Mercurial > repos > iuc > edger
annotate edger.xml @ 6:7cf6248bc173 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 21f0bc6c64129122212a6d182fdf3e360617e629
| author | iuc |
|---|---|
| date | Sat, 09 Feb 2019 07:19:54 -0500 |
| parents | a261c79b6556 |
| children | 47094543a5ff |
| rev | line source |
|---|---|
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a261c79b6556
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 91bdcc6a5a46173be6546d590cdf3f311c2b1476
iuc
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1 <tool id="edger" name="edgeR" version="3.24.1"> |
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1844cd48af49
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
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2 <description> |
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1844cd48af49
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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1844cd48af49
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
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4 </description> |
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1844cd48af49
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
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5 |
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1844cd48af49
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
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6 <requirements> |
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a261c79b6556
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 91bdcc6a5a46173be6546d590cdf3f311c2b1476
iuc
parents:
4
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7 <requirement type="package" version="3.24.1">bioconductor-edger</requirement> |
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a261c79b6556
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 91bdcc6a5a46173be6546d590cdf3f311c2b1476
iuc
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8 <requirement type="package" version="3.38.3">bioconductor-limma</requirement> |
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9a62dbdb122b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 230fc767e2e402ee460440afab0e348f2ccab179
iuc
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9 <requirement type="package" version="0.2.20">r-rjson</requirement> |
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9a62dbdb122b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 230fc767e2e402ee460440afab0e348f2ccab179
iuc
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10 <requirement type="package" version="1.20.2">r-getopt</requirement> |
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c469357cf454
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 22882a8eabae0dcc15938423852d1325303b0b78
iuc
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11 <requirement type="package" version="1.4.30">r-statmod</requirement> |
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1844cd48af49
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
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12 <!-- required for alpha function used with plotMD --> |
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9a62dbdb122b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 230fc767e2e402ee460440afab0e348f2ccab179
iuc
parents:
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13 <requirement type="package" version="1.0.0">r-scales</requirement> |
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1844cd48af49
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
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14 </requirements> |
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1844cd48af49
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
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15 |
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1844cd48af49
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
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16 <version_command><![CDATA[ |
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3de72f1f78aa
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 910ffba48cb5f981aad1e00b77056bbbec7f9617
iuc
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17 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" $(R --vanilla --slave -e "library(getopt); cat(sessionInfo()\$otherPkgs\$getopt\$Version)" 2> /dev/null | grep -v -i "WARNING: ") |
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1844cd48af49
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
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18 ]]></version_command> |
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1844cd48af49
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
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19 |
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1844cd48af49
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
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20 <command detect_errors="exit_code"><![CDATA[ |
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1844cd48af49
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
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21 #import json |
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1844cd48af49
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
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22 Rscript '$__tool_directory__/edger.R' |
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1844cd48af49
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
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23 |
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1844cd48af49
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
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24 -R '$outReport' |
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1844cd48af49
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
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25 -o '$outReport.files_path' |
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1844cd48af49
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
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26 |
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1844cd48af49
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
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27 #if $input.format=="files": |
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1844cd48af49
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
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28 |
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1844cd48af49
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
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29 ## Adapted from DESeq2 wrapper |
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1844cd48af49
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
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30 #set $temp_factor_names = list() |
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1844cd48af49
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
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31 #for $fact in $input.rep_factor: |
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1844cd48af49
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
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32 #set $temp_factor = list() |
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1844cd48af49
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
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33 #for $g in $fact.rep_group: |
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1844cd48af49
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
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34 #set $count_files = list() |
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1844cd48af49
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
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35 #for $file in $g.countsFile: |
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1844cd48af49
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
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36 $count_files.append(str($file)) |
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1844cd48af49
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
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37 #end for |
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1844cd48af49
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
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38 $temp_factor.append( {str($g.groupName): $count_files} ) |
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1844cd48af49
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
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39 #end for |
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1844cd48af49
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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1844cd48af49
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
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41 $temp_factor.reverse() |
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1844cd48af49
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
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42 $temp_factor_names.append([str($fact.factorName), $temp_factor]) |
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1844cd48af49
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
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43 #end for |
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1844cd48af49
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
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44 -j '#echo json.dumps(temp_factor_names)#' |
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1844cd48af49
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
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45 |
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1844cd48af49
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
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46 #elif $input.format=="matrix": |
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1844cd48af49
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
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47 -m '$input.counts' |
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1844cd48af49
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
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48 #if $input.fact.ffile=='yes': |
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1844cd48af49
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
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49 -f '$input.fact.finfo' |
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1844cd48af49
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
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50 #else: |
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1844cd48af49
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
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51 -i '${ '|'.join( ['%s::%s' % ($x.factorName, $x.groupNames) for x in $input.fact.rep_factor] ) }' |
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1844cd48af49
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
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52 #end if |
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1844cd48af49
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
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53 #end if |
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1844cd48af49
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
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54 |
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1844cd48af49
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
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55 #if $anno.annoOpt=='yes': |
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1844cd48af49
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
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56 -a '$anno.geneanno' |
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1844cd48af49
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
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57 #end if |
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1844cd48af49
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
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58 |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
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59 -C '${ ','.join( ['%s' % $x.contrast for x in $rep_contrast] ) }' |
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1844cd48af49
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
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60 |
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1844cd48af49
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
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61 #if $f.filt.filt_select == 'yes': |
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1844cd48af49
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
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62 #if $f.filt.cformat.format_select == 'cpm': |
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1844cd48af49
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
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63 -c '$f.filt.cformat.cpmReq' |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
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64 -s '$f.filt.cformat.cpmSampleReq' |
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1844cd48af49
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
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65 #elif $f.filt.cformat.format_select == 'counts': |
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1844cd48af49
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
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66 -z '$f.filt.cformat.cntReq' |
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1844cd48af49
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
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67 #if $f.filt.cformat.samples.count_select == 'total': |
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1844cd48af49
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
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68 -y |
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1844cd48af49
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
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69 #elif $f.filt.cformat.samples.count_select == 'sample': |
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1844cd48af49
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
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70 -s '$f.filt.cformat.samples.cntSampleReq' |
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1844cd48af49
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
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71 #end if |
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1844cd48af49
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
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72 #end if |
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1844cd48af49
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
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73 #end if |
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1844cd48af49
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
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74 |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
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75 #if $out.normCounts: |
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1844cd48af49
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
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76 -x |
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1844cd48af49
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
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77 #end if |
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1844cd48af49
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
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78 #if $out.rdaOption: |
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1844cd48af49
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
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79 -r |
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80 #end if |
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81 |
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82 -l '$adv.lfc' |
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83 -p '$adv.pVal' |
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84 -d '$adv.pAdjust' |
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85 -n '$adv.normalisationOption' |
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86 #if $adv.robOption: |
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87 -b |
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88 #end if |
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89 #if $adv.lrtOption: |
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90 -t |
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91 #end if |
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92 |
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93 && |
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94 mkdir ./output_dir |
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95 |
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96 && |
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97 cp '$outReport.files_path'/*.tsv output_dir/ |
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2
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98 |
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99 #if $out.rscript: |
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100 && cp '$__tool_directory__/edger.R' '$rscript' |
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101 #end if |
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0
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102 ]]></command> |
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103 |
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104 <inputs> |
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105 |
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106 <!-- Counts and Factors --> |
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107 <conditional name="input"> |
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108 <param name="format" type="select" label="Count Files or Matrix?" |
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109 help="You can choose to input either separate count files (one per sample) or a single count matrix"> |
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110 <option value="files">Separate Count Files</option> |
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111 <option value="matrix">Single Count Matrix</option> |
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112 </param> |
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113 |
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114 <when value="files"> |
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115 <repeat name="rep_factor" title="Factor" min="1"> |
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6
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116 <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"> |
|
0
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117 <sanitizer> |
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118 <valid initial="string.letters,string.digits"><add value="_" /></valid> |
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119 </sanitizer> |
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120 </param> |
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121 <repeat name="rep_group" title="Group" min="2" default="2"> |
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122 <param name="groupName" type="text" label="Name" |
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6
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123 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"> |
|
0
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124 <sanitizer> |
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125 <valid initial="string.letters,string.digits"><add value="_" /></valid> |
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126 </sanitizer> |
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127 </param> |
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3
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128 <param name="countsFile" type="data" format="tabular" multiple="true" label="Counts files"/> |
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0
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129 </repeat> |
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130 </repeat> |
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131 </when> |
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132 |
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133 <when value="matrix"> |
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134 <param name="counts" type="data" format="tabular" label="Count Matrix"/> |
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135 |
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136 <conditional name="fact"> |
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137 <param name="ffile" type="select" label="Input factor information from file?" |
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6
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138 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
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139 <option value="no">No</option> |
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140 <option value="yes">Yes</option> |
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141 </param> |
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142 <when value="yes"> |
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143 <param name="finfo" type="data" format="tabular" label="Factor File"/> |
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144 </when> |
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145 <when value="no" > |
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146 <repeat name="rep_factor" title="Factor" min="1"> |
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147 <param name="factorName" type="text" label="Factor Name" |
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6
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148 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"> |
|
0
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149 <validator type="empty_field" /> |
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150 <validator type="regex" message="Please only use letters, numbers or underscores">^[\w]+$</validator> |
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151 </param> |
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152 <param name="groupNames" type="text" label="Groups" |
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6
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153 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"> |
|
0
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154 <validator type="empty_field" /> |
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155 <validator type="regex" message="Please only use letters, numbers or underscores, and separate levels by commas">^[\w,]+$</validator> |
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156 </param> |
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157 </repeat> |
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158 </when> |
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159 </conditional> |
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160 </when> |
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161 </conditional> |
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162 |
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163 <!-- Gene Annotations --> |
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164 <conditional name="anno"> |
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165 <param name="annoOpt" type="select" label="Use Gene Annotations?" |
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166 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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167 <option value="no">No</option> |
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168 <option value="yes">Yes</option> |
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169 </param> |
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170 <when value="yes"> |
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171 <param name="geneanno" type="data" format="tabular" label="Gene Annotations"/> |
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172 </when> |
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173 <when value="no" /> |
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174 </conditional> |
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175 |
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176 <!-- Contrasts --> |
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177 <repeat name="rep_contrast" title="Contrast" min="1" default="1"> |
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178 <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 more info, see Chapter 8 in the limma User's guide: https://www.bioconductor.org/packages/release/bioc/vignettes/limma/inst/doc/usersguide.pdf"> |
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179 <validator type="empty_field" /> |
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180 <validator type="regex" message="Please only use letters, numbers or underscores">^[\w-]+$</validator> |
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181 </param> |
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182 </repeat> |
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183 |
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184 <!-- Filter Options --> |
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185 <section name="f" expanded="false" title="Filter Low Counts"> |
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186 <conditional name="filt"> |
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187 <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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188 <option value="no" selected="true">No</option> |
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189 <option value="yes">Yes</option> |
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190 </param> |
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191 <when value="yes"> |
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192 <conditional name="cformat"> |
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193 <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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194 <option value="cpm">CPM</option> |
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195 <option value="counts">Counts</option> |
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196 </param> |
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197 <when value="cpm"> |
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198 <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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199 <param name="cpmSampleReq" type="integer" value="0" min="0" label="Minimum Samples" |
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200 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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201 </when> |
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202 <when value="counts"> |
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203 <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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204 <conditional name="samples"> |
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205 <param name="count_select" type="select" label="Filter on Total Count or per Sample Count values?" > |
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206 <option value="total">Total</option> |
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207 <option value="sample">Sample</option> |
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208 </param> |
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209 <when value="total"> |
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210 <param name="totReq" type="boolean" truevalue="1" falsevalue="0" checked="false" label="Filter on Total Count" help="Apply the Minimum Count filter to genes after summing counts for all samples. See the Filter Low Counts section below for more information." /> |
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211 </when> |
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212 <when value="sample"> |
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213 <param name="cntSampleReq" type="integer" value="0" min="0" label="Minimum Samples" |
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214 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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215 </when> |
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216 </conditional> |
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217 </when> |
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218 </conditional> |
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219 </when> |
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220 <when value="no" /> |
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221 </conditional> |
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222 </section> |
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223 |
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224 <!-- Output Options --> |
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225 <section name="out" expanded="false" title="Output Options"> |
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226 <param name="normCounts" type="boolean" truevalue="1" falsevalue="0" checked="false" |
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227 label="Output Normalised Counts Table?" |
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228 help="Output a file containing the normalised counts, these are in log2 counts per million (logCPM). Default: No"> |
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229 </param> |
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2
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230 <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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0
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231 <param name="rdaOption" type="boolean" truevalue="1" falsevalue="0" checked="false" |
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232 label="Output RData file?" |
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233 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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234 </param> |
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235 </section> |
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236 |
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237 <!-- Advanced Options --> |
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238 <section name="adv" expanded="false" title="Advanced Options"> |
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239 <param name="lfc" type="float" value="0" min="0" |
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240 label="Minimum Log2 Fold Change" |
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241 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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242 <param name="pVal" type="float" value="0.05" min="0" max="1" |
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243 label="P-Value Adjusted Threshold" |
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244 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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245 <param name="pAdjust" type="select" label="P-Value Adjustment Method" help="Default: BH"> |
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246 <option value="BH" selected="true">Benjamini and Hochberg (1995)</option> |
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247 <option value="BY">Benjamini and Yekutieli (2001)</option> |
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248 <option value="holm">Holm (1979)</option> |
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249 <option value="none">None</option> |
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250 </param> |
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251 <param name="normalisationOption" type="select" label="Normalisation Method" help="Default: TMM"> |
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252 <option value="TMM" selected="true">TMM</option> |
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253 <option value="RLE">RLE</option> |
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254 <option value="upperquartile">Upperquartile</option> |
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255 <option value="none">None (Don't normalise)</option> |
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256 </param> |
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257 <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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258 <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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259 </section> |
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260 |
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261 </inputs> |
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262 |
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263 <outputs> |
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264 <data name="outReport" format="html" label="${tool.name} on ${on_string}: Report" /> |
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265 <collection name="outTables" type="list" label="${tool.name} on ${on_string}: Tables"> |
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266 <discover_datasets pattern="(?P<name>.+)\.tsv$" format="tabular" directory="output_dir" visible="false" /> |
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267 </collection> |
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2
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268 <data name="rscript" format="txt" label="${tool.name} on ${on_string}: Rscript"> |
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269 <filter>out['rscript']</filter> |
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270 </data> |
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0
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271 </outputs> |
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272 |
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273 <tests> |
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274 <!-- Ensure report is output --> |
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275 <test> |
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276 <param name="format" value="matrix" /> |
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277 <param name="counts" value="matrix.txt" /> |
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278 <repeat name="rep_factor"> |
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279 <param name="factorName" value="Genotype"/> |
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280 <param name="groupNames" value="Mut,Mut,Mut,WT,WT,WT" /> |
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281 </repeat> |
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282 <repeat name="rep_contrast"> |
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283 <param name="contrast" value="Mut-WT" /> |
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284 </repeat> |
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285 <repeat name="rep_contrast"> |
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286 <param name="contrast" value="WT-Mut" /> |
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287 </repeat> |
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288 <param name="normalisationOption" value="TMM" /> |
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289 <output_collection name="outTables" count="2"> |
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2
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290 <element name="edgeR_Mut-WT" ftype="tabular" > |
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291 <assert_contents> |
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292 <has_text_matching expression="GeneID.*logFC.*logCPM.*F.*PValue.*FDR" /> |
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293 <has_text_matching expression="11304.*0.4582" /> |
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294 </assert_contents> |
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295 </element> |
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296 <element name="edgeR_WT-Mut" ftype="tabular" > |
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297 <assert_contents> |
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298 <has_text_matching expression="GeneID.*logFC.*logCPM.*F.*PValue.*FDR" /> |
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299 <has_text_matching expression="11304.*-0.4582" /> |
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300 </assert_contents> |
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301 </element> |
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0
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302 </output_collection> |
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303 <output name="outReport" > |
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304 <assert_contents> |
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305 <has_text text="edgeR Analysis Output" /> |
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306 <has_text text="quasi-likelihood" /> |
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307 <not_has_text text="likelihood ratio" /> |
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308 <not_has_text text="RData" /> |
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309 </assert_contents> |
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310 </output> |
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311 </test> |
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312 <!-- Ensure annotation file input works --> |
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313 <test> |
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314 <param name="format" value="matrix" /> |
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315 <param name="annoOpt" value="yes" /> |
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316 <param name="geneanno" value="anno.txt" /> |
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317 <param name="counts" value="matrix.txt" /> |
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318 <repeat name="rep_factor"> |
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319 <param name="factorName" value="Genotype"/> |
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1844cd48af49
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff
changeset
|
320 <param name="groupNames" value="Mut,Mut,Mut,WT,WT,WT" /> |
|
1844cd48af49
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff
changeset
|
321 </repeat> |
|
1844cd48af49
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff
changeset
|
322 <repeat name="rep_contrast"> |
|
1844cd48af49
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff
changeset
|
323 <param name="contrast" value="Mut-WT" /> |
|
1844cd48af49
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff
changeset
|
324 </repeat> |
|
1844cd48af49
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff
changeset
|
325 <param name="normalisationOption" value="TMM" /> |
|
1844cd48af49
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff
changeset
|
326 <output_collection name="outTables" count="1"> |
|
2
3de72f1f78aa
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 910ffba48cb5f981aad1e00b77056bbbec7f9617
iuc
parents:
1
diff
changeset
|
327 <element name="edgeR_Mut-WT" ftype="tabular" > |
|
3de72f1f78aa
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 910ffba48cb5f981aad1e00b77056bbbec7f9617
iuc
parents:
1
diff
changeset
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328 <assert_contents> |
|
3de72f1f78aa
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 910ffba48cb5f981aad1e00b77056bbbec7f9617
iuc
parents:
1
diff
changeset
|
329 <has_text_matching expression="EntrezID.*Symbol.*logFC.*logCPM.*F.*PValue.*FDR" /> |
|
3de72f1f78aa
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 910ffba48cb5f981aad1e00b77056bbbec7f9617
iuc
parents:
1
diff
changeset
|
330 <has_text_matching expression="11304.*Abca4.*0.4582" /> |
|
3de72f1f78aa
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 910ffba48cb5f981aad1e00b77056bbbec7f9617
iuc
parents:
1
diff
changeset
|
331 </assert_contents> |
|
3de72f1f78aa
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 910ffba48cb5f981aad1e00b77056bbbec7f9617
iuc
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1
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changeset
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332 </element> |
|
0
1844cd48af49
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff
changeset
|
333 </output_collection> |
|
1844cd48af49
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff
changeset
|
334 </test> |
|
2
3de72f1f78aa
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 910ffba48cb5f981aad1e00b77056bbbec7f9617
iuc
parents:
1
diff
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|
335 <!-- Ensure RScript and RData file can be output --> |
|
0
1844cd48af49
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
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diff
changeset
|
336 <test> |
|
1844cd48af49
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
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diff
changeset
|
337 <param name="format" value="matrix" /> |
|
2
3de72f1f78aa
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 910ffba48cb5f981aad1e00b77056bbbec7f9617
iuc
parents:
1
diff
changeset
|
338 <param name="rscript" value="True"/> |
|
0
1844cd48af49
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
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changeset
|
339 <param name="rdaOption" value="true" /> |
|
1844cd48af49
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff
changeset
|
340 <param name="counts" value="matrix.txt" /> |
|
1844cd48af49
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff
changeset
|
341 <repeat name="rep_factor"> |
|
1844cd48af49
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff
changeset
|
342 <param name="factorName" value="Genotype"/> |
|
1844cd48af49
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff
changeset
|
343 <param name="groupNames" value="Mut,Mut,Mut,WT,WT,WT" /> |
|
1844cd48af49
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
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diff
changeset
|
344 </repeat> |
|
1844cd48af49
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
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diff
changeset
|
345 <repeat name="rep_contrast"> |
|
1844cd48af49
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
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diff
changeset
|
346 <param name="contrast" value="Mut-WT" /> |
|
1844cd48af49
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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347 </repeat> |
|
1844cd48af49
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
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diff
changeset
|
348 <param name="normalisationOption" value="TMM" /> |
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1844cd48af49
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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349 <output name="outReport" > |
|
1844cd48af49
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
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diff
changeset
|
350 <assert_contents> |
|
1844cd48af49
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
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diff
changeset
|
351 <has_text text="RData" /> |
|
1844cd48af49
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff
changeset
|
352 </assert_contents> |
|
1844cd48af49
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff
changeset
|
353 </output> |
|
4
9a62dbdb122b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 230fc767e2e402ee460440afab0e348f2ccab179
iuc
parents:
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diff
changeset
|
354 <output name="rscript"> |
|
9a62dbdb122b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 230fc767e2e402ee460440afab0e348f2ccab179
iuc
parents:
3
diff
changeset
|
355 <assert_contents> |
|
9a62dbdb122b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 230fc767e2e402ee460440afab0e348f2ccab179
iuc
parents:
3
diff
changeset
|
356 <has_text_matching expression="Task run time" /> |
|
9a62dbdb122b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 230fc767e2e402ee460440afab0e348f2ccab179
iuc
parents:
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diff
changeset
|
357 </assert_contents> |
|
9a62dbdb122b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 230fc767e2e402ee460440afab0e348f2ccab179
iuc
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diff
changeset
|
358 </output> |
|
0
1844cd48af49
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff
changeset
|
359 </test> |
|
1844cd48af49
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
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diff
changeset
|
360 <!-- Ensure secondary factors work --> |
|
1844cd48af49
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff
changeset
|
361 <test> |
|
1844cd48af49
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff
changeset
|
362 <param name="format" value="matrix" /> |
|
1844cd48af49
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff
changeset
|
363 <param name="counts" value="matrix.txt" /> |
|
1844cd48af49
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff
changeset
|
364 <repeat name="rep_factor"> |
|
1844cd48af49
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff
changeset
|
365 <param name="factorName" value="Genotype"/> |
|
1844cd48af49
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff
changeset
|
366 <param name="groupNames" value="Mut,Mut,Mut,WT,WT,WT" /> |
|
1844cd48af49
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff
changeset
|
367 </repeat> |
|
1844cd48af49
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff
changeset
|
368 <repeat name="rep_factor"> |
|
1844cd48af49
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
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diff
changeset
|
369 <param name="factorName" value="Batch"/> |
|
1844cd48af49
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff
changeset
|
370 <param name="groupNames" value="b1,b2,b3,b1,b2,b3"/> |
|
1844cd48af49
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff
changeset
|
371 </repeat> |
|
1844cd48af49
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff
changeset
|
372 <repeat name="rep_contrast"> |
|
1844cd48af49
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
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diff
changeset
|
373 <param name="contrast" value="Mut-WT" /> |
|
1844cd48af49
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
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diff
changeset
|
374 </repeat> |
|
1844cd48af49
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff
changeset
|
375 <param name="normalisationOption" value="TMM" /> |
|
1844cd48af49
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
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diff
changeset
|
376 <output_collection name="outTables" count="1" > |
|
2
3de72f1f78aa
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 910ffba48cb5f981aad1e00b77056bbbec7f9617
iuc
parents:
1
diff
changeset
|
377 <element name="edgeR_Mut-WT" ftype="tabular" > |
|
3de72f1f78aa
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 910ffba48cb5f981aad1e00b77056bbbec7f9617
iuc
parents:
1
diff
changeset
|
378 <assert_contents> |
|
3de72f1f78aa
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 910ffba48cb5f981aad1e00b77056bbbec7f9617
iuc
parents:
1
diff
changeset
|
379 <has_text_matching expression="GeneID.*logFC.*logCPM.*F.*PValue.*FDR" /> |
|
3de72f1f78aa
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 910ffba48cb5f981aad1e00b77056bbbec7f9617
iuc
parents:
1
diff
changeset
|
380 <has_text_matching expression="11304.*0.4584" /> |
|
3de72f1f78aa
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 910ffba48cb5f981aad1e00b77056bbbec7f9617
iuc
parents:
1
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|
381 </assert_contents> |
|
3de72f1f78aa
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 910ffba48cb5f981aad1e00b77056bbbec7f9617
iuc
parents:
1
diff
changeset
|
382 </element> |
|
0
1844cd48af49
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
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diff
changeset
|
383 </output_collection> |
|
1844cd48af49
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff
changeset
|
384 </test> |
|
4
9a62dbdb122b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 230fc767e2e402ee460440afab0e348f2ccab179
iuc
parents:
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diff
changeset
|
385 <!-- Ensure factors file with unordered samples works --> |
|
0
1844cd48af49
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff
changeset
|
386 <test> |
|
1844cd48af49
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
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diff
changeset
|
387 <param name="format" value="matrix" /> |
|
1844cd48af49
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
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diff
changeset
|
388 <param name="ffile" value="yes" /> |
|
1844cd48af49
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff
changeset
|
389 <param name="finfo" value="factorinfo.txt" /> |
|
1844cd48af49
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff
changeset
|
390 <param name="counts" value="matrix.txt" /> |
|
1844cd48af49
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff
changeset
|
391 <repeat name="rep_contrast"> |
|
1844cd48af49
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff
changeset
|
392 <param name="contrast" value="Mut-WT" /> |
|
1844cd48af49
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff
changeset
|
393 </repeat> |
|
1844cd48af49
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff
changeset
|
394 <param name="normalisationOption" value="TMM" /> |
|
1844cd48af49
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff
changeset
|
395 <output_collection name="outTables" count="1"> |
|
2
3de72f1f78aa
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 910ffba48cb5f981aad1e00b77056bbbec7f9617
iuc
parents:
1
diff
changeset
|
396 <element name="edgeR_Mut-WT" ftype="tabular" > |
|
3de72f1f78aa
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 910ffba48cb5f981aad1e00b77056bbbec7f9617
iuc
parents:
1
diff
changeset
|
397 <assert_contents> |
|
3de72f1f78aa
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 910ffba48cb5f981aad1e00b77056bbbec7f9617
iuc
parents:
1
diff
changeset
|
398 <has_text_matching expression="GeneID.*logFC.*logCPM.*F.*PValue.*FDR" /> |
|
3de72f1f78aa
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 910ffba48cb5f981aad1e00b77056bbbec7f9617
iuc
parents:
1
diff
changeset
|
399 <has_text_matching expression="11304.*0.4584" /> |
|
3de72f1f78aa
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 910ffba48cb5f981aad1e00b77056bbbec7f9617
iuc
parents:
1
diff
changeset
|
400 </assert_contents> |
|
3de72f1f78aa
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 910ffba48cb5f981aad1e00b77056bbbec7f9617
iuc
parents:
1
diff
changeset
|
401 </element> |
|
0
1844cd48af49
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff
changeset
|
402 </output_collection> |
|
1844cd48af49
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff
changeset
|
403 </test> |
|
1844cd48af49
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff
changeset
|
404 <!-- Ensure normalised counts file output works--> |
|
1844cd48af49
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff
changeset
|
405 <test> |
|
1844cd48af49
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff
changeset
|
406 <param name="format" value="matrix" /> |
|
1844cd48af49
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff
changeset
|
407 <param name="normCounts" value="true" /> |
|
1844cd48af49
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff
changeset
|
408 <param name="counts" value="matrix.txt" /> |
|
1844cd48af49
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff
changeset
|
409 <repeat name="rep_factor"> |
|
1844cd48af49
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff
changeset
|
410 <param name="factorName" value="Genotype"/> |
|
1844cd48af49
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff
changeset
|
411 <param name="groupNames" value="Mut,Mut,Mut,WT,WT,WT" /> |
|
1844cd48af49
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff
changeset
|
412 </repeat> |
|
1844cd48af49
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff
changeset
|
413 <repeat name="rep_contrast"> |
|
1844cd48af49
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff
changeset
|
414 <param name="contrast" value="Mut-WT" /> |
|
1844cd48af49
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff
changeset
|
415 </repeat> |
|
1844cd48af49
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff
changeset
|
416 <param name="normalisationOption" value="TMM" /> |
|
1844cd48af49
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff
changeset
|
417 <output_collection name="outTables" count="2"> |
|
2
3de72f1f78aa
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 910ffba48cb5f981aad1e00b77056bbbec7f9617
iuc
parents:
1
diff
changeset
|
418 <element name="edgeR_Mut-WT" ftype="tabular" > |
|
3de72f1f78aa
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 910ffba48cb5f981aad1e00b77056bbbec7f9617
iuc
parents:
1
diff
changeset
|
419 <assert_contents> |
|
3de72f1f78aa
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 910ffba48cb5f981aad1e00b77056bbbec7f9617
iuc
parents:
1
diff
changeset
|
420 <has_text_matching expression="GeneID.*logFC.*logCPM.*F.*PValue.*FDR" /> |
|
3de72f1f78aa
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 910ffba48cb5f981aad1e00b77056bbbec7f9617
iuc
parents:
1
diff
changeset
|
421 <has_text_matching expression="11304.*0.4582" /> |
|
3de72f1f78aa
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 910ffba48cb5f981aad1e00b77056bbbec7f9617
iuc
parents:
1
diff
changeset
|
422 </assert_contents> |
|
3de72f1f78aa
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 910ffba48cb5f981aad1e00b77056bbbec7f9617
iuc
parents:
1
diff
changeset
|
423 </element> |
|
3de72f1f78aa
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 910ffba48cb5f981aad1e00b77056bbbec7f9617
iuc
parents:
1
diff
changeset
|
424 <element name="edgeR_normcounts" ftype="tabular" > |
|
3de72f1f78aa
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 910ffba48cb5f981aad1e00b77056bbbec7f9617
iuc
parents:
1
diff
changeset
|
425 <assert_contents> |
|
3de72f1f78aa
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 910ffba48cb5f981aad1e00b77056bbbec7f9617
iuc
parents:
1
diff
changeset
|
426 <has_text_matching expression="GeneID.*Mut1.*Mut2.*Mut3.*WT1.*WT2.*WT3" /> |
|
5
a261c79b6556
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 91bdcc6a5a46173be6546d590cdf3f311c2b1476
iuc
parents:
4
diff
changeset
|
427 <has_text_matching expression="11304.*15.75" /> |
|
2
3de72f1f78aa
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 910ffba48cb5f981aad1e00b77056bbbec7f9617
iuc
parents:
1
diff
changeset
|
428 </assert_contents> |
|
3de72f1f78aa
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 910ffba48cb5f981aad1e00b77056bbbec7f9617
iuc
parents:
1
diff
changeset
|
429 </element> |
|
0
1844cd48af49
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff
changeset
|
430 </output_collection> |
|
1844cd48af49
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff
changeset
|
431 </test> |
|
1844cd48af49
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff
changeset
|
432 <!-- Ensure likelihood ratio option works --> |
|
1844cd48af49
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff
changeset
|
433 <test> |
|
1844cd48af49
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff
changeset
|
434 <param name="format" value="matrix" /> |
|
1844cd48af49
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff
changeset
|
435 <param name="counts" value="matrix.txt" /> |
|
1844cd48af49
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff
changeset
|
436 <repeat name="rep_factor"> |
|
1844cd48af49
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff
changeset
|
437 <param name="factorName" value="Genotype"/> |
|
1844cd48af49
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff
changeset
|
438 <param name="groupNames" value="Mut,Mut,Mut,WT,WT,WT" /> |
|
1844cd48af49
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff
changeset
|
439 </repeat> |
|
1844cd48af49
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff
changeset
|
440 <repeat name="rep_contrast"> |
|
1844cd48af49
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff
changeset
|
441 <param name="contrast" value="Mut-WT" /> |
|
1844cd48af49
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff
changeset
|
442 </repeat> |
|
1844cd48af49
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff
changeset
|
443 <param name="normalisationOption" value="TMM" /> |
|
1844cd48af49
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff
changeset
|
444 <param name="lrtOption" value="true" /> |
|
1844cd48af49
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff
changeset
|
445 <output name="outReport" > |
|
1844cd48af49
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff
changeset
|
446 <assert_contents> |
|
1844cd48af49
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff
changeset
|
447 <has_text text="likelihood ratio" /> |
|
1844cd48af49
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff
changeset
|
448 <not_has_text text="quasi-likelihood" /> |
|
1844cd48af49
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff
changeset
|
449 </assert_contents> |
|
1844cd48af49
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff
changeset
|
450 </output> |
|
1844cd48af49
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff
changeset
|
451 </test> |
|
1844cd48af49
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff
changeset
|
452 <!-- Ensure multiple counts files input works --> |
|
1844cd48af49
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff
changeset
|
453 <test> |
|
1844cd48af49
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff
changeset
|
454 <param name="format" value="files" /> |
|
1844cd48af49
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff
changeset
|
455 <repeat name="rep_factor"> |
|
1844cd48af49
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff
changeset
|
456 <param name="factorName" value="Genotype"/> |
|
1844cd48af49
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff
changeset
|
457 <repeat name="rep_group"> |
|
1844cd48af49
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff
changeset
|
458 <param name="groupName" value="WT"/> |
|
1844cd48af49
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff
changeset
|
459 <param name="countsFile" value="WT1.counts,WT2.counts,WT3.counts"/> |
|
1844cd48af49
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff
changeset
|
460 </repeat> |
|
1844cd48af49
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff
changeset
|
461 <repeat name="rep_group"> |
|
1844cd48af49
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff
changeset
|
462 <param name="groupName" value="Mut"/> |
|
1844cd48af49
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff
changeset
|
463 <param name="countsFile" value="Mut1.counts,Mut2.counts,Mut3.counts"/> |
|
1844cd48af49
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff
changeset
|
464 </repeat> |
|
1844cd48af49
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff
changeset
|
465 </repeat> |
|
1844cd48af49
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff
changeset
|
466 <repeat name="rep_factor"> |
|
1844cd48af49
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff
changeset
|
467 <param name="factorName" value="Batch"/> |
|
1844cd48af49
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff
changeset
|
468 <repeat name="rep_group"> |
|
1844cd48af49
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff
changeset
|
469 <param name="groupName" value="b1"/> |
|
1844cd48af49
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff
changeset
|
470 <param name="countsFile" value="WT1.counts,Mut1.counts"/> |
|
1844cd48af49
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff
changeset
|
471 </repeat> |
|
1844cd48af49
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff
changeset
|
472 <repeat name="rep_group"> |
|
1844cd48af49
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff
changeset
|
473 <param name="groupName" value="b2"/> |
|
1844cd48af49
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff
changeset
|
474 <param name="countsFile" value="WT2.counts,Mut2.counts"/> |
|
1844cd48af49
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff
changeset
|
475 </repeat> |
|
1844cd48af49
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff
changeset
|
476 <repeat name="rep_group"> |
|
1844cd48af49
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff
changeset
|
477 <param name="groupName" value="b3"/> |
|
1844cd48af49
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff
changeset
|
478 <param name="countsFile" value="WT3.counts,Mut3.counts"/> |
|
1844cd48af49
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff
changeset
|
479 </repeat> |
|
1844cd48af49
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff
changeset
|
480 </repeat> |
|
1844cd48af49
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff
changeset
|
481 <param name="annoOpt" value="yes" /> |
|
1844cd48af49
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff
changeset
|
482 <param name="geneanno" value="anno.txt" /> |
|
1844cd48af49
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff
changeset
|
483 <repeat name="rep_contrast"> |
|
1844cd48af49
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff
changeset
|
484 <param name="contrast" value="Mut-WT" /> |
|
1844cd48af49
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff
changeset
|
485 </repeat> |
|
1844cd48af49
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff
changeset
|
486 <repeat name="rep_contrast"> |
|
1844cd48af49
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff
changeset
|
487 <param name="contrast" value="WT-Mut" /> |
|
1844cd48af49
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff
changeset
|
488 </repeat> |
|
1844cd48af49
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff
changeset
|
489 <param name="normCounts" value="true" /> |
|
1844cd48af49
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff
changeset
|
490 <output_collection name="outTables" count="3"> |
|
2
3de72f1f78aa
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 910ffba48cb5f981aad1e00b77056bbbec7f9617
iuc
parents:
1
diff
changeset
|
491 <element name="edgeR_Mut-WT" ftype="tabular" > |
|
3de72f1f78aa
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 910ffba48cb5f981aad1e00b77056bbbec7f9617
iuc
parents:
1
diff
changeset
|
492 <assert_contents> |
|
3de72f1f78aa
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 910ffba48cb5f981aad1e00b77056bbbec7f9617
iuc
parents:
1
diff
changeset
|
493 <has_text_matching expression="EntrezID.*Symbol.*logFC.*logCPM.*F.*PValue.*FDR" /> |
|
3de72f1f78aa
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 910ffba48cb5f981aad1e00b77056bbbec7f9617
iuc
parents:
1
diff
changeset
|
494 <has_text_matching expression="11304.*Abca4.*0.4584" /> |
|
3de72f1f78aa
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 910ffba48cb5f981aad1e00b77056bbbec7f9617
iuc
parents:
1
diff
changeset
|
495 </assert_contents> |
|
3de72f1f78aa
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 910ffba48cb5f981aad1e00b77056bbbec7f9617
iuc
parents:
1
diff
changeset
|
496 </element> |
|
3de72f1f78aa
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 910ffba48cb5f981aad1e00b77056bbbec7f9617
iuc
parents:
1
diff
changeset
|
497 <element name="edgeR_WT-Mut" ftype="tabular" > |
|
3de72f1f78aa
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 910ffba48cb5f981aad1e00b77056bbbec7f9617
iuc
parents:
1
diff
changeset
|
498 <assert_contents> |
|
3de72f1f78aa
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 910ffba48cb5f981aad1e00b77056bbbec7f9617
iuc
parents:
1
diff
changeset
|
499 <has_text_matching expression="logFC.*logCPM.*F.*PValue.*FDR" /> |
|
3de72f1f78aa
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 910ffba48cb5f981aad1e00b77056bbbec7f9617
iuc
parents:
1
diff
changeset
|
500 <has_text_matching expression="11304.*Abca4.*-0.4584" /> |
|
3de72f1f78aa
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 910ffba48cb5f981aad1e00b77056bbbec7f9617
iuc
parents:
1
diff
changeset
|
501 </assert_contents> |
|
3de72f1f78aa
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 910ffba48cb5f981aad1e00b77056bbbec7f9617
iuc
parents:
1
diff
changeset
|
502 </element> |
|
3de72f1f78aa
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 910ffba48cb5f981aad1e00b77056bbbec7f9617
iuc
parents:
1
diff
changeset
|
503 <element name="edgeR_normcounts" ftype="tabular" > |
|
3de72f1f78aa
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 910ffba48cb5f981aad1e00b77056bbbec7f9617
iuc
parents:
1
diff
changeset
|
504 <assert_contents> |
|
3de72f1f78aa
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 910ffba48cb5f981aad1e00b77056bbbec7f9617
iuc
parents:
1
diff
changeset
|
505 <has_text_matching expression="Mut1.*Mut2.*Mut3.*WT1.*WT2.*WT3" /> |
|
5
a261c79b6556
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 91bdcc6a5a46173be6546d590cdf3f311c2b1476
iuc
parents:
4
diff
changeset
|
506 <has_text_matching expression="11304.*Abca4.*15.75" /> |
|
2
3de72f1f78aa
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 910ffba48cb5f981aad1e00b77056bbbec7f9617
iuc
parents:
1
diff
changeset
|
507 </assert_contents> |
|
3de72f1f78aa
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 910ffba48cb5f981aad1e00b77056bbbec7f9617
iuc
parents:
1
diff
changeset
|
508 </element> |
|
0
1844cd48af49
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff
changeset
|
509 </output_collection> |
|
1844cd48af49
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff
changeset
|
510 </test> |
|
1844cd48af49
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff
changeset
|
511 <!-- Ensure filtering on CPM in Mnimum Samples works --> |
|
1844cd48af49
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff
changeset
|
512 <test> |
|
1844cd48af49
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff
changeset
|
513 <param name="format" value="matrix" /> |
|
1844cd48af49
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff
changeset
|
514 <param name="counts" value="matrix.txt" /> |
|
1844cd48af49
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff
changeset
|
515 <repeat name="rep_factor"> |
|
1844cd48af49
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff
changeset
|
516 <param name="factorName" value="Genotype"/> |
|
1844cd48af49
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff
changeset
|
517 <param name="groupNames" value="Mut,Mut,Mut,WT,WT,WT" /> |
|
1844cd48af49
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff
changeset
|
518 </repeat> |
|
1844cd48af49
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff
changeset
|
519 <repeat name="rep_contrast"> |
|
1844cd48af49
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff
changeset
|
520 <param name="contrast" value="Mut-WT" /> |
|
1844cd48af49
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff
changeset
|
521 </repeat> |
|
1844cd48af49
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff
changeset
|
522 <param name="normalisationOption" value="TMM" /> |
|
1844cd48af49
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff
changeset
|
523 <param name="filt_select" value="yes" /> |
|
1844cd48af49
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff
changeset
|
524 <param name="format_select" value="cpm" /> |
|
1844cd48af49
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff
changeset
|
525 <!-- real cpmReq values would be a lot lower |
|
1844cd48af49
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff
changeset
|
526 this is just for this tiny test dataset --> |
|
1844cd48af49
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff
changeset
|
527 <param name="cpmReq" value="1000" /> |
|
1844cd48af49
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff
changeset
|
528 <param name="cpmSampleReq" value="3" /> |
|
1844cd48af49
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff
changeset
|
529 <output name="outReport" > |
|
1844cd48af49
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff
changeset
|
530 <assert_contents> |
|
1844cd48af49
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff
changeset
|
531 <has_text text="CPM in at least" /> |
|
1844cd48af49
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff
changeset
|
532 <not_has_text text="after summing counts for all samples" /> |
|
1844cd48af49
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff
changeset
|
533 <not_has_text text="counts in at least" /> |
|
1844cd48af49
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff
changeset
|
534 </assert_contents> |
|
1844cd48af49
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff
changeset
|
535 </output> |
|
1844cd48af49
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff
changeset
|
536 <output_collection name="outTables" count="1" > |
|
2
3de72f1f78aa
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 910ffba48cb5f981aad1e00b77056bbbec7f9617
iuc
parents:
1
diff
changeset
|
537 <element name="edgeR_Mut-WT" ftype="tabular" > |
|
3de72f1f78aa
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 910ffba48cb5f981aad1e00b77056bbbec7f9617
iuc
parents:
1
diff
changeset
|
538 <assert_contents> |
|
3de72f1f78aa
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 910ffba48cb5f981aad1e00b77056bbbec7f9617
iuc
parents:
1
diff
changeset
|
539 <has_text_matching expression="GeneID.*logFC.*logCPM.*F.*PValue.*FDR" /> |
|
3de72f1f78aa
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 910ffba48cb5f981aad1e00b77056bbbec7f9617
iuc
parents:
1
diff
changeset
|
540 <has_text_matching expression="11304.*0.4568" /> |
|
3de72f1f78aa
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 910ffba48cb5f981aad1e00b77056bbbec7f9617
iuc
parents:
1
diff
changeset
|
541 <not_has_text text="-0.0682" /> |
|
3de72f1f78aa
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 910ffba48cb5f981aad1e00b77056bbbec7f9617
iuc
parents:
1
diff
changeset
|
542 </assert_contents> |
|
3de72f1f78aa
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 910ffba48cb5f981aad1e00b77056bbbec7f9617
iuc
parents:
1
diff
changeset
|
543 </element> |
|
0
1844cd48af49
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff
changeset
|
544 </output_collection> |
|
1844cd48af49
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff
changeset
|
545 </test> |
|
1844cd48af49
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff
changeset
|
546 <!-- Ensure filtering on Count in Minmum Samples works --> |
|
1844cd48af49
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff
changeset
|
547 <test> |
|
1844cd48af49
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff
changeset
|
548 <param name="format" value="matrix" /> |
|
1844cd48af49
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff
changeset
|
549 <param name="counts" value="matrix.txt" /> |
|
1844cd48af49
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff
changeset
|
550 <repeat name="rep_factor"> |
|
1844cd48af49
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff
changeset
|
551 <param name="factorName" value="Genotype"/> |
|
1844cd48af49
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff
changeset
|
552 <param name="groupNames" value="Mut,Mut,Mut,WT,WT,WT" /> |
|
1844cd48af49
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff
changeset
|
553 </repeat> |
|
1844cd48af49
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff
changeset
|
554 <repeat name="rep_contrast"> |
|
1844cd48af49
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff
changeset
|
555 <param name="contrast" value="Mut-WT" /> |
|
1844cd48af49
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff
changeset
|
556 </repeat> |
|
1844cd48af49
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff
changeset
|
557 <param name="normalisationOption" value="TMM" /> |
|
1844cd48af49
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff
changeset
|
558 <param name="filt_select" value="yes" /> |
|
1844cd48af49
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff
changeset
|
559 <param name="format_select" value="counts" /> |
|
1844cd48af49
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff
changeset
|
560 <param name="cntReq" value="10" /> |
|
1844cd48af49
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff
changeset
|
561 <param name="count_select" value="sample" /> |
|
1844cd48af49
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff
changeset
|
562 <param name="cntSampleReq" value="3" /> |
|
1844cd48af49
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff
changeset
|
563 <output name="outReport" > |
|
1844cd48af49
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff
changeset
|
564 <assert_contents> |
|
1844cd48af49
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff
changeset
|
565 <has_text text="counts in at least" /> |
|
1844cd48af49
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff
changeset
|
566 <not_has_text text="after summing counts for all samples" /> |
|
1844cd48af49
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff
changeset
|
567 <not_has_text text="CPM in at least" /> |
|
1844cd48af49
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff
changeset
|
568 </assert_contents> |
|
1844cd48af49
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff
changeset
|
569 </output> |
|
1844cd48af49
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff
changeset
|
570 <output_collection name="outTables" count="1" > |
|
2
3de72f1f78aa
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 910ffba48cb5f981aad1e00b77056bbbec7f9617
iuc
parents:
1
diff
changeset
|
571 <element name="edgeR_Mut-WT" ftype="tabular" > |
|
3de72f1f78aa
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 910ffba48cb5f981aad1e00b77056bbbec7f9617
iuc
parents:
1
diff
changeset
|
572 <assert_contents> |
|
3de72f1f78aa
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 910ffba48cb5f981aad1e00b77056bbbec7f9617
iuc
parents:
1
diff
changeset
|
573 <has_text_matching expression="GeneID.*logFC.*logCPM.*F.*PValue.*FDR" /> |
|
3de72f1f78aa
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 910ffba48cb5f981aad1e00b77056bbbec7f9617
iuc
parents:
1
diff
changeset
|
574 <has_text_matching expression="11304.*0.4568" /> |
|
3de72f1f78aa
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 910ffba48cb5f981aad1e00b77056bbbec7f9617
iuc
parents:
1
diff
changeset
|
575 <not_has_text text="-0.0682" /> |
|
3de72f1f78aa
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 910ffba48cb5f981aad1e00b77056bbbec7f9617
iuc
parents:
1
diff
changeset
|
576 </assert_contents> |
|
3de72f1f78aa
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 910ffba48cb5f981aad1e00b77056bbbec7f9617
iuc
parents:
1
diff
changeset
|
577 </element> |
|
3de72f1f78aa
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 910ffba48cb5f981aad1e00b77056bbbec7f9617
iuc
parents:
1
diff
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|
578 |
|
0
1844cd48af49
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
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changeset
|
579 </output_collection> |
|
1844cd48af49
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
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changeset
|
580 </test> |
|
1844cd48af49
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
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changeset
|
581 <!-- Ensure filtering on Total Count works --> |
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1844cd48af49
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
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changeset
|
582 <test> |
|
1844cd48af49
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
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changeset
|
583 <param name="format" value="matrix" /> |
|
1844cd48af49
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
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diff
changeset
|
584 <param name="counts" value="matrix.txt" /> |
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1844cd48af49
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
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changeset
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585 <repeat name="rep_factor"> |
|
1844cd48af49
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
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changeset
|
586 <param name="factorName" value="Genotype"/> |
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1844cd48af49
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
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changeset
|
587 <param name="groupNames" value="Mut,Mut,Mut,WT,WT,WT" /> |
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1844cd48af49
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
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changeset
|
588 </repeat> |
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1844cd48af49
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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589 <repeat name="rep_contrast"> |
|
1844cd48af49
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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590 <param name="contrast" value="Mut-WT" /> |
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1844cd48af49
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
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591 </repeat> |
|
1844cd48af49
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
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592 <param name="normalisationOption" value="TMM" /> |
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1844cd48af49
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
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593 <param name="filt_select" value="yes" /> |
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1844cd48af49
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
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|
594 <param name="format_select" value="counts" /> |
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1844cd48af49
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
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595 <!-- real cntReq values would be a lot lower |
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1844cd48af49
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
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|
596 this is just for this tiny test dataset --> |
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1844cd48af49
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
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|
597 <param name="cntReq" value="1000" /> |
|
1844cd48af49
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
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|
598 <param name="count_select" value="total" /> |
|
1844cd48af49
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
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599 <param name="totReq" value="true" /> |
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1844cd48af49
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
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600 <output name="outReport" > |
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1844cd48af49
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
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601 <assert_contents> |
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1844cd48af49
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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602 <has_text text="after summing counts for all samples" /> |
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1844cd48af49
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
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603 <not_has_text text="counts in at least" /> |
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1844cd48af49
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
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604 <not_has_text text="CPM in at least" /> |
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1844cd48af49
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
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605 </assert_contents> |
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1844cd48af49
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
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606 </output> |
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1844cd48af49
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
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607 <output_collection name="outTables" count="1" > |
|
2
3de72f1f78aa
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 910ffba48cb5f981aad1e00b77056bbbec7f9617
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608 <element name="edgeR_Mut-WT" ftype="tabular" > |
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3de72f1f78aa
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 910ffba48cb5f981aad1e00b77056bbbec7f9617
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609 <assert_contents> |
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3de72f1f78aa
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 910ffba48cb5f981aad1e00b77056bbbec7f9617
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610 <has_text_matching expression="GeneID.*logFC.*logCPM.*F.*PValue.*FDR" /> |
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3de72f1f78aa
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 910ffba48cb5f981aad1e00b77056bbbec7f9617
iuc
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611 <has_text_matching expression="11304.*0.4568" /> |
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3de72f1f78aa
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 910ffba48cb5f981aad1e00b77056bbbec7f9617
iuc
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612 <not_has_text text="-0.0682" /> |
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3de72f1f78aa
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 910ffba48cb5f981aad1e00b77056bbbec7f9617
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613 </assert_contents> |
|
3de72f1f78aa
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 910ffba48cb5f981aad1e00b77056bbbec7f9617
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614 </element> |
|
0
1844cd48af49
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
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615 </output_collection> |
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1844cd48af49
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
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616 </test> |
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1844cd48af49
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617 </tests> |
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618 |
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1844cd48af49
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619 <help><![CDATA[ |
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1844cd48af49
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
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620 .. class:: infomark |
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621 |
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1844cd48af49
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622 **What it does** |
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623 |
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1844cd48af49
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
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624 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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625 produces plots and tables useful in the analysis of differential gene expression. |
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1844cd48af49
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
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626 |
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1844cd48af49
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
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627 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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628 |
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1844cd48af49
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
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629 .. _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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630 .. _edgeR workflow article: https://f1000research.com/articles/5-1438 |
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631 |
|
1844cd48af49
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632 ----- |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
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633 |
|
1844cd48af49
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
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634 **Inputs** |
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635 |
|
1844cd48af49
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
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636 **Counts Data:** |
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1844cd48af49
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
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637 |
|
6
7cf6248bc173
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 21f0bc6c64129122212a6d182fdf3e360617e629
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638 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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0
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639 |
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640 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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641 |
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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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643 **GeneID** **WT1** |
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1844cd48af49
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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1844cd48af49
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff
changeset
|
645 11287 1699 |
|
1844cd48af49
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff
changeset
|
646 11298 1905 |
|
1844cd48af49
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff
changeset
|
647 11302 6 |
|
1844cd48af49
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff
changeset
|
648 11303 2099 |
|
1844cd48af49
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff
changeset
|
649 11304 356 |
|
1844cd48af49
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff
changeset
|
650 11305 2528 |
|
1844cd48af49
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff
changeset
|
651 ========== ======= |
|
1844cd48af49
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff
changeset
|
652 |
|
1844cd48af49
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff
changeset
|
653 Example - **Single Count Matrix**: |
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1844cd48af49
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff
changeset
|
654 |
|
1844cd48af49
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff
changeset
|
655 ========== ======= ======= ======= ======== ======== ======== |
|
1844cd48af49
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff
changeset
|
656 **GeneID** **WT1** **WT2** **WT3** **Mut1** **Mut2** **Mut3** |
|
1844cd48af49
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff
changeset
|
657 ---------- ------- ------- ------- -------- -------- -------- |
|
1844cd48af49
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff
changeset
|
658 11287 1699 1528 1601 1463 1441 1495 |
|
1844cd48af49
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff
changeset
|
659 11298 1905 1744 1834 1345 1291 1346 |
|
1844cd48af49
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff
changeset
|
660 11302 6 8 7 5 6 5 |
|
1844cd48af49
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff
changeset
|
661 11303 2099 1974 2100 1574 1519 1654 |
|
1844cd48af49
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff
changeset
|
662 11304 356 312 337 361 397 346 |
|
1844cd48af49
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff
changeset
|
663 11305 2528 2438 2493 1762 1942 2027 |
|
1844cd48af49
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff
changeset
|
664 ========== ======= ======= ======= ======== ======== ======== |
|
1844cd48af49
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff
changeset
|
665 |
|
1844cd48af49
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff
changeset
|
666 |
|
1844cd48af49
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff
changeset
|
667 **Gene Annotations:** |
|
1844cd48af49
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff
changeset
|
668 Optional input for gene annotations, this can contain more |
|
1844cd48af49
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff
changeset
|
669 information about the genes than just an ID number. The annotations will |
|
3
2aa9dd87aad3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit e646be741e315df9332b5206cec1e47c11370ff1
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parents:
2
diff
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|
670 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
1844cd48af49
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff
changeset
|
671 |
|
1844cd48af49
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
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changeset
|
672 Example: |
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1844cd48af49
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff
changeset
|
673 |
|
1844cd48af49
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff
changeset
|
674 ========== ========== =================================================== |
|
1844cd48af49
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff
changeset
|
675 **GeneID** **Symbol** **GeneName** |
|
1844cd48af49
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff
changeset
|
676 ---------- ---------- --------------------------------------------------- |
|
3
2aa9dd87aad3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit e646be741e315df9332b5206cec1e47c11370ff1
iuc
parents:
2
diff
changeset
|
677 11287 Pzp pregnancy zone protein |
|
2aa9dd87aad3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit e646be741e315df9332b5206cec1e47c11370ff1
iuc
parents:
2
diff
changeset
|
678 11298 Aanat arylalkylamine N-acetyltransferase |
|
2aa9dd87aad3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit e646be741e315df9332b5206cec1e47c11370ff1
iuc
parents:
2
diff
changeset
|
679 11302 Aatk apoptosis-associated tyrosine kinase |
|
2aa9dd87aad3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit e646be741e315df9332b5206cec1e47c11370ff1
iuc
parents:
2
diff
changeset
|
680 11303 Abca1 ATP-binding cassette, sub-family A (ABC1), member 1 |
|
2aa9dd87aad3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit e646be741e315df9332b5206cec1e47c11370ff1
iuc
parents:
2
diff
changeset
|
681 11304 Abca4 ATP-binding cassette, sub-family A (ABC1), member 4 |
|
2aa9dd87aad3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit e646be741e315df9332b5206cec1e47c11370ff1
iuc
parents:
2
diff
changeset
|
682 11305 Abca2 ATP-binding cassette, sub-family A (ABC1), member 2 |
|
0
1844cd48af49
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff
changeset
|
683 ========== ========== =================================================== |
|
1844cd48af49
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff
changeset
|
684 |
|
4
9a62dbdb122b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 230fc767e2e402ee460440afab0e348f2ccab179
iuc
parents:
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changeset
|
685 **Factor Information:** |
|
9a62dbdb122b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 230fc767e2e402ee460440afab0e348f2ccab179
iuc
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changeset
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686 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. |
|
9a62dbdb122b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 230fc767e2e402ee460440afab0e348f2ccab179
iuc
parents:
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changeset
|
687 |
|
9a62dbdb122b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 230fc767e2e402ee460440afab0e348f2ccab179
iuc
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688 Example: |
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9a62dbdb122b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 230fc767e2e402ee460440afab0e348f2ccab179
iuc
parents:
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changeset
|
689 |
|
9a62dbdb122b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 230fc767e2e402ee460440afab0e348f2ccab179
iuc
parents:
3
diff
changeset
|
690 ========== ============ ========= |
|
9a62dbdb122b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 230fc767e2e402ee460440afab0e348f2ccab179
iuc
parents:
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changeset
|
691 **Sample** **Genotype** **Batch** |
|
9a62dbdb122b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 230fc767e2e402ee460440afab0e348f2ccab179
iuc
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changeset
|
692 ---------- ------------ --------- |
|
9a62dbdb122b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 230fc767e2e402ee460440afab0e348f2ccab179
iuc
parents:
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changeset
|
693 WT1 WT b1 |
|
9a62dbdb122b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 230fc767e2e402ee460440afab0e348f2ccab179
iuc
parents:
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diff
changeset
|
694 WT2 WT b2 |
|
9a62dbdb122b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 230fc767e2e402ee460440afab0e348f2ccab179
iuc
parents:
3
diff
changeset
|
695 WT3 WT b3 |
|
9a62dbdb122b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 230fc767e2e402ee460440afab0e348f2ccab179
iuc
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changeset
|
696 Mut1 Mut b1 |
|
9a62dbdb122b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 230fc767e2e402ee460440afab0e348f2ccab179
iuc
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changeset
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697 Mut2 Mut b2 |
|
9a62dbdb122b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 230fc767e2e402ee460440afab0e348f2ccab179
iuc
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changeset
|
698 Mut3 Mut b3 |
|
9a62dbdb122b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 230fc767e2e402ee460440afab0e348f2ccab179
iuc
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changeset
|
699 ========== ============ ========= |
|
9a62dbdb122b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 230fc767e2e402ee460440afab0e348f2ccab179
iuc
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changeset
|
700 |
|
6
7cf6248bc173
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 21f0bc6c64129122212a6d182fdf3e360617e629
iuc
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changeset
|
701 *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
9a62dbdb122b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 230fc767e2e402ee460440afab0e348f2ccab179
iuc
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changeset
|
702 |
|
6
7cf6248bc173
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 21f0bc6c64129122212a6d182fdf3e360617e629
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changeset
|
703 *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
9a62dbdb122b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 230fc767e2e402ee460440afab0e348f2ccab179
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changeset
|
704 |
|
0
1844cd48af49
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
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changeset
|
705 **Contrasts of Interest:** |
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1844cd48af49
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
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changeset
|
706 The contrasts you wish to make between levels. |
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1844cd48af49
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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707 A common contrast would be a simple difference between two levels: "Mut-WT" |
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1844cd48af49
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
|
708 represents the difference between the mutant and wild type genotypes. |
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1844cd48af49
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
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changeset
|
709 Multiple contrasts must be entered separately using the Insert Contrast button, spaces must not be used. |
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1844cd48af49
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
|
710 |
|
1844cd48af49
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
|
711 **Filter Low Counts:** |
|
1844cd48af49
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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712 Genes with very low counts across all libraries provide little evidence for differential expression. |
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1844cd48af49
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
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changeset
|
713 In the biological point of view, a gene must be expressed at some minimal level before |
|
1844cd48af49
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
|
714 it is likely to be translated into a protein or to be biologically important. In addition, the |
|
1844cd48af49
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
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changeset
|
715 pronounced discreteness of these counts interferes with some of the statistical approximations |
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1844cd48af49
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
|
716 that are used later in the pipeline. These genes should be filtered out prior to further |
|
1844cd48af49
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
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changeset
|
717 analysis. |
|
1844cd48af49
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
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changeset
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718 As a rule of thumb, genes are dropped if they can’t possibly be expressed in all the samples |
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1844cd48af49
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
|
719 for any of the conditions. Users can set their own definition of genes being expressed. Usually |
|
1844cd48af49
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
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changeset
|
720 a gene is required to have a count of 5-10 in a library to be considered expressed in that |
|
1844cd48af49
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
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changeset
|
721 library. Users should also filter with count-per-million (CPM) rather than filtering on the |
|
1844cd48af49
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
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changeset
|
722 counts directly, as the latter does not account for differences in library sizes between samples. |
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1844cd48af49
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
|
723 |
|
1844cd48af49
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
|
724 Option to ignore the genes that do not show significant levels of |
|
1844cd48af49
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
|
725 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: |
|
1844cd48af49
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff
changeset
|
726 |
|
1844cd48af49
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff
changeset
|
727 * **Minimum CPM:** This is the minimum count per million that a gene must have in at |
|
1844cd48af49
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff
changeset
|
728 least the number of samples specified under Minimum Samples. |
|
1844cd48af49
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff
changeset
|
729 |
|
1844cd48af49
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff
changeset
|
730 * **Minimum Count:** This is the minimum count that a gene must have. It can be combined with either Filter |
|
1844cd48af49
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff
changeset
|
731 on Total Count or Minimum Samples. |
|
1844cd48af49
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff
changeset
|
732 |
|
1844cd48af49
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff
changeset
|
733 * **Filter on Total Count:** This can be used with the Minimum Count filter to keep genes |
|
1844cd48af49
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff
changeset
|
734 with a minimum total read count. |
|
1844cd48af49
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff
changeset
|
735 |
|
1844cd48af49
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff
changeset
|
736 * **Minimum Samples:** This is the number of samples in which the Minimum CPM/Count |
|
1844cd48af49
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff
changeset
|
737 requirement must be met in order for that gene to be kept. |
|
1844cd48af49
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff
changeset
|
738 |
|
1844cd48af49
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff
changeset
|
739 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 |
|
1844cd48af49
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff
changeset
|
740 ensure that the sample requirement is appropriate. In the case of an experiment |
|
1844cd48af49
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff
changeset
|
741 with two experimental groups each with two members, if there is a change from |
|
1844cd48af49
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff
changeset
|
742 insignificant CPM/count to significant CPM/count but the sample requirement is set to 3, |
|
1844cd48af49
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff
changeset
|
743 then this will cause that gene to fail the criteria. When in doubt simply do not |
|
1844cd48af49
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff
changeset
|
744 filter or consult the `edgeR workflow article`_ for filtering recommendations. |
|
1844cd48af49
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff
changeset
|
745 |
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1844cd48af49
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
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changeset
|
746 **Advanced Options:** |
|
1844cd48af49
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff
changeset
|
747 |
|
1844cd48af49
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff
changeset
|
748 By default error rate for multiple testing is controlled using Benjamini and |
|
1844cd48af49
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff
changeset
|
749 Hochberg's false discovery rate control at a threshold value of 0.05. However |
|
1844cd48af49
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
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changeset
|
750 there are options to change this to custom values. |
|
1844cd48af49
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff
changeset
|
751 |
|
1844cd48af49
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
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parents:
diff
changeset
|
752 * **Minimum log2-fold-change Required:** |
|
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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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753 In addition to meeting the requirement for the adjusted statistic for |
|
1844cd48af49
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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754 multiple testing, the observation must have an absolute log2-fold-change |
|
1844cd48af49
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff
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|
755 greater than this threshold to be considered significant, thus highlighted |
|
1844cd48af49
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
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parents:
diff
changeset
|
756 in the MD plot. |
|
1844cd48af49
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff
changeset
|
757 |
|
1844cd48af49
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff
changeset
|
758 * **Adjusted Threshold:** |
|
1844cd48af49
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
|
759 Set the threshold for the resulting value of the multiple testing control |
|
1844cd48af49
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
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parents:
diff
changeset
|
760 method. Only observations whose statistic falls below this value is |
|
1844cd48af49
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
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parents:
diff
changeset
|
761 considered significant, thus highlighted in the MD plot. |
|
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
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|
762 |
|
1844cd48af49
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
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changeset
|
763 * **P-Value Adjustment Method:** |
|
1844cd48af49
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
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changeset
|
764 Change the multiple testing control method, the options are BH(1995) and |
|
1844cd48af49
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
|
765 BY(2001) which are both false discovery rate controls. There is also |
|
1844cd48af49
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
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changeset
|
766 Holm(1979) which is a method for family-wise error rate control. |
|
1844cd48af49
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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|
767 |
|
1844cd48af49
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
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|
768 **Normalisation Method:** |
|
1844cd48af49
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
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parents:
diff
changeset
|
769 The most obvious technical factor that affects the read counts, other than gene expression |
|
1844cd48af49
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
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|
770 levels, is the sequencing depth of each RNA sample. edgeR adjusts any differential expression |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
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parents:
diff
changeset
|
771 analysis for varying sequencing depths as represented by differing library sizes. This is |
|
1844cd48af49
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
|
772 part of the basic modeling procedure and flows automatically into fold-change or p-value |
|
1844cd48af49
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
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|
773 calculations. It is always present, and doesn’t require any user intervention. |
|
1844cd48af49
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
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parents:
diff
changeset
|
774 The second most important technical influence on differential expression is one that is less |
|
1844cd48af49
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff
changeset
|
775 obvious. RNA-seq provides a measure of the relative abundance of each gene in each RNA |
|
1844cd48af49
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
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changeset
|
776 sample, but does not provide any measure of the total RNA output on a per-cell basis. |
|
1844cd48af49
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff
changeset
|
777 This commonly becomes important when a small number of genes are very highly expressed |
|
1844cd48af49
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff
changeset
|
778 in one sample, but not in another. The highly expressed genes can consume a substantial |
|
1844cd48af49
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff
changeset
|
779 proportion of the total library size, causing the remaining genes to be under-sampled in that |
|
1844cd48af49
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff
changeset
|
780 sample. Unless this RNA composition effect is adjusted for, the remaining genes may falsely |
|
1844cd48af49
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff
changeset
|
781 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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parents:
diff
changeset
|
782 |
|
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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
|
783 **Robust Settings** |
|
1844cd48af49
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
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changeset
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784 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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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
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changeset
|
785 |
|
1844cd48af49
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
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changeset
|
786 **Test Method** |
|
1844cd48af49
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
|
787 Option to use the likelihood ratio test instead of the quasi-likelihood F test. For more information, see the `edgeR workflow article`_. |
|
1844cd48af49
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff
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|
788 |
|
1844cd48af49
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff
changeset
|
789 .. _edgeR User's Guide: http://www.bioconductor.org/packages/release/bioc/html/edgeR.html |
|
1844cd48af49
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iuc
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|
790 |
|
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
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|
791 ----- |
|
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parents:
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changeset
|
792 |
|
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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
|
793 **Outputs** |
|
1844cd48af49
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
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|
794 |
|
1844cd48af49
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff
changeset
|
795 This tool outputs |
|
1844cd48af49
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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|
796 |
|
1844cd48af49
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff
changeset
|
797 * a table of differentially expressed genes for each contrast of interest |
|
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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
|
798 * a HTML report with plots and additional information |
|
1844cd48af49
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
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parents:
diff
changeset
|
799 |
|
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
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parents:
diff
changeset
|
800 Optionally, under **Output Options** you can choose to output |
|
1844cd48af49
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
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changeset
|
801 |
|
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
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changeset
|
802 * a normalised counts table |
|
2
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1
diff
changeset
|
803 * the R script used by this tool |
|
0
1844cd48af49
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iuc
parents:
diff
changeset
|
804 * an RData file |
|
1844cd48af49
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
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805 |
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806 ----- |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
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807 |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
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808 **Citations** |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
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809 |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
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810 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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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
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811 |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
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812 ]]></help> |
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813 <citations> |
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814 <citation type="doi">10.1093/bioinformatics/btp616</citation> |
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815 <citation type="doi">10.1093/nar/gkv412</citation> |
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816 </citations> |
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817 </tool> |