
|
718 A common contrast would be a simple difference between two levels: "Mut-WT" |
|
9bdff28ae1b1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff
changeset
|
719 represents the difference between the mutant and wild type genotypes. |
|
9bdff28ae1b1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff
changeset
|
720 Multiple contrasts must be entered separately using the Insert Contrast button, spaces must not be used. |
|
9bdff28ae1b1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff
changeset
|
721 |
|
9bdff28ae1b1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff
changeset
|
722 **Filter Low Counts:** |
|
9bdff28ae1b1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff
changeset
|
723 Genes with very low counts across all libraries provide little evidence for differential expression. |
|
9bdff28ae1b1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff
changeset
|
724 In the biological point of view, a gene must be expressed at some minimal level before |
|
9bdff28ae1b1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff
changeset
|
725 it is likely to be translated into a protein or to be biologically important. In addition, the |
|
9bdff28ae1b1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff
changeset
|
726 pronounced discreteness of these counts interferes with some of the statistical approximations |
|
9bdff28ae1b1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff
changeset
|
727 that are used later in the pipeline. These genes should be filtered out prior to further |
|
9bdff28ae1b1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff
changeset
|
728 analysis. |
|
9bdff28ae1b1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff
changeset
|
729 As a rule of thumb, genes are dropped if they can’t possibly be expressed in all the samples |
|
9bdff28ae1b1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff
changeset
|
730 for any of the conditions. Users can set their own definition of genes being expressed. Usually |
|
9bdff28ae1b1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff
changeset
|
731 a gene is required to have a count of 5-10 in a library to be considered expressed in that |
|
9bdff28ae1b1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff
changeset
|
732 library. Users should also filter with count-per-million (CPM) rather than filtering on the |
|
9bdff28ae1b1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff
changeset
|
733 counts directly, as the latter does not account for differences in library sizes between samples. |
|
9bdff28ae1b1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff
changeset
|
734 |
|
9bdff28ae1b1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff
changeset
|
735 Option to ignore the genes that do not show significant levels of |
|
9bdff28ae1b1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff
changeset
|
736 expression, this filtering is dependent on two criteria: CPM/count and number of samples. You can specify to filter on CPM (Minimum CPM) or count (Minimum Count) values: |
|
9bdff28ae1b1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff
changeset
|
737 |
|
9bdff28ae1b1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff
changeset
|
738 * **Minimum CPM:** This is the minimum count per million that a gene must have in at |
|
9bdff28ae1b1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff
changeset
|
739 least the number of samples specified under Minimum Samples. |
|
9bdff28ae1b1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff
changeset
|
740 |
|
9bdff28ae1b1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff
changeset
|
741 * **Minimum Count:** This is the minimum count that a gene must have. It can be combined with either Filter |
|
9bdff28ae1b1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff
changeset
|
742 on Total Count or Minimum Samples. |
|
9bdff28ae1b1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff
changeset
|
743 |
|
9bdff28ae1b1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff
changeset
|
744 * **Filter on Total Count:** This can be used with the Minimum Count filter to keep genes |
|
9bdff28ae1b1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff
changeset
|
745 with a minimum total read count. |
|
9bdff28ae1b1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff
changeset
|
746 |
|
9bdff28ae1b1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff
changeset
|
747 * **Minimum Samples:** This is the number of samples in which the Minimum CPM/Count |
|
9bdff28ae1b1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff
changeset
|
748 requirement must be met in order for that gene to be kept. |
|
9bdff28ae1b1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff
changeset
|
749 |
|
9bdff28ae1b1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff
changeset
|
750 If the Minimum Samples filter is applied, only genes that exhibit a CPM/count greater than the required amount in at least the number of samples specified will be used for analysis. Care should be taken to |
|
9bdff28ae1b1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff
changeset
|
751 ensure that the sample requirement is appropriate. In the case of an experiment |
|
9bdff28ae1b1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff
changeset
|
752 with two experimental groups each with two members, if there is a change from |
|
9bdff28ae1b1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff
changeset
|
753 insignificant CPM/count to significant CPM/count but the sample requirement is set to 3, |
|
9bdff28ae1b1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff
changeset
|
754 then this will cause that gene to fail the criteria. When in doubt simply do not |
|
9bdff28ae1b1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff
changeset
|
755 filter or consult the `edgeR workflow article`_ for filtering recommendations. |
|
9bdff28ae1b1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
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parents:
diff
changeset
|
756 |
|
9bdff28ae1b1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff
changeset
|
757 **Advanced Options:** |
|
9bdff28ae1b1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff
changeset
|
758 |
|
9bdff28ae1b1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff
changeset
|
759 By default error rate for multiple testing is controlled using Benjamini and |
|
9bdff28ae1b1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff
changeset
|
760 Hochberg's false discovery rate control at a threshold value of 0.05. However |
|
9bdff28ae1b1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff
changeset
|
761 there are options to change this to custom values. |
|
9bdff28ae1b1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
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changeset
|
762 |
|
9bdff28ae1b1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff
changeset
|
763 * **Minimum log2-fold-change Required:** |
|
9bdff28ae1b1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
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diff
changeset
|
764 In addition to meeting the requirement for the adjusted statistic for |
|
9bdff28ae1b1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
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changeset
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765 multiple testing, the observation must have an absolute log2-fold-change |
|
9bdff28ae1b1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff
changeset
|
766 greater than this threshold to be considered significant, thus highlighted |
|
9bdff28ae1b1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff
changeset
|
767 in the MD plot. |
|
9bdff28ae1b1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
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parents:
diff
changeset
|
768 |
|
9bdff28ae1b1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff
changeset
|
769 * **Adjusted Threshold:** |
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9bdff28ae1b1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
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changeset
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770 Set the threshold for the resulting value of the multiple testing control |
|
9bdff28ae1b1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
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parents:
diff
changeset
|
771 method. Only observations whose statistic falls below this value is |
|
9bdff28ae1b1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff
changeset
|
772 considered significant, thus highlighted in the MD plot. |
|
9bdff28ae1b1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff
changeset
|
773 |
|
9bdff28ae1b1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff
changeset
|
774 * **P-Value Adjustment Method:** |
|
9bdff28ae1b1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff
changeset
|
775 Change the multiple testing control method, the options are BH(1995) and |
|
9bdff28ae1b1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff
changeset
|
776 BY(2001) which are both false discovery rate controls. There is also |
|
9bdff28ae1b1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff
changeset
|
777 Holm(1979) which is a method for family-wise error rate control. |
|
9bdff28ae1b1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff
changeset
|
778 |
|
9bdff28ae1b1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff
changeset
|
779 **Normalisation Method:** |
|
9bdff28ae1b1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff
changeset
|
780 The most obvious technical factor that affects the read counts, other than gene expression |
|
9bdff28ae1b1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff
changeset
|
781 levels, is the sequencing depth of each RNA sample. edgeR adjusts any differential expression |
|
9bdff28ae1b1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff
changeset
|
782 analysis for varying sequencing depths as represented by differing library sizes. This is |
|
9bdff28ae1b1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff
changeset
|
783 part of the basic modeling procedure and flows automatically into fold-change or p-value |
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784 calculations. It is always present, and doesn’t require any user intervention. |
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785 The second most important technical influence on differential expression is one that is less |
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786 obvious. RNA-seq provides a measure of the relative abundance of each gene in each RNA |
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787 sample, but does not provide any measure of the total RNA output on a per-cell basis. |
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788 This commonly becomes important when a small number of genes are very highly expressed |
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789 in one sample, but not in another. The highly expressed genes can consume a substantial |
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790 proportion of the total library size, causing the remaining genes to be under-sampled in that |
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791 sample. Unless this RNA composition effect is adjusted for, the remaining genes may falsely |
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792 appear to be down-regulated in that sample . The edgeR `calcNormFactors` function normalizes for RNA composition by finding a set of scaling factors for the library sizes that minimize the log-fold changes between the samples for most genes. The default method for computing these scale factors uses a trimmed mean of M values (TMM) between each pair of samples. We call the product of the original library size and the scaling factor the *effective library size*. The effective library size replaces the original library size in all downsteam analyses. TMM is the recommended method for most RNA-Seq data where the majority (more than half) of the genes are believed not differentially expressed between any pair of the samples. You can change the normalisation method under **Advanced Options** above. For more information, see the `calcNormFactors` section in the `edgeR User's Guide`_. |
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793 |
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794 **Robust Settings** |
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795 Option to use robust settings. Using robust settings (robust=TRUE) with the edgeR estimateDisp and glmQLFit functions is usually recommended to protect against outlier genes. This is turned on by default. Note that it is only used with the quasi-likelihood F test method. For more information, see the `edgeR workflow article`_. |
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796 |
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797 **Test Method** |
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798 Option to use the likelihood ratio test instead of the quasi-likelihood F test. For more information, see the `edgeR workflow article`_. |
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799 |
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800 .. _edgeR User's Guide: http://www.bioconductor.org/packages/release/bioc/html/edgeR.html |
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801 |
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802 ----- |
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803 |
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804 **Outputs** |
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805 |
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806 This tool outputs |
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807 |
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808 * a table of differentially expressed genes for each contrast of interest |
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809 * a HTML report with plots and additional information |
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810 |
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811 Optionally, under **Output Options** you can choose to output |
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812 |
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813 * a normalised counts table |
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814 * the R script used by this tool |
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815 * an RData file |
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816 |
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817 ----- |
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818 |
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819 **Citations** |
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820 |
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821 Please try to cite the appropriate articles when you publish results obtained using software, as such citation is the main means by which the authors receive credit for their work. For the edgeR method itself, please cite Robinson et al., 2010, and for this tool (which was developed from the Galaxy limma-voom tool) please cite Liu et al., 2015. |
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822 |
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823 ]]></help> |
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824 <citations> |
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825 <citation type="doi">10.1093/bioinformatics/btp616</citation> |
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826 <citation type="doi">10.1093/nar/gkv412</citation> |
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827 </citations> |
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828 </tool> |