Mercurial > repos > iuc > limma_voom
annotate limma_voom.xml @ 8:00a42b66e522 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
| author | iuc |
|---|---|
| date | Tue, 15 May 2018 02:36:36 -0400 |
| parents | e6a4ff41af6b |
| children | 4255881bebb1 |
| rev | line source |
|---|---|
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8
00a42b66e522
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
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changeset
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1 <tool id="limma_voom" name="limma" version="3.34.9.4"> |
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bdebdea5f6a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
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2 <description> |
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3
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
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3 Perform differential expression with limma-voom or limma-trend |
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bdebdea5f6a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
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4 </description> |
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76d01fe0ec36
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 58c05c0ce9334f8b9c800283cfd1f40573546edd
iuc
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5 |
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bdebdea5f6a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
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6 <requirements> |
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a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
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7 <requirement type="package" version="3.34.9">bioconductor-limma</requirement> |
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38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
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8 <requirement type="package" version="3.20.7">bioconductor-edger</requirement> |
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38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
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9 <requirement type="package" version="1.4.30">r-statmod</requirement> |
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38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents:
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10 <requirement type="package" version="0.5.0">r-scales</requirement> |
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38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents:
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11 <requirement type="package" version="0.2.15">r-rjson</requirement> |
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38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
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12 <requirement type="package" version="1.20.0">r-getopt</requirement> |
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e6a4ff41af6b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit cf399638ebca4250bcc15f468238a9964de97b33
iuc
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13 <requirement type="package" version="3.0.1">r-gplots</requirement> |
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bdebdea5f6a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
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14 </requirements> |
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bdebdea5f6a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
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15 |
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1
76d01fe0ec36
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 58c05c0ce9334f8b9c800283cfd1f40573546edd
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16 <version_command><![CDATA[ |
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e6a4ff41af6b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit cf399638ebca4250bcc15f468238a9964de97b33
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17 echo $(R --version | grep version | grep -v GNU)", limma version" $(R --vanilla --slave -e "library(limma); cat(sessionInfo()\$otherPkgs\$limma\$Version)" 2> /dev/null | grep -v -i "WARNING: ")", edgeR version" $(R --vanilla --slave -e "library(edgeR); cat(sessionInfo()\$otherPkgs\$edgeR\$Version)" 2> /dev/null | grep -v -i "WARNING: ")", statmod version" $(R --vanilla --slave -e "library(statmod); cat(sessionInfo()\$otherPkgs\$statmod\$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: ")", gplots version" $(R --vanilla --slave -e "library(gplots); cat(sessionInfo()\$otherPkgs\$gplots\$Version)" 2> /dev/null | grep -v -i "WARNING: ") |
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76d01fe0ec36
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 58c05c0ce9334f8b9c800283cfd1f40573546edd
iuc
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18 ]]></version_command> |
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76d01fe0ec36
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 58c05c0ce9334f8b9c800283cfd1f40573546edd
iuc
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19 |
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76d01fe0ec36
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 58c05c0ce9334f8b9c800283cfd1f40573546edd
iuc
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20 <command detect_errors="exit_code"><![CDATA[ |
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38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
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21 #import json |
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76d01fe0ec36
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 58c05c0ce9334f8b9c800283cfd1f40573546edd
iuc
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22 Rscript '$__tool_directory__/limma_voom.R' |
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38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
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23 |
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38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
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24 -R '$outReport' |
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38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
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25 -o '$outReport.files_path' |
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38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
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26 |
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38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
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27 #if $input.format=="files": |
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38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
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28 |
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38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
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29 ## Adapted from DESeq2 wrapper |
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38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
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30 #set $temp_factor_names = list() |
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38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents:
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31 #for $fact in $input.rep_factor: |
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38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents:
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32 #set $temp_factor = list() |
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38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
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33 #for $g in $fact.rep_group: |
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38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
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34 #set $count_files = list() |
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38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
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35 #for $file in $g.countsFile: |
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38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
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36 $count_files.append(str($file)) |
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38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
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37 #end for |
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38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
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38 $temp_factor.append( {str($g.groupName): $count_files} ) |
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38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
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39 #end for |
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38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
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40 |
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38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
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41 $temp_factor.reverse() |
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38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
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42 $temp_factor_names.append([str($fact.factorName), $temp_factor]) |
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38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
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43 #end for |
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38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
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44 -j '#echo json.dumps(temp_factor_names)#' |
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38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
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45 |
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38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
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46 #elif $input.format=="matrix": |
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38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
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47 -m '$input.counts' |
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38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
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48 #if $input.fact.ffile=='yes': |
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38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
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49 -f '$input.fact.finfo' |
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38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
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50 #else: |
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38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
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51 -i '${ '|'.join( ['%s::%s' % ($x.factorName, $x.groupNames) for x in $input.fact.rep_factor] ) }' |
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38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
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52 #end if |
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38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
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53 #end if |
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1
76d01fe0ec36
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 58c05c0ce9334f8b9c800283cfd1f40573546edd
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54 |
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76d01fe0ec36
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 58c05c0ce9334f8b9c800283cfd1f40573546edd
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55 #if $anno.annoOpt=='yes': |
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38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
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56 -a '$anno.geneanno' |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 58c05c0ce9334f8b9c800283cfd1f40573546edd
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57 #end if |
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76d01fe0ec36
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 58c05c0ce9334f8b9c800283cfd1f40573546edd
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58 |
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3
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
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59 -C '${ ','.join( ['%s' % $x.contrast for x in $rep_contrast] ) }' |
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1
76d01fe0ec36
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 58c05c0ce9334f8b9c800283cfd1f40573546edd
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60 |
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3
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
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61 #if $f.filt.filt_select == 'yes': |
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38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
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62 #if $f.filt.cformat.format_select == 'cpm': |
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38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
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63 -c '$f.filt.cformat.cpmReq' |
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38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
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64 -s '$f.filt.cformat.cpmSampleReq' |
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38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
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65 #elif $f.filt.cformat.format_select == 'counts': |
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38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
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66 -z '$f.filt.cformat.cntReq' |
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38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
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67 #if $f.filt.cformat.samples.count_select == 'total': |
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38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
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68 -y |
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38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
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69 #elif $f.filt.cformat.samples.count_select == 'sample': |
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38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
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70 -s '$f.filt.cformat.samples.cntSampleReq' |
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38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
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71 #end if |
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38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
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72 #end if |
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38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
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changeset
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73 #end if |
|
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents:
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diff
changeset
|
74 |
|
8
00a42b66e522
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents:
7
diff
changeset
|
75 #if $out.plots: |
|
00a42b66e522
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents:
7
diff
changeset
|
76 -P $out.plots |
|
00a42b66e522
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents:
7
diff
changeset
|
77 #end if |
|
00a42b66e522
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents:
7
diff
changeset
|
78 |
|
3
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
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changeset
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79 #if $out.normCounts: |
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38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
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changeset
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80 -x |
|
1
76d01fe0ec36
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 58c05c0ce9334f8b9c800283cfd1f40573546edd
iuc
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81 #end if |
|
0
bdebdea5f6a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
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diff
changeset
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82 |
|
3
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
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changeset
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83 #if $out.rdaOption: |
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38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
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changeset
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84 -r |
|
1
76d01fe0ec36
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 58c05c0ce9334f8b9c800283cfd1f40573546edd
iuc
parents:
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changeset
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85 #end if |
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76d01fe0ec36
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 58c05c0ce9334f8b9c800283cfd1f40573546edd
iuc
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86 |
|
3
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
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changeset
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87 -l '$adv.lfc' |
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38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
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changeset
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88 -p '$adv.pVal' |
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38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
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changeset
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89 -d '$adv.pAdjust' |
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7
e6a4ff41af6b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit cf399638ebca4250bcc15f468238a9964de97b33
iuc
parents:
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changeset
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90 -G '$adv.topgenes' |
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6
39fa12a6d885
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 60cae222b10f43f830936c19298bd723ac47e43d
iuc
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91 #if $adv.treat: |
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39fa12a6d885
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 60cae222b10f43f830936c19298bd723ac47e43d
iuc
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92 -T |
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39fa12a6d885
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 60cae222b10f43f830936c19298bd723ac47e43d
iuc
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93 #end if |
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0
bdebdea5f6a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
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94 |
|
3
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
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95 #if $deMethod.de_select == 'voom': |
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38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
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96 #if $deMethod.weightOption: |
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38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
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97 -w |
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38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
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98 #end if |
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38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
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99 #elif $deMethod.de_select == 'trend': |
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38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
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100 -t $deMethod.prior_count |
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38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
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101 #end if |
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38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
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102 |
|
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
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103 -n '$adv.normalisationOption' |
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38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
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104 |
|
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
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105 #if $adv.robOption: |
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38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
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106 -b |
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1
76d01fe0ec36
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 58c05c0ce9334f8b9c800283cfd1f40573546edd
iuc
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107 #end if |
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0
bdebdea5f6a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
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108 |
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1
76d01fe0ec36
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 58c05c0ce9334f8b9c800283cfd1f40573546edd
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109 && |
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76d01fe0ec36
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 58c05c0ce9334f8b9c800283cfd1f40573546edd
iuc
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110 mkdir ./output_dir |
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76d01fe0ec36
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 58c05c0ce9334f8b9c800283cfd1f40573546edd
iuc
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111 |
|
76d01fe0ec36
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 58c05c0ce9334f8b9c800283cfd1f40573546edd
iuc
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112 && |
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2
a330ddf43861
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 346319bd01bfd51f02d656e653a93f0bd1e954aa
iuc
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113 cp '$outReport.files_path'/*.tsv output_dir/ |
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4
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
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114 |
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a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
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115 #if $out.rscript: |
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a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
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116 && cp '$__tool_directory__/limma_voom.R' '$rscript' |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
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117 #end if |
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1
76d01fe0ec36
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 58c05c0ce9334f8b9c800283cfd1f40573546edd
iuc
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118 ]]></command> |
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76d01fe0ec36
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 58c05c0ce9334f8b9c800283cfd1f40573546edd
iuc
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119 |
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0
bdebdea5f6a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
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120 <inputs> |
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3
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
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121 |
|
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
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122 <!-- DE Method Option --> |
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38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
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123 <conditional name="deMethod"> |
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38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
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124 <param name="de_select" type="select" label="Differential Expression Method" help="Select the limma-voom or limma-trend method. See Help section below for more information. Default: limma-voom"> |
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38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
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125 <option value="voom" selected="True">limma-voom</option> |
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38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
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126 <option value="trend">limma-trend</option> |
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38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
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127 </param> |
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38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
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128 <when value="voom"> |
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38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
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129 <param name="weightOption" type="boolean" truevalue="1" falsevalue="0" checked="false" label="Apply voom with sample quality weights?" |
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38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
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130 help="Apply weights if outliers are present (voomWithQualityWeights). Default: False."> |
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38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
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131 </param> |
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38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
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132 </when> |
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38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
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133 <when value="trend"> |
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38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
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134 <param name="prior_count" type="float" min="0" value="3" label="Prior count" help="Average count to be added to each observation to avoid taking log of zero. Default: 3." /> |
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38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
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135 </when> |
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38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
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136 </conditional> |
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38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
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137 <!-- Counts and Factors --> |
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38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
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138 <conditional name="input"> |
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38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
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139 <param name="format" type="select" label="Count Files or Matrix?" |
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38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
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140 help="You can choose to input either separate count files (one per sample) or a single count matrix"> |
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38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
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141 <option value="files">Separate Count Files</option> |
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38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
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142 <option value="matrix">Single Count Matrix</option> |
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38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
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143 </param> |
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1
76d01fe0ec36
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 58c05c0ce9334f8b9c800283cfd1f40573546edd
iuc
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144 |
|
3
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
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145 <when value="files"> |
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38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
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146 <repeat name="rep_factor" title="Factor" min="1"> |
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38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
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147 <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."> |
|
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
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148 <sanitizer> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
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149 <valid initial="string.letters,string.digits"><add value="_" /></valid> |
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38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
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150 </sanitizer> |
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38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
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151 </param> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
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152 <repeat name="rep_group" title="Group" min="2" default="2"> |
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153 <param name="groupName" type="text" label="Name" |
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154 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)."> |
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3
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155 <sanitizer> |
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156 <valid initial="string.letters,string.digits"><add value="_" /></valid> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
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157 </sanitizer> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
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158 </param> |
|
4
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159 <param name="countsFile" type="data" format="tabular" multiple="true" label="Counts files"/> |
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3
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
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160 </repeat> |
|
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
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161 </repeat> |
|
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
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162 </when> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
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163 |
|
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164 <when value="matrix"> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
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165 <param name="counts" type="data" format="tabular" label="Count Matrix"/> |
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166 |
|
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167 <conditional name="fact"> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
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168 <param name="ffile" type="select" label="Input factor information from file?" |
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169 help="You can choose to input the factor and group information for the samples from a file or manually enter below."> |
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170 <option value="no">No</option> |
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171 <option value="yes">Yes</option> |
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172 </param> |
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173 <when value="yes"> |
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174 <param name="finfo" type="data" format="tabular" label="Factor File"/> |
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175 </when> |
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176 <when value="no" > |
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177 <repeat name="rep_factor" title="Factor" min="1"> |
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178 <param name="factorName" type="text" label="Factor Name" |
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179 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."> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
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180 <validator type="empty_field" /> |
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181 <validator type="regex" message="Please only use letters, numbers or underscores">^[\w]+$</validator> |
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182 </param> |
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183 <param name="groupNames" type="text" label="Groups" |
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184 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)."> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
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185 <validator type="empty_field" /> |
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186 <validator type="regex" message="Please only use letters, numbers or underscores, and separate levels by commas">^[\w,]+$</validator> |
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187 </param> |
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188 </repeat> |
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189 </when> |
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190 </conditional> |
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191 </when> |
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192 </conditional> |
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193 |
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194 <!-- Gene Annotations --> |
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0
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195 <conditional name="anno"> |
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196 <param name="annoOpt" type="select" label="Use Gene Annotations?" |
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197 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, and used to label the top genes in the Volcano plot. See Help section below."> |
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0
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
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198 <option value="no">No</option> |
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199 <option value="yes">Yes</option> |
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200 </param> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
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201 <when value="yes"> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
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202 <param name="geneanno" type="data" format="tabular" label="Gene Annotations"/> |
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203 </when> |
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204 <when value="no" /> |
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205 </conditional> |
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206 |
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3
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207 <!-- Contrasts --> |
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208 <repeat name="rep_contrast" title="Contrast" min="1" default="1"> |
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8
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209 <param name="contrast" type="text" label="Contrast of Interest" help="Names of two groups to compare separated by a hyphen e.g. Mut-WT. If the order is Mut-WT the fold changes in the results will be up/down in Mut relative to WT. If you have more than one contrast enter each separately using the Insert Contrast button below. For differences between contrasts use e.g. (Mut1-WT)-(Mut2-WT). 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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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
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210 <validator type="empty_field" /> |
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8
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211 <validator type="regex" message="Please only use letters, numbers or underscores">^[\(\w\)-]+$</validator> |
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0
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212 </param> |
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3
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213 </repeat> |
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1
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214 |
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3
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215 <!-- Filter Options --> |
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216 <section name="f" expanded="false" title="Filter Low Counts"> |
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217 <conditional name="filt"> |
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218 <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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219 <option value="no" selected="true">No</option> |
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220 <option value="yes">Yes</option> |
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221 </param> |
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222 <when value="yes"> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
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223 <conditional name="cformat"> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
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224 <param name="format_select" type="select" label="Filter on CPM or Count values?" help="It is slightly better to base the filtering on count-per-million (CPM) rather than the raw count values so as to avoid favoring genes expressed in samples sequenced to a higher depth. "> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
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225 <option value="cpm">CPM</option> |
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226 <option value="counts">Counts</option> |
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227 </param> |
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228 <when value="cpm"> |
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229 <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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230 <param name="cpmSampleReq" type="integer" value="0" min="0" label="Minimum Samples" |
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231 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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232 </when> |
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233 <when value="counts"> |
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234 <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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235 <conditional name="samples"> |
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236 <param name="count_select" type="select" label="Filter on Total Count or per Sample Count values?" > |
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237 <option value="total">Total</option> |
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238 <option value="sample">Sample</option> |
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239 </param> |
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240 <when value="total"> |
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241 <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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242 </when> |
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243 <when value="sample"> |
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244 <param name="cntSampleReq" type="integer" value="0" min="0" label="Minimum Samples" |
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245 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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246 </when> |
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247 </conditional> |
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248 </when> |
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249 </conditional> |
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250 </when> |
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251 <when value="no" /> |
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252 </conditional> |
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253 </section> |
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1
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254 |
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3
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255 <!-- Output Options --> |
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256 <section name="out" expanded="false" title="Output Options"> |
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257 <param name="plots" type="select" display="checkboxes" multiple="True" optional="True" label="Additional Plots" help="Select additional plots to output in the report and as PDFs"> |
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258 <option value="d">Density Plots (if filtering)</option> |
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259 <option value="c">CpmsVsCounts Plots (if filtering on cpms)</option> |
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260 <option value="b">Box Plots (if normalising)</option> |
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261 <option value="x">MDS Extra (Dims 2vs3 and 3vs4)</option> |
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262 <option value="m">MD Plots for individual samples</option> |
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263 <option value="h">Heatmaps (top DE genes) </option> |
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264 <option value="s">Stripcharts (top DE genes)</option> |
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265 </param> |
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266 <param name="normCounts" type="boolean" truevalue="1" falsevalue="0" checked="false" |
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267 label="Output Normalised Counts Table?" |
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268 help="Output a file containing the normalised counts, these are in log2 counts per million (logCPM). Default: No"> |
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1
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269 </param> |
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4
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270 <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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271 <param name="rdaOption" type="boolean" truevalue="1" falsevalue="0" checked="false" |
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272 label="Output RData file?" |
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273 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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274 </param> |
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275 </section> |
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276 |
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277 <!-- Advanced Options --> |
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278 <section name="adv" expanded="false" title="Advanced Options"> |
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279 <param name="lfc" type="float" value="0" min="0" |
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280 label="Minimum Log2 Fold Change" |
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281 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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282 <param name="pVal" type="float" value="0.05" min="0" max="1" |
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283 label="P-Value Adjusted Threshold" |
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284 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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285 <param name="pAdjust" type="select" label="P-Value Adjustment Method" help="Default: BH"> |
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286 <option value="BH" selected="true">Benjamini and Hochberg (1995)</option> |
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287 <option value="BY">Benjamini and Yekutieli (2001)</option> |
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288 <option value="holm">Holm (1979)</option> |
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289 <option value="none">None</option> |
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290 </param> |
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6
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291 <param name="treat" type="boolean" truevalue="1" falsevalue="0" checked="False" |
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292 label="Test significance relative to a fold-change threshold (TREAT)" |
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293 help="If you want to apply a cut-off on a fold change the TREAT function can be used, see Help section below. Default: No"/> |
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294 <param name="topgenes" type="integer" value="10" min="0" max="100" |
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295 label="Number of genes to highlight in Volcano plot, Heatmap and Stripcharts" |
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296 help="The top DE genes will be highlighted in the Volcano plot for each contrast and can be output in heatmap and stripchart PDFs (max 100). Default: 10."/> |
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3
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297 <param name="normalisationOption" type="select" label="Normalisation Method" help="Default: TMM"> |
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38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
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298 <option value="TMM" selected="true">TMM</option> |
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38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
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299 <option value="RLE">RLE</option> |
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38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
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300 <option value="upperquartile">Upperquartile</option> |
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38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
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301 <option value="none">None (Don't normalise)</option> |
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38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
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302 </param> |
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38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
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303 <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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38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
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304 </section> |
|
0
bdebdea5f6a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
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305 |
|
bdebdea5f6a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
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306 </inputs> |
|
1
76d01fe0ec36
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 58c05c0ce9334f8b9c800283cfd1f40573546edd
iuc
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changeset
|
307 |
|
0
bdebdea5f6a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
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308 <outputs> |
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1
76d01fe0ec36
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 58c05c0ce9334f8b9c800283cfd1f40573546edd
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309 <data name="outReport" format="html" label="${tool.name} on ${on_string}: Report" /> |
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76d01fe0ec36
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 58c05c0ce9334f8b9c800283cfd1f40573546edd
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310 <collection name="outTables" type="list" label="${tool.name} on ${on_string}: Tables"> |
|
0
bdebdea5f6a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
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311 <discover_datasets pattern="(?P<name>.+)\.tsv$" format="tabular" directory="output_dir" visible="false" /> |
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bdebdea5f6a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
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312 </collection> |
|
4
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
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313 <data name="rscript" format="txt" label="${tool.name} on ${on_string}: Rscript"> |
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a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
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314 <filter>out['rscript']</filter> |
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a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
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315 </data> |
|
0
bdebdea5f6a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
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316 </outputs> |
|
bdebdea5f6a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
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317 |
|
bdebdea5f6a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
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318 <tests> |
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3
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
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319 <!-- Ensure report is output --> |
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0
bdebdea5f6a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
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320 <test> |
|
3
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
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321 <param name="format" value="matrix" /> |
|
0
bdebdea5f6a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
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322 <param name="counts" value="matrix.txt" /> |
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3
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
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323 <repeat name="rep_factor"> |
|
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
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324 <param name="factorName" value="Genotype"/> |
|
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
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325 <param name="groupNames" value="Mut,Mut,Mut,WT,WT,WT" /> |
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38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
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326 </repeat> |
|
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
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327 <repeat name="rep_contrast"> |
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38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
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328 <param name="contrast" value="Mut-WT" /> |
|
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
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329 </repeat> |
|
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
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330 <repeat name="rep_contrast"> |
|
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
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331 <param name="contrast" value="WT-Mut" /> |
|
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
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332 </repeat> |
|
0
bdebdea5f6a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
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333 <param name="normalisationOption" value="TMM" /> |
|
7
e6a4ff41af6b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit cf399638ebca4250bcc15f468238a9964de97b33
iuc
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334 <param name="topgenes" value="6" /> |
|
1
76d01fe0ec36
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 58c05c0ce9334f8b9c800283cfd1f40573546edd
iuc
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335 <output_collection name="outTables" count="2"> |
|
4
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
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336 <element name="limma-voom_Mut-WT" ftype="tabular" > |
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a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
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337 <assert_contents> |
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a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
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338 <has_text_matching expression="GeneID.*logFC.*AveExpr.*t.*P.Value.*adj.P.Val.*B" /> |
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a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
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339 <has_text_matching expression="11304.*0.4573" /> |
|
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
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340 </assert_contents> |
|
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
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341 </element> |
|
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
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342 <element name="limma-voom_WT-Mut" ftype="tabular" > |
|
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
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343 <assert_contents> |
|
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
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344 <has_text_matching expression="GeneID.*logFC.*AveExpr.*t.*P.Value.*adj.P.Val.*B" /> |
|
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
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345 <has_text_matching expression="11304.*-0.4573" /> |
|
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
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346 </assert_contents> |
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a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
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347 </element> |
|
1
76d01fe0ec36
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 58c05c0ce9334f8b9c800283cfd1f40573546edd
iuc
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348 </output_collection> |
|
0
bdebdea5f6a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
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349 <output name="outReport" > |
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bdebdea5f6a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
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350 <assert_contents> |
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3
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
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351 <has_text text="Limma Analysis Output" /> |
|
0
bdebdea5f6a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
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352 <not_has_text text="RData" /> |
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bdebdea5f6a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
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353 </assert_contents> |
|
1
76d01fe0ec36
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 58c05c0ce9334f8b9c800283cfd1f40573546edd
iuc
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354 </output> |
|
4
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
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355 </test> |
|
3
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
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356 <!-- Ensure annotation file input works --> |
|
0
bdebdea5f6a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
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357 <test> |
|
3
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
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358 <param name="format" value="matrix" /> |
|
0
bdebdea5f6a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
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359 <param name="annoOpt" value="yes" /> |
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bdebdea5f6a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
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|
360 <param name="geneanno" value="anno.txt" /> |
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bdebdea5f6a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
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|
361 <param name="counts" value="matrix.txt" /> |
|
3
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
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changeset
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362 <repeat name="rep_factor"> |
|
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents:
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changeset
|
363 <param name="factorName" value="Genotype"/> |
|
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents:
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364 <param name="groupNames" value="Mut,Mut,Mut,WT,WT,WT" /> |
|
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents:
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365 </repeat> |
|
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents:
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diff
changeset
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366 <repeat name="rep_contrast"> |
|
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents:
2
diff
changeset
|
367 <param name="contrast" value="Mut-WT" /> |
|
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents:
2
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changeset
|
368 </repeat> |
|
0
bdebdea5f6a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
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changeset
|
369 <param name="normalisationOption" value="TMM" /> |
|
7
e6a4ff41af6b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit cf399638ebca4250bcc15f468238a9964de97b33
iuc
parents:
6
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changeset
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370 <param name="topgenes" value="6" /> |
|
3
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents:
2
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changeset
|
371 <output_collection name="outTables" count="1"> |
|
4
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
3
diff
changeset
|
372 <element name="limma-voom_Mut-WT" ftype="tabular" > |
|
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
3
diff
changeset
|
373 <assert_contents> |
|
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
3
diff
changeset
|
374 <has_text_matching expression="EntrezID.*Symbol.*logFC.*AveExpr.*t.*P.Value.*adj.P.Val.*B" /> |
|
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
3
diff
changeset
|
375 <has_text_matching expression="11304.*Abca4.*0.4573" /> |
|
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
3
diff
changeset
|
376 </assert_contents> |
|
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
3
diff
changeset
|
377 </element> |
|
1
76d01fe0ec36
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 58c05c0ce9334f8b9c800283cfd1f40573546edd
iuc
parents:
0
diff
changeset
|
378 </output_collection> |
|
0
bdebdea5f6a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff
changeset
|
379 </test> |
|
4
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
3
diff
changeset
|
380 <!-- Ensure Rscript and RData file can be output --> |
|
0
bdebdea5f6a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff
changeset
|
381 <test> |
|
3
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents:
2
diff
changeset
|
382 <param name="format" value="matrix" /> |
|
4
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
3
diff
changeset
|
383 <param name="rscript" value="True"/> |
|
3
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents:
2
diff
changeset
|
384 <param name="rdaOption" value="true" /> |
|
1
76d01fe0ec36
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 58c05c0ce9334f8b9c800283cfd1f40573546edd
iuc
parents:
0
diff
changeset
|
385 <param name="counts" value="matrix.txt" /> |
|
3
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents:
2
diff
changeset
|
386 <repeat name="rep_factor"> |
|
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents:
2
diff
changeset
|
387 <param name="factorName" value="Genotype"/> |
|
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents:
2
diff
changeset
|
388 <param name="groupNames" value="Mut,Mut,Mut,WT,WT,WT" /> |
|
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents:
2
diff
changeset
|
389 </repeat> |
|
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents:
2
diff
changeset
|
390 <repeat name="rep_contrast"> |
|
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents:
2
diff
changeset
|
391 <param name="contrast" value="Mut-WT" /> |
|
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents:
2
diff
changeset
|
392 </repeat> |
|
0
bdebdea5f6a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff
changeset
|
393 <param name="normalisationOption" value="TMM" /> |
|
7
e6a4ff41af6b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit cf399638ebca4250bcc15f468238a9964de97b33
iuc
parents:
6
diff
changeset
|
394 <param name="topgenes" value="6" /> |
|
0
bdebdea5f6a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff
changeset
|
395 <output name="outReport" > |
|
bdebdea5f6a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff
changeset
|
396 <assert_contents> |
|
bdebdea5f6a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff
changeset
|
397 <has_text text="RData" /> |
|
bdebdea5f6a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff
changeset
|
398 </assert_contents> |
|
bdebdea5f6a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff
changeset
|
399 </output> |
|
4
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
3
diff
changeset
|
400 <output name="rscript" value="out_rscript.txt"/> |
|
0
bdebdea5f6a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff
changeset
|
401 </test> |
|
3
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents:
2
diff
changeset
|
402 <!-- Ensure secondary factors work --> |
|
1
76d01fe0ec36
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 58c05c0ce9334f8b9c800283cfd1f40573546edd
iuc
parents:
0
diff
changeset
|
403 <test> |
|
3
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents:
2
diff
changeset
|
404 <param name="format" value="matrix" /> |
|
1
76d01fe0ec36
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 58c05c0ce9334f8b9c800283cfd1f40573546edd
iuc
parents:
0
diff
changeset
|
405 <param name="counts" value="matrix.txt" /> |
|
3
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents:
2
diff
changeset
|
406 <repeat name="rep_factor"> |
|
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents:
2
diff
changeset
|
407 <param name="factorName" value="Genotype"/> |
|
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents:
2
diff
changeset
|
408 <param name="groupNames" value="Mut,Mut,Mut,WT,WT,WT" /> |
|
1
76d01fe0ec36
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 58c05c0ce9334f8b9c800283cfd1f40573546edd
iuc
parents:
0
diff
changeset
|
409 </repeat> |
|
3
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents:
2
diff
changeset
|
410 <repeat name="rep_factor"> |
|
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents:
2
diff
changeset
|
411 <param name="factorName" value="Batch"/> |
|
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents:
2
diff
changeset
|
412 <param name="groupNames" value="b1,b2,b3,b1,b2,b3"/> |
|
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents:
2
diff
changeset
|
413 </repeat> |
|
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents:
2
diff
changeset
|
414 <repeat name="rep_contrast"> |
|
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents:
2
diff
changeset
|
415 <param name="contrast" value="Mut-WT" /> |
|
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents:
2
diff
changeset
|
416 </repeat> |
|
1
76d01fe0ec36
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 58c05c0ce9334f8b9c800283cfd1f40573546edd
iuc
parents:
0
diff
changeset
|
417 <param name="normalisationOption" value="TMM" /> |
|
7
e6a4ff41af6b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit cf399638ebca4250bcc15f468238a9964de97b33
iuc
parents:
6
diff
changeset
|
418 <param name="topgenes" value="6" /> |
|
3
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents:
2
diff
changeset
|
419 <output_collection name="outTables" count="1" > |
|
4
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
3
diff
changeset
|
420 <element name="limma-voom_Mut-WT" ftype="tabular" > |
|
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
3
diff
changeset
|
421 <assert_contents> |
|
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
3
diff
changeset
|
422 <has_text_matching expression="GeneID.*logFC.*AveExpr.*t.*P.Value.*adj.P.Val.*B" /> |
|
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
3
diff
changeset
|
423 <has_text_matching expression="11304.*0.4590" /> |
|
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
3
diff
changeset
|
424 </assert_contents> |
|
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
3
diff
changeset
|
425 </element> |
|
1
76d01fe0ec36
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 58c05c0ce9334f8b9c800283cfd1f40573546edd
iuc
parents:
0
diff
changeset
|
426 </output_collection> |
|
76d01fe0ec36
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 58c05c0ce9334f8b9c800283cfd1f40573546edd
iuc
parents:
0
diff
changeset
|
427 </test> |
|
3
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents:
2
diff
changeset
|
428 <!-- Ensure factors file input works --> |
|
1
76d01fe0ec36
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 58c05c0ce9334f8b9c800283cfd1f40573546edd
iuc
parents:
0
diff
changeset
|
429 <test> |
|
3
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents:
2
diff
changeset
|
430 <param name="format" value="matrix" /> |
|
1
76d01fe0ec36
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 58c05c0ce9334f8b9c800283cfd1f40573546edd
iuc
parents:
0
diff
changeset
|
431 <param name="ffile" value="yes" /> |
|
76d01fe0ec36
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 58c05c0ce9334f8b9c800283cfd1f40573546edd
iuc
parents:
0
diff
changeset
|
432 <param name="finfo" value="factorinfo.txt" /> |
|
76d01fe0ec36
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 58c05c0ce9334f8b9c800283cfd1f40573546edd
iuc
parents:
0
diff
changeset
|
433 <param name="counts" value="matrix.txt" /> |
|
3
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents:
2
diff
changeset
|
434 <repeat name="rep_contrast"> |
|
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents:
2
diff
changeset
|
435 <param name="contrast" value="Mut-WT" /> |
|
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents:
2
diff
changeset
|
436 </repeat> |
|
1
76d01fe0ec36
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 58c05c0ce9334f8b9c800283cfd1f40573546edd
iuc
parents:
0
diff
changeset
|
437 <param name="normalisationOption" value="TMM" /> |
|
7
e6a4ff41af6b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit cf399638ebca4250bcc15f468238a9964de97b33
iuc
parents:
6
diff
changeset
|
438 <param name="topgenes" value="6" /> |
|
3
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents:
2
diff
changeset
|
439 <output_collection name="outTables" count="1"> |
|
4
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
3
diff
changeset
|
440 <element name="limma-voom_Mut-WT" ftype="tabular" > |
|
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
3
diff
changeset
|
441 <assert_contents> |
|
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
3
diff
changeset
|
442 <has_text_matching expression="GeneID.*logFC.*AveExpr.*t.*P.Value.*adj.P.Val.*B" /> |
|
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
3
diff
changeset
|
443 <has_text_matching expression="11304.*0.4590" /> |
|
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
3
diff
changeset
|
444 </assert_contents> |
|
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
3
diff
changeset
|
445 </element> |
|
1
76d01fe0ec36
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 58c05c0ce9334f8b9c800283cfd1f40573546edd
iuc
parents:
0
diff
changeset
|
446 </output_collection> |
|
76d01fe0ec36
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 58c05c0ce9334f8b9c800283cfd1f40573546edd
iuc
parents:
0
diff
changeset
|
447 </test> |
|
3
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents:
2
diff
changeset
|
448 <!-- Ensure normalised counts file output works--> |
|
1
76d01fe0ec36
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 58c05c0ce9334f8b9c800283cfd1f40573546edd
iuc
parents:
0
diff
changeset
|
449 <test> |
|
3
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents:
2
diff
changeset
|
450 <param name="format" value="matrix" /> |
|
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents:
2
diff
changeset
|
451 <param name="normCounts" value="true" /> |
|
1
76d01fe0ec36
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 58c05c0ce9334f8b9c800283cfd1f40573546edd
iuc
parents:
0
diff
changeset
|
452 <param name="counts" value="matrix.txt" /> |
|
3
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents:
2
diff
changeset
|
453 <repeat name="rep_factor"> |
|
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents:
2
diff
changeset
|
454 <param name="factorName" value="Genotype"/> |
|
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents:
2
diff
changeset
|
455 <param name="groupNames" value="Mut,Mut,Mut,WT,WT,WT" /> |
|
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents:
2
diff
changeset
|
456 </repeat> |
|
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents:
2
diff
changeset
|
457 <repeat name="rep_contrast"> |
|
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents:
2
diff
changeset
|
458 <param name="contrast" value="Mut-WT" /> |
|
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents:
2
diff
changeset
|
459 </repeat> |
|
1
76d01fe0ec36
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 58c05c0ce9334f8b9c800283cfd1f40573546edd
iuc
parents:
0
diff
changeset
|
460 <param name="normalisationOption" value="TMM" /> |
|
7
e6a4ff41af6b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit cf399638ebca4250bcc15f468238a9964de97b33
iuc
parents:
6
diff
changeset
|
461 <param name="topgenes" value="6" /> |
|
1
76d01fe0ec36
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 58c05c0ce9334f8b9c800283cfd1f40573546edd
iuc
parents:
0
diff
changeset
|
462 <output_collection name="outTables" count="2"> |
|
4
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
3
diff
changeset
|
463 <element name="limma-voom_Mut-WT" ftype="tabular" > |
|
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
3
diff
changeset
|
464 <assert_contents> |
|
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
3
diff
changeset
|
465 <has_text_matching expression="GeneID.*logFC.*AveExpr.*t.*P.Value.*adj.P.Val.*B" /> |
|
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
3
diff
changeset
|
466 <has_text_matching expression="11304.*0.4573" /> |
|
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
3
diff
changeset
|
467 </assert_contents> |
|
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
3
diff
changeset
|
468 </element> |
|
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
3
diff
changeset
|
469 <element name="limma-voom_normcounts" ftype="tabular" > |
|
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
3
diff
changeset
|
470 <assert_contents> |
|
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
3
diff
changeset
|
471 <has_text_matching expression="GeneID.*Mut1.*Mut2.*Mut3.*WT1.*WT2.*WT3" /> |
|
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
3
diff
changeset
|
472 <has_text_matching expression="11304.*15.7545" /> |
|
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
3
diff
changeset
|
473 </assert_contents> |
|
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
3
diff
changeset
|
474 </element> |
|
1
76d01fe0ec36
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 58c05c0ce9334f8b9c800283cfd1f40573546edd
iuc
parents:
0
diff
changeset
|
475 </output_collection> |
|
76d01fe0ec36
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 58c05c0ce9334f8b9c800283cfd1f40573546edd
iuc
parents:
0
diff
changeset
|
476 </test> |
|
3
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents:
2
diff
changeset
|
477 <!-- Ensure multiple counts files input works --> |
|
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents:
2
diff
changeset
|
478 <test> |
|
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents:
2
diff
changeset
|
479 <param name="format" value="files" /> |
|
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents:
2
diff
changeset
|
480 <repeat name="rep_factor"> |
|
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents:
2
diff
changeset
|
481 <param name="factorName" value="Genotype"/> |
|
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents:
2
diff
changeset
|
482 <repeat name="rep_group"> |
|
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents:
2
diff
changeset
|
483 <param name="groupName" value="WT"/> |
|
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents:
2
diff
changeset
|
484 <param name="countsFile" value="WT1.counts,WT2.counts,WT3.counts"/> |
|
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents:
2
diff
changeset
|
485 </repeat> |
|
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents:
2
diff
changeset
|
486 <repeat name="rep_group"> |
|
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents:
2
diff
changeset
|
487 <param name="groupName" value="Mut"/> |
|
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents:
2
diff
changeset
|
488 <param name="countsFile" value="Mut1.counts,Mut2.counts,Mut3.counts"/> |
|
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents:
2
diff
changeset
|
489 </repeat> |
|
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents:
2
diff
changeset
|
490 </repeat> |
|
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents:
2
diff
changeset
|
491 <repeat name="rep_factor"> |
|
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents:
2
diff
changeset
|
492 <param name="factorName" value="Batch"/> |
|
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents:
2
diff
changeset
|
493 <repeat name="rep_group"> |
|
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents:
2
diff
changeset
|
494 <param name="groupName" value="b1"/> |
|
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents:
2
diff
changeset
|
495 <param name="countsFile" value="WT1.counts,Mut1.counts"/> |
|
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents:
2
diff
changeset
|
496 </repeat> |
|
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents:
2
diff
changeset
|
497 <repeat name="rep_group"> |
|
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents:
2
diff
changeset
|
498 <param name="groupName" value="b2"/> |
|
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents:
2
diff
changeset
|
499 <param name="countsFile" value="WT2.counts,Mut2.counts"/> |
|
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents:
2
diff
changeset
|
500 </repeat> |
|
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents:
2
diff
changeset
|
501 <repeat name="rep_group"> |
|
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents:
2
diff
changeset
|
502 <param name="groupName" value="b3"/> |
|
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents:
2
diff
changeset
|
503 <param name="countsFile" value="WT3.counts,Mut3.counts"/> |
|
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents:
2
diff
changeset
|
504 </repeat> |
|
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents:
2
diff
changeset
|
505 </repeat> |
|
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents:
2
diff
changeset
|
506 <param name="annoOpt" value="yes" /> |
|
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents:
2
diff
changeset
|
507 <param name="geneanno" value="anno.txt" /> |
|
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents:
2
diff
changeset
|
508 <repeat name="rep_contrast"> |
|
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents:
2
diff
changeset
|
509 <param name="contrast" value="Mut-WT" /> |
|
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents:
2
diff
changeset
|
510 </repeat> |
|
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents:
2
diff
changeset
|
511 <repeat name="rep_contrast"> |
|
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents:
2
diff
changeset
|
512 <param name="contrast" value="WT-Mut" /> |
|
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents:
2
diff
changeset
|
513 </repeat> |
|
7
e6a4ff41af6b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit cf399638ebca4250bcc15f468238a9964de97b33
iuc
parents:
6
diff
changeset
|
514 <param name="topgenes" value="6" /> |
|
3
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents:
2
diff
changeset
|
515 <param name="normCounts" value="true" /> |
|
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents:
2
diff
changeset
|
516 <output_collection name="outTables" count="3"> |
|
4
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
3
diff
changeset
|
517 <element name="limma-voom_Mut-WT" ftype="tabular" > |
|
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
3
diff
changeset
|
518 <assert_contents> |
|
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
3
diff
changeset
|
519 <has_text_matching expression="logFC.*AveExpr.*t.*P.Value.*adj.P.Val.*B" /> |
|
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
3
diff
changeset
|
520 <has_text_matching expression="11304.*Abca4.*0.4590" /> |
|
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
3
diff
changeset
|
521 </assert_contents> |
|
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
3
diff
changeset
|
522 </element> |
|
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
3
diff
changeset
|
523 <element name="limma-voom_WT-Mut" ftype="tabular" > |
|
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
3
diff
changeset
|
524 <assert_contents> |
|
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
3
diff
changeset
|
525 <has_text_matching expression="EntrezID.*Symbol.*logFC.*AveExpr.*t.*P.Value.*adj.P.Val.*B" /> |
|
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
3
diff
changeset
|
526 <has_text_matching expression="11304.*Abca4.*-0.4590" /> |
|
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
3
diff
changeset
|
527 </assert_contents> |
|
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
3
diff
changeset
|
528 </element> |
|
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
3
diff
changeset
|
529 <element name="limma-voom_normcounts" ftype="tabular" > |
|
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
3
diff
changeset
|
530 <assert_contents> |
|
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
3
diff
changeset
|
531 <has_text_matching expression="EntrezID.*Symbol.*Mut1.*Mut2.*Mut3.*WT1.*WT2.*WT3" /> |
|
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
3
diff
changeset
|
532 <has_text_matching expression="11304.*Abca4.*15.7545" /> |
|
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
3
diff
changeset
|
533 </assert_contents> |
|
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
3
diff
changeset
|
534 </element> |
|
3
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents:
2
diff
changeset
|
535 </output_collection> |
|
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents:
2
diff
changeset
|
536 </test> |
|
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents:
2
diff
changeset
|
537 <!-- Ensure limma-trend option works --> |
|
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents:
2
diff
changeset
|
538 <test> |
|
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents:
2
diff
changeset
|
539 <param name="format" value="matrix" /> |
|
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents:
2
diff
changeset
|
540 <param name="counts" value="matrix.txt" /> |
|
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents:
2
diff
changeset
|
541 <repeat name="rep_factor"> |
|
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents:
2
diff
changeset
|
542 <param name="factorName" value="Genotype"/> |
|
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents:
2
diff
changeset
|
543 <param name="groupNames" value="Mut,Mut,Mut,WT,WT,WT" /> |
|
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents:
2
diff
changeset
|
544 </repeat> |
|
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents:
2
diff
changeset
|
545 <repeat name="rep_contrast"> |
|
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents:
2
diff
changeset
|
546 <param name="contrast" value="Mut-WT" /> |
|
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents:
2
diff
changeset
|
547 </repeat> |
|
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents:
2
diff
changeset
|
548 <param name="normalisationOption" value="TMM" /> |
|
7
e6a4ff41af6b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit cf399638ebca4250bcc15f468238a9964de97b33
iuc
parents:
6
diff
changeset
|
549 <param name="topgenes" value="6" /> |
|
3
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents:
2
diff
changeset
|
550 <param name="de_select" value="trend" /> |
|
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents:
2
diff
changeset
|
551 <param name="rdaOption" value="true" /> |
|
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents:
2
diff
changeset
|
552 <output name="outReport" > |
|
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents:
2
diff
changeset
|
553 <assert_contents> |
|
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents:
2
diff
changeset
|
554 <has_text text="The limma-trend method was used" /> |
|
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents:
2
diff
changeset
|
555 </assert_contents> |
|
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents:
2
diff
changeset
|
556 </output> |
|
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents:
2
diff
changeset
|
557 <output_collection name="outTables" count="1"> |
|
4
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
3
diff
changeset
|
558 <element name="limma-trend_Mut-WT" ftype="tabular" > |
|
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
3
diff
changeset
|
559 <assert_contents> |
|
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
3
diff
changeset
|
560 <has_text_matching expression="GeneID.*logFC.*AveExpr.*t.*P.Value.*adj.P.Val.*B" /> |
|
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
3
diff
changeset
|
561 <has_text_matching expression="11304.*0.4540" /> |
|
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
3
diff
changeset
|
562 </assert_contents> |
|
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
3
diff
changeset
|
563 </element> |
|
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
3
diff
changeset
|
564 </output_collection> |
|
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
3
diff
changeset
|
565 </test> |
|
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
3
diff
changeset
|
566 <!-- Ensure limma-trend option with annotation works --> |
|
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
3
diff
changeset
|
567 <test> |
|
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
3
diff
changeset
|
568 <param name="format" value="matrix" /> |
|
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
3
diff
changeset
|
569 <param name="counts" value="matrix.txt" /> |
|
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
3
diff
changeset
|
570 <param name="annoOpt" value="yes" /> |
|
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
3
diff
changeset
|
571 <param name="geneanno" value="anno.txt" /> |
|
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
3
diff
changeset
|
572 <repeat name="rep_factor"> |
|
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
3
diff
changeset
|
573 <param name="factorName" value="Genotype"/> |
|
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
3
diff
changeset
|
574 <param name="groupNames" value="Mut,Mut,Mut,WT,WT,WT" /> |
|
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
3
diff
changeset
|
575 </repeat> |
|
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
3
diff
changeset
|
576 <repeat name="rep_contrast"> |
|
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
3
diff
changeset
|
577 <param name="contrast" value="Mut-WT" /> |
|
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
3
diff
changeset
|
578 </repeat> |
|
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
3
diff
changeset
|
579 <param name="normalisationOption" value="TMM" /> |
|
7
e6a4ff41af6b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit cf399638ebca4250bcc15f468238a9964de97b33
iuc
parents:
6
diff
changeset
|
580 <param name="topgenes" value="6" /> |
|
4
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
3
diff
changeset
|
581 <param name="de_select" value="trend" /> |
|
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
3
diff
changeset
|
582 <param name="rdaOption" value="true" /> |
|
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
3
diff
changeset
|
583 <output name="outReport" > |
|
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
3
diff
changeset
|
584 <assert_contents> |
|
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
3
diff
changeset
|
585 <has_text text="The limma-trend method was used" /> |
|
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
3
diff
changeset
|
586 </assert_contents> |
|
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
3
diff
changeset
|
587 </output> |
|
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
3
diff
changeset
|
588 <output_collection name="outTables" count="1"> |
|
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
3
diff
changeset
|
589 <element name="limma-trend_Mut-WT" ftype="tabular" > |
|
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
3
diff
changeset
|
590 <assert_contents> |
|
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
3
diff
changeset
|
591 <has_text_matching expression="EntrezID.*Symbol.*logFC.*AveExpr.*t.*P.Value.*adj.P.Val.*B" /> |
|
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
3
diff
changeset
|
592 <has_text_matching expression="11304.*0.4540" /> |
|
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
3
diff
changeset
|
593 </assert_contents> |
|
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
3
diff
changeset
|
594 </element> |
|
3
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents:
2
diff
changeset
|
595 </output_collection> |
|
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents:
2
diff
changeset
|
596 </test> |
|
0
bdebdea5f6a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff
changeset
|
597 </tests> |
|
1
76d01fe0ec36
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 58c05c0ce9334f8b9c800283cfd1f40573546edd
iuc
parents:
0
diff
changeset
|
598 |
|
76d01fe0ec36
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 58c05c0ce9334f8b9c800283cfd1f40573546edd
iuc
parents:
0
diff
changeset
|
599 <help><![CDATA[ |
|
0
bdebdea5f6a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff
changeset
|
600 .. class:: infomark |
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bdebdea5f6a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff
changeset
|
601 |
|
bdebdea5f6a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff
changeset
|
602 **What it does** |
|
bdebdea5f6a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff
changeset
|
603 |
|
3
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents:
2
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changeset
|
604 Given a matrix of counts (e.g. from featureCounts) and optional information about the genes, performs differential expression (DE) using the limma_ Bioconductor package and produces plots and tables useful in DE analysis. |
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38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents:
2
diff
changeset
|
605 |
|
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents:
2
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changeset
|
606 In the `limma approach`_ to RNA-seq, read counts are converted to log2-counts-per-million (logCPM) and the mean-variance relationship is modelled either with precision weights or with an empirical Bayes prior trend. The precision weights approach is called “voom” and the prior trend approach is called “limma-trend”. For more information, see the Help section below. |
|
0
bdebdea5f6a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff
changeset
|
607 |
|
bdebdea5f6a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff
changeset
|
608 ----- |
|
bdebdea5f6a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff
changeset
|
609 |
|
bdebdea5f6a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff
changeset
|
610 **Inputs** |
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bdebdea5f6a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff
changeset
|
611 |
|
3
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents:
2
diff
changeset
|
612 **Differential Expression Method:** |
|
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents:
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diff
changeset
|
613 Option to use the limma-voom or limma-trend approach for differential expression. The default is limma-voom. |
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38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents:
2
diff
changeset
|
614 If the sequencing depth is reasonably consistent across the RNA samples, then the simplest and most |
|
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents:
2
diff
changeset
|
615 robust approach to differential expression is to use limma-trend. This approach will usually work well if the |
|
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents:
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changeset
|
616 ratio of the largest library size to the smallest is not more than about 3-fold. When the library sizes are quite variable between samples, then the voom approach is theoretically more powerful than limma-trend. For more information see the excellent `limma User's Guide`_. |
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38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents:
2
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changeset
|
617 |
|
0
bdebdea5f6a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff
changeset
|
618 **Counts Data:** |
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3
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents:
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changeset
|
619 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. Gene identifiers can be of any type but must be unique and not repeated within a counts file. |
|
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents:
2
diff
changeset
|
620 |
|
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents:
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diff
changeset
|
621 Example - **Separate Count Files**: |
|
0
bdebdea5f6a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff
changeset
|
622 |
|
3
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents:
2
diff
changeset
|
623 ========== ======= |
|
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents:
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diff
changeset
|
624 **GeneID** **WT1** |
|
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents:
2
diff
changeset
|
625 ---------- ------- |
|
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents:
2
diff
changeset
|
626 11287 1699 |
|
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents:
2
diff
changeset
|
627 11298 1905 |
|
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents:
2
diff
changeset
|
628 11302 6 |
|
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents:
2
diff
changeset
|
629 11303 2099 |
|
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents:
2
diff
changeset
|
630 11304 356 |
|
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents:
2
diff
changeset
|
631 11305 2528 |
|
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents:
2
diff
changeset
|
632 ========== ======= |
|
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents:
2
diff
changeset
|
633 |
|
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents:
2
diff
changeset
|
634 Example - **Single Count Matrix**: |
|
0
bdebdea5f6a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff
changeset
|
635 |
|
bdebdea5f6a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff
changeset
|
636 ========== ======= ======= ======= ======== ======== ======== |
|
bdebdea5f6a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff
changeset
|
637 **GeneID** **WT1** **WT2** **WT3** **Mut1** **Mut2** **Mut3** |
|
bdebdea5f6a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff
changeset
|
638 ---------- ------- ------- ------- -------- -------- -------- |
|
1
76d01fe0ec36
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 58c05c0ce9334f8b9c800283cfd1f40573546edd
iuc
parents:
0
diff
changeset
|
639 11287 1699 1528 1601 1463 1441 1495 |
|
76d01fe0ec36
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 58c05c0ce9334f8b9c800283cfd1f40573546edd
iuc
parents:
0
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changeset
|
640 11298 1905 1744 1834 1345 1291 1346 |
|
76d01fe0ec36
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 58c05c0ce9334f8b9c800283cfd1f40573546edd
iuc
parents:
0
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changeset
|
641 11302 6 8 7 5 6 5 |
|
76d01fe0ec36
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 58c05c0ce9334f8b9c800283cfd1f40573546edd
iuc
parents:
0
diff
changeset
|
642 11303 2099 1974 2100 1574 1519 1654 |
|
76d01fe0ec36
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 58c05c0ce9334f8b9c800283cfd1f40573546edd
iuc
parents:
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changeset
|
643 11304 356 312 337 361 397 346 |
|
76d01fe0ec36
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 58c05c0ce9334f8b9c800283cfd1f40573546edd
iuc
parents:
0
diff
changeset
|
644 11305 2528 2438 2493 1762 1942 2027 |
|
0
bdebdea5f6a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff
changeset
|
645 ========== ======= ======= ======= ======== ======== ======== |
|
bdebdea5f6a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff
changeset
|
646 |
|
bdebdea5f6a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff
changeset
|
647 **Gene Annotations:** |
|
bdebdea5f6a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff
changeset
|
648 Optional input for gene annotations, this can contain more |
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bdebdea5f6a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff
changeset
|
649 information about the genes than just an ID number. The annotations will |
|
6
39fa12a6d885
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 60cae222b10f43f830936c19298bd723ac47e43d
iuc
parents:
5
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changeset
|
650 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 second column will be used to label the genes in the Volcano plot instead of the default Gene IDs. 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
bdebdea5f6a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff
changeset
|
651 |
|
bdebdea5f6a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff
changeset
|
652 Example: |
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bdebdea5f6a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff
changeset
|
653 |
|
bdebdea5f6a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff
changeset
|
654 ========== ========== =================================================== |
|
bdebdea5f6a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff
changeset
|
655 **GeneID** **Symbol** **GeneName** |
|
bdebdea5f6a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
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changeset
|
656 ---------- ---------- --------------------------------------------------- |
|
4
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
3
diff
changeset
|
657 11287 Pzp pregnancy zone protein |
|
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
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changeset
|
658 11298 Aanat arylalkylamine N-acetyltransferase |
|
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
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changeset
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659 11302 Aatk apoptosis-associated tyrosine kinase |
|
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
3
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changeset
|
660 11303 Abca1 ATP-binding cassette, sub-family A (ABC1), member 1 |
|
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
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changeset
|
661 11304 Abca4 ATP-binding cassette, sub-family A (ABC1), member 4 |
|
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
3
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changeset
|
662 11305 Abca2 ATP-binding cassette, sub-family A (ABC1), member 2 |
|
0
bdebdea5f6a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff
changeset
|
663 ========== ========== =================================================== |
|
bdebdea5f6a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
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changeset
|
664 |
|
1
76d01fe0ec36
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 58c05c0ce9334f8b9c800283cfd1f40573546edd
iuc
parents:
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changeset
|
665 **Factor Information:** |
|
3
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents:
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666 Enter factor names and groups in the tool form, or provide a tab-separated file that has the samples in the same order as listed in the columns of the counts matrix. The second column should contain the primary factor levels (e.g. WT, Mut) with optional additional columns for any secondary factors. |
|
1
76d01fe0ec36
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 58c05c0ce9334f8b9c800283cfd1f40573546edd
iuc
parents:
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changeset
|
667 |
|
76d01fe0ec36
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 58c05c0ce9334f8b9c800283cfd1f40573546edd
iuc
parents:
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changeset
|
668 Example: |
|
0
bdebdea5f6a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff
changeset
|
669 |
|
1
76d01fe0ec36
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 58c05c0ce9334f8b9c800283cfd1f40573546edd
iuc
parents:
0
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changeset
|
670 ========== ============ ========= |
|
76d01fe0ec36
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 58c05c0ce9334f8b9c800283cfd1f40573546edd
iuc
parents:
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changeset
|
671 **Sample** **Genotype** **Batch** |
|
76d01fe0ec36
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 58c05c0ce9334f8b9c800283cfd1f40573546edd
iuc
parents:
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changeset
|
672 ---------- ------------ --------- |
|
76d01fe0ec36
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 58c05c0ce9334f8b9c800283cfd1f40573546edd
iuc
parents:
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diff
changeset
|
673 WT1 WT b1 |
|
76d01fe0ec36
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 58c05c0ce9334f8b9c800283cfd1f40573546edd
iuc
parents:
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diff
changeset
|
674 WT2 WT b2 |
|
76d01fe0ec36
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 58c05c0ce9334f8b9c800283cfd1f40573546edd
iuc
parents:
0
diff
changeset
|
675 WT3 WT b3 |
|
76d01fe0ec36
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 58c05c0ce9334f8b9c800283cfd1f40573546edd
iuc
parents:
0
diff
changeset
|
676 Mut1 Mut b1 |
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76d01fe0ec36
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 58c05c0ce9334f8b9c800283cfd1f40573546edd
iuc
parents:
0
diff
changeset
|
677 Mut2 Mut b2 |
|
76d01fe0ec36
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 58c05c0ce9334f8b9c800283cfd1f40573546edd
iuc
parents:
0
diff
changeset
|
678 Mut3 Mut b3 |
|
76d01fe0ec36
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 58c05c0ce9334f8b9c800283cfd1f40573546edd
iuc
parents:
0
diff
changeset
|
679 ========== ============ ========= |
|
0
bdebdea5f6a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff
changeset
|
680 |
|
3
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents:
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changeset
|
681 *Factor Name:* The name of the experimental factor being investigated e.g. Genotype, Treatment. One factor must be entered 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, edgeR will fit an additive linear model. |
|
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents:
2
diff
changeset
|
682 |
|
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents:
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changeset
|
683 *Groups:* The names of the groups for the factor. These must be entered in the same order as the samples (to which the groups correspond) are listed in the columns of the counts matrix. Spaces must not be used and if entered into the tool form above, the values should be separated by commas. |
|
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents:
2
diff
changeset
|
684 |
|
1
76d01fe0ec36
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 58c05c0ce9334f8b9c800283cfd1f40573546edd
iuc
parents:
0
diff
changeset
|
685 |
|
0
bdebdea5f6a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff
changeset
|
686 **Contrasts of Interest:** |
|
1
76d01fe0ec36
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 58c05c0ce9334f8b9c800283cfd1f40573546edd
iuc
parents:
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687 The contrasts you wish to make between levels. |
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76d01fe0ec36
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 58c05c0ce9334f8b9c800283cfd1f40573546edd
iuc
parents:
0
diff
changeset
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688 A common contrast would be a simple difference between two levels: "Mut-WT" |
|
0
bdebdea5f6a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff
changeset
|
689 represents the difference between the mutant and wild type genotypes. |
|
3
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents:
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diff
changeset
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690 Multiple contrasts must be entered separately using the Insert Contrast button, spaces must not be used. |
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0
bdebdea5f6a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff
changeset
|
691 |
|
3
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents:
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changeset
|
692 **Filter Low Counts:** |
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38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents:
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diff
changeset
|
693 Genes with very low counts across all libraries provide little evidence for differential expression. |
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38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents:
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diff
changeset
|
694 In the biological point of view, a gene must be expressed at some minimal level before |
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38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents:
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changeset
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695 it is likely to be translated into a protein or to be biologically important. In addition, the |
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38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents:
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changeset
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696 pronounced discreteness of these counts interferes with some of the statistical approximations |
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38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents:
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changeset
|
697 that are used later in the pipeline. These genes should be filtered out prior to further |
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38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents:
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changeset
|
698 analysis. |
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38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents:
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changeset
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699 As a rule of thumb, genes are dropped if they can’t possibly be expressed in all the samples |
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38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents:
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diff
changeset
|
700 for any of the conditions. Users can set their own definition of genes being expressed. Usually |
|
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents:
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diff
changeset
|
701 a gene is required to have a count of 5-10 in a library to be considered expressed in that |
|
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents:
2
diff
changeset
|
702 library. Users should also filter with count-per-million (CPM) rather than filtering on the |
|
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents:
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diff
changeset
|
703 counts directly, as the latter does not account for differences in library sizes between samples. |
|
0
bdebdea5f6a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff
changeset
|
704 |
|
3
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents:
2
diff
changeset
|
705 Option to ignore the genes that do not show significant levels of |
|
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents:
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changeset
|
706 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: |
|
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents:
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diff
changeset
|
707 |
|
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents:
2
diff
changeset
|
708 * **Minimum CPM:** This is the minimum count per million that a gene must have in at |
|
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents:
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diff
changeset
|
709 least the number of samples specified under Minimum Samples. |
|
0
bdebdea5f6a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff
changeset
|
710 |
|
3
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents:
2
diff
changeset
|
711 * **Minimum Count:** This is the minimum count that a gene must have. It can be combined with either Filter |
|
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents:
2
diff
changeset
|
712 on Total Count or Minimum Samples. |
|
0
bdebdea5f6a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff
changeset
|
713 |
|
3
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents:
2
diff
changeset
|
714 * **Filter on Total Count:** This can be used with the Minimum Count filter to keep genes |
|
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents:
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diff
changeset
|
715 with a minimum total read count. |
|
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents:
2
diff
changeset
|
716 |
|
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents:
2
diff
changeset
|
717 * **Minimum Samples:** This is the number of samples in which the Minimum CPM/Count |
|
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents:
2
diff
changeset
|
718 requirement must be met in order for that gene to be kept. |
|
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents:
2
diff
changeset
|
719 |
|
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents:
2
diff
changeset
|
720 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 |
|
0
bdebdea5f6a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff
changeset
|
721 ensure that the sample requirement is appropriate. In the case of an experiment |
|
bdebdea5f6a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff
changeset
|
722 with two experimental groups each with two members, if there is a change from |
|
3
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents:
2
diff
changeset
|
723 insignificant CPM/count to significant CPM/count but the sample requirement is set to 3, |
|
0
bdebdea5f6a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff
changeset
|
724 then this will cause that gene to fail the criteria. When in doubt simply do not |
|
3
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents:
2
diff
changeset
|
725 filter or consult the `limma User's Guide`_ for filtering recommendations. |
|
0
bdebdea5f6a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff
changeset
|
726 |
|
3
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents:
2
diff
changeset
|
727 **Advanced Options:** |
|
0
bdebdea5f6a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff
changeset
|
728 |
|
bdebdea5f6a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff
changeset
|
729 By default error rate for multiple testing is controlled using Benjamini and |
|
bdebdea5f6a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff
changeset
|
730 Hochberg's false discovery rate control at a threshold value of 0.05. However |
|
bdebdea5f6a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff
changeset
|
731 there are options to change this to custom values. |
|
bdebdea5f6a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff
changeset
|
732 |
|
3
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents:
2
diff
changeset
|
733 * **Minimum log2-fold-change Required:** |
|
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents:
2
diff
changeset
|
734 In addition to meeting the requirement for the adjusted statistic for |
|
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents:
2
diff
changeset
|
735 multiple testing, the observation must have an absolute log2-fold-change |
|
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents:
2
diff
changeset
|
736 greater than this threshold to be considered significant, thus highlighted |
|
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents:
2
diff
changeset
|
737 in the MD plot. |
|
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents:
2
diff
changeset
|
738 |
|
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents:
2
diff
changeset
|
739 * **Adjusted Threshold:** |
|
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents:
2
diff
changeset
|
740 Set the threshold for the resulting value of the multiple testing control |
|
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents:
2
diff
changeset
|
741 method. Only observations whose statistic falls below this value is |
|
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents:
2
diff
changeset
|
742 considered significant, thus highlighted in the MD plot. |
|
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents:
2
diff
changeset
|
743 |
|
0
bdebdea5f6a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff
changeset
|
744 * **P-Value Adjustment Method:** |
|
1
76d01fe0ec36
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 58c05c0ce9334f8b9c800283cfd1f40573546edd
iuc
parents:
0
diff
changeset
|
745 Change the multiple testing control method, the options are BH(1995) and |
|
0
bdebdea5f6a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff
changeset
|
746 BY(2001) which are both false discovery rate controls. There is also |
|
bdebdea5f6a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff
changeset
|
747 Holm(1979) which is a method for family-wise error rate control. |
|
1
76d01fe0ec36
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 58c05c0ce9334f8b9c800283cfd1f40573546edd
iuc
parents:
0
diff
changeset
|
748 |
|
6
39fa12a6d885
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 60cae222b10f43f830936c19298bd723ac47e43d
iuc
parents:
5
diff
changeset
|
749 **Testing relative to a threshold (TREAT):** |
|
39fa12a6d885
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 60cae222b10f43f830936c19298bd723ac47e43d
iuc
parents:
5
diff
changeset
|
750 If there are a lot of differentially expressed genes, a fold change threshold can be applied in addition to the P-value threshold to select genes that are more likely to be biologically significant. However, ranking by P-value and discarding genes with small logFCs can increase the false discovery rate. Using the limma TREAT function performs this analysis correctly (`McCarthy and Smyth, 2009`_). |
|
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 60cae222b10f43f830936c19298bd723ac47e43d
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751 |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
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752 **Normalisation Method:** |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
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753 The most obvious technical factor that affects the read counts, other than gene expression |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
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754 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/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
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755 analysis for varying sequencing depths as represented by differing library sizes. This is |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
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756 part of the basic modeling procedure and flows automatically into fold-change or p-value |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
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757 calculations. It is always present, and doesn’t require any user intervention. |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
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758 The second most important technical influence on differential expression is one that is less |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
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759 obvious. RNA-seq provides a measure of the relative abundance of each gene in each RNA |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
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760 sample, but does not provide any measure of the total RNA output on a per-cell basis. |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
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761 This commonly becomes important when a small number of genes are very highly expressed |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
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762 in one sample, but not in another. The highly expressed genes can consume a substantial |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
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763 proportion of the total library size, causing the remaining genes to be under-sampled in that |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
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764 sample. Unless this RNA composition effect is adjusted for, the remaining genes may falsely |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
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765 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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766 |
|
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
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767 **Robust Settings** |
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768 Option to use robust settings with eBayes or TREAT, used by both limma-voom and limma-trend. Using robust settings is usually recommended to protect against outlier genes, for more information see the `limma User's Guide`_ and `Phipson et al. 2016`_. This is turned on by default. |
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769 |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
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770 **Prior Count:** |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
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771 If the limma-trend method is used, a count (`prior.count`) is added to all counts to avoid taking a log of zero, and damp down the variances of logarithms of low counts. A default of 3 is used, as recommended in the `limma User's Guide`_. |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
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772 |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
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773 **Apply Sample Weights:** |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
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774 If the limma-voom method is used, an option is available to downweight outlier samples, such that their information is still |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
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775 used in the statistical analysis but their impact is reduced. Use this |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
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776 whenever significant outliers are present. The MDS plotting tool in this package |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
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777 is useful for identifying outliers. For more information on this option see Liu et al. (2015). |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
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778 |
|
0
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|
779 |
|
1
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780 **Outputs** |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 58c05c0ce9334f8b9c800283cfd1f40573546edd
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781 |
|
3
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
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782 This tool outputs |
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783 |
|
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
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784 * 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/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
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785 * a HTML report with plots and additional information |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
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786 |
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787 Optionally, under **Output Options** you can choose to output |
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788 |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
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789 * a normalised counts table |
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4
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790 * the R script used by this tool |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
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791 * an RData file |
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1
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792 |
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793 ----- |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
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794 |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
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795 **Citations:** |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
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796 |
|
3
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797 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. |
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0
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798 |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
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799 limma |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
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800 |
|
1
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801 Please cite the paper below for the limma software itself. Please also try |
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0
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802 to cite the appropriate methodology articles that describe the statistical |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
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803 methods implemented in limma, depending on which limma functions you are |
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804 using. The methodology articles are listed in Section 2.1 of the `limma |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
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805 User's Guide`_. |
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806 |
|
1
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 58c05c0ce9334f8b9c800283cfd1f40573546edd
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807 * Smyth GK (2005). Limma: linear models for microarray data. In: |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 58c05c0ce9334f8b9c800283cfd1f40573546edd
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808 'Bioinformatics and Computational Biology Solutions using R and |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 58c05c0ce9334f8b9c800283cfd1f40573546edd
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809 Bioconductor'. R. Gentleman, V. Carey, S. Dudoit, R. Irizarry, |
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0
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810 W. Huber (eds), Springer, New York, pages 397-420. |
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811 |
|
0
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
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812 * Law CW, Chen Y, Shi W, and Smyth GK (2014). Voom: |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
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|
813 precision weights unlock linear model analysis tools for |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
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814 RNA-seq read counts. Genome Biology 15, R29. |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
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|
815 |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
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816 * Liu R, Holik AZ, Su S, Jansz N, Chen K, Leong HS, Blewitt ME, Asselin-Labat ML, Smyth GK, Ritchie ME (2015). Why weight? Modelling sample and observational level variability improves power in RNA-seq analyses. Nucleic Acids Research, 43(15), e97. |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
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817 |
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1
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818 * Ritchie, M. E., Diyagama, D., Neilson, J., van Laar, R., Dobrovic, |
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0
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819 A., Holloway, A., and Smyth, G. K. (2006). Empirical array quality weights |
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820 for microarray data. BMC Bioinformatics 7, Article 261. |
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821 |
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822 |
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823 edgeR |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
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824 |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
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825 Please cite the first paper for the software itself and the other papers for |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 58c05c0ce9334f8b9c800283cfd1f40573546edd
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826 the various original statistical methods implemented in edgeR. See |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
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827 Section 1.2 in the `edgeR User's Guide`_ for more detail. |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
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828 |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 58c05c0ce9334f8b9c800283cfd1f40573546edd
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829 * Robinson MD, McCarthy DJ and Smyth GK (2010). edgeR: a Bioconductor |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 58c05c0ce9334f8b9c800283cfd1f40573546edd
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830 package for differential expression analysis of digital gene expression |
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0
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
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831 data. Bioinformatics 26, 139-140 |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 58c05c0ce9334f8b9c800283cfd1f40573546edd
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832 |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 58c05c0ce9334f8b9c800283cfd1f40573546edd
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833 * Robinson MD and Smyth GK (2007). Moderated statistical tests for assessing |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
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834 differences in tag abundance. Bioinformatics 23, 2881-2887 |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 58c05c0ce9334f8b9c800283cfd1f40573546edd
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835 |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 58c05c0ce9334f8b9c800283cfd1f40573546edd
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836 * Robinson MD and Smyth GK (2008). Small-sample estimation of negative |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
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837 binomial dispersion, with applications to SAGE data. |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
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838 Biostatistics, 9, 321-332 |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 58c05c0ce9334f8b9c800283cfd1f40573546edd
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839 |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 58c05c0ce9334f8b9c800283cfd1f40573546edd
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840 * McCarthy DJ, Chen Y and Smyth GK (2012). Differential expression analysis |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 58c05c0ce9334f8b9c800283cfd1f40573546edd
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841 of multifactor RNA-Seq experiments with respect to biological variation. |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
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842 Nucleic Acids Research 40, 4288-4297 |
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843 |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
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844 Please report problems or suggestions to: su.s@wehi.edu.au |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
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845 |
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846 .. _limma: http://www.bioconductor.org/packages/release/bioc/html/limma.html |
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847 .. _limma approach: https://www.ncbi.nlm.nih.gov/pubmed/25605792 |
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848 .. _limma User's Guide: http://bioconductor.org/packages/release/bioc/vignettes/limma/inst/doc/usersguide.pdf |
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849 .. _edgeR: http://www.bioconductor.org/packages/release/bioc/html/edgeR.html |
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3
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
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850 .. _edgeR User's Guide: https://bioconductor.org/packages/release/bioc/vignettes/edgeR/inst/doc/edgeRUsersGuide.pdf |
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851 .. _McCarthy and Smyth, 2009: https://www.ncbi.nlm.nih.gov/pubmed/19176553 |
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852 .. _Phipson et al. 2016: https://www.ncbi.nlm.nih.gov/pubmed/28367255 |
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853 ]]></help> |
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854 <citations> |
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855 <citation type="doi">10.1186/gb-2014-15-2-r29</citation> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
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856 <citation type="doi">10.1093/nar/gkv412</citation> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
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857 </citations> |
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858 </tool> |