Mercurial > repos > iuc > limma_voom
annotate limma_voom.xml @ 26:119b069fc845 draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit b4d788c0f159d507159117a063b1f867b243c738
| author | iuc |
|---|---|
| date | Fri, 09 Feb 2024 17:06:25 +0000 |
| parents | d6f5fa4ee473 |
| children |
| rev | line source |
|---|---|
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26
119b069fc845
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit b4d788c0f159d507159117a063b1f867b243c738
iuc
parents:
25
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changeset
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1 <tool id="limma_voom" name="limma" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@"> |
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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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0
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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e827f9aae031
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 38cf93fd693c810b4150c5d8aa3763aebc988b07"
iuc
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5 <macros> |
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26
119b069fc845
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit b4d788c0f159d507159117a063b1f867b243c738
iuc
parents:
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changeset
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6 <token name="@TOOL_VERSION@">3.58.1</token> |
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119b069fc845
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit b4d788c0f159d507159117a063b1f867b243c738
iuc
parents:
25
diff
changeset
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7 <token name="@VERSION_SUFFIX@">0</token> |
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119b069fc845
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit b4d788c0f159d507159117a063b1f867b243c738
iuc
parents:
25
diff
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8 <token name="@PROFILE@">23.0</token> |
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23
e827f9aae031
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 38cf93fd693c810b4150c5d8aa3763aebc988b07"
iuc
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9 </macros> |
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21
58c35179ebf0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 127882bd6729d92500ce2a7a51eb5f8949a4c2b5"
iuc
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10 <edam_topics> |
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58c35179ebf0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 127882bd6729d92500ce2a7a51eb5f8949a4c2b5"
iuc
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11 <edam_topic>topic_3308</edam_topic> |
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58c35179ebf0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 127882bd6729d92500ce2a7a51eb5f8949a4c2b5"
iuc
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12 </edam_topics> |
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58c35179ebf0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 127882bd6729d92500ce2a7a51eb5f8949a4c2b5"
iuc
parents:
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13 <edam_operations> |
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58c35179ebf0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 127882bd6729d92500ce2a7a51eb5f8949a4c2b5"
iuc
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14 <edam_operation>operation_3563</edam_operation> |
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58c35179ebf0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 127882bd6729d92500ce2a7a51eb5f8949a4c2b5"
iuc
parents:
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changeset
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15 <edam_operation>operation_3223</edam_operation> |
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58c35179ebf0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 127882bd6729d92500ce2a7a51eb5f8949a4c2b5"
iuc
parents:
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16 </edam_operations> |
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26
119b069fc845
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit b4d788c0f159d507159117a063b1f867b243c738
iuc
parents:
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changeset
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17 <xrefs> |
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119b069fc845
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit b4d788c0f159d507159117a063b1f867b243c738
iuc
parents:
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changeset
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18 <xref type="bio.tools">limma</xref> |
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119b069fc845
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit b4d788c0f159d507159117a063b1f867b243c738
iuc
parents:
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changeset
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19 <xref type="bioconductor">limma</xref> |
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119b069fc845
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit b4d788c0f159d507159117a063b1f867b243c738
iuc
parents:
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changeset
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20 </xrefs> |
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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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21 |
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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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22 <requirements> |
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e827f9aae031
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 38cf93fd693c810b4150c5d8aa3763aebc988b07"
iuc
parents:
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23 <requirement type="package" version="@TOOL_VERSION@">bioconductor-limma</requirement> |
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119b069fc845
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit b4d788c0f159d507159117a063b1f867b243c738
iuc
parents:
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diff
changeset
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24 <requirement type="package" version="4.0.2">bioconductor-edger</requirement> |
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119b069fc845
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit b4d788c0f159d507159117a063b1f867b243c738
iuc
parents:
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changeset
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25 <requirement type="package" version="1.5.0">r-statmod</requirement> |
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119b069fc845
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit b4d788c0f159d507159117a063b1f867b243c738
iuc
parents:
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diff
changeset
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26 <requirement type="package" version="1.3.0">r-scales</requirement> |
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25
d6f5fa4ee473
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 55ecaab6d53c6a3f0769f802a4d68a45291f51e9"
iuc
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27 <requirement type="package" version="0.2.21">r-rjson</requirement> |
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26
119b069fc845
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit b4d788c0f159d507159117a063b1f867b243c738
iuc
parents:
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diff
changeset
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28 <requirement type="package" version="1.20.4">r-getopt</requirement> |
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119b069fc845
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit b4d788c0f159d507159117a063b1f867b243c738
iuc
parents:
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diff
changeset
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29 <requirement type="package" version="3.1.3.1">r-gplots</requirement> |
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119b069fc845
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit b4d788c0f159d507159117a063b1f867b243c738
iuc
parents:
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diff
changeset
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30 <requirement type="package" version="2.12.0">bioconductor-glimma</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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31 </requirements> |
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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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32 |
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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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33 <version_command><![CDATA[ |
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4255881bebb1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 5f8052ab47b789da5ea47feb48e1b8e08b5fc1e0
iuc
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34 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: ")", Glimma version" $(R --vanilla --slave -e "library(Glimma); cat(sessionInfo()\$otherPkgs\$Glimma\$Version)" 2> /dev/null | grep -v -i "WARNING: ") |
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1
76d01fe0ec36
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 58c05c0ce9334f8b9c800283cfd1f40573546edd
iuc
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35 ]]></version_command> |
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76d01fe0ec36
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 58c05c0ce9334f8b9c800283cfd1f40573546edd
iuc
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36 |
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76d01fe0ec36
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 58c05c0ce9334f8b9c800283cfd1f40573546edd
iuc
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37 <command detect_errors="exit_code"><![CDATA[ |
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3
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
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38 #import json |
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1
76d01fe0ec36
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 58c05c0ce9334f8b9c800283cfd1f40573546edd
iuc
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39 Rscript '$__tool_directory__/limma_voom.R' |
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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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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 -R '$outReport' |
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38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
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42 -o '$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
parents:
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43 |
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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 #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
parents:
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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 ## 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
parents:
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47 #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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48 #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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49 #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
parents:
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50 #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
parents:
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51 #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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52 #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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53 $count_files.append(str($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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54 #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
parents:
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55 $temp_factor.append( {str($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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56 #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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57 |
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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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58 $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
parents:
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59 $temp_factor_names.append([str($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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60 #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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61 -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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62 |
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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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63 #elif $input.format=="matrix": |
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38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
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64 -m '$input.counts' |
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38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
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65 #if $input.fact.ffile=='yes': |
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38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
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66 -f '$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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67 #else: |
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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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68 -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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69 #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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70 #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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71 |
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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
|
72 #if $anno.annoOpt=='yes': |
|
3
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents:
2
diff
changeset
|
73 -a '$anno.geneanno' |
|
1
76d01fe0ec36
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 58c05c0ce9334f8b9c800283cfd1f40573546edd
iuc
parents:
0
diff
changeset
|
74 #end if |
|
76d01fe0ec36
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 58c05c0ce9334f8b9c800283cfd1f40573546edd
iuc
parents:
0
diff
changeset
|
75 |
|
19
c9c6427edfe9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 4c0406815cb76175d7d90b2874310635694126f5
iuc
parents:
18
diff
changeset
|
76 #if $cont.cfile=='yes': |
|
c9c6427edfe9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 4c0406815cb76175d7d90b2874310635694126f5
iuc
parents:
18
diff
changeset
|
77 -C '$cont.cinfo' |
|
c9c6427edfe9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 4c0406815cb76175d7d90b2874310635694126f5
iuc
parents:
18
diff
changeset
|
78 #else: |
|
c9c6427edfe9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 4c0406815cb76175d7d90b2874310635694126f5
iuc
parents:
18
diff
changeset
|
79 -D '${ ','.join( ['%s' % $x.contrast for x in $cont.rep_contrast] ) }' |
|
c9c6427edfe9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 4c0406815cb76175d7d90b2874310635694126f5
iuc
parents:
18
diff
changeset
|
80 #end if |
|
1
76d01fe0ec36
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 58c05c0ce9334f8b9c800283cfd1f40573546edd
iuc
parents:
0
diff
changeset
|
81 |
|
3
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents:
2
diff
changeset
|
82 #if $f.filt.filt_select == 'yes': |
|
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents:
2
diff
changeset
|
83 #if $f.filt.cformat.format_select == 'cpm': |
|
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents:
2
diff
changeset
|
84 -c '$f.filt.cformat.cpmReq' |
|
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents:
2
diff
changeset
|
85 -s '$f.filt.cformat.cpmSampleReq' |
|
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents:
2
diff
changeset
|
86 #elif $f.filt.cformat.format_select == 'counts': |
|
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents:
2
diff
changeset
|
87 -z '$f.filt.cformat.cntReq' |
|
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents:
2
diff
changeset
|
88 #if $f.filt.cformat.samples.count_select == 'total': |
|
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents:
2
diff
changeset
|
89 -y |
|
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents:
2
diff
changeset
|
90 #elif $f.filt.cformat.samples.count_select == 'sample': |
|
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents:
2
diff
changeset
|
91 -s '$f.filt.cformat.samples.cntSampleReq' |
|
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents:
2
diff
changeset
|
92 #end if |
|
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents:
2
diff
changeset
|
93 #end if |
|
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents:
2
diff
changeset
|
94 #end if |
|
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents:
2
diff
changeset
|
95 |
|
8
00a42b66e522
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents:
7
diff
changeset
|
96 #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
|
97 -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
|
98 #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
|
99 |
|
12
81796eb60bd0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 33651907e4d5d6672537b80142c022d2b4951e8c
iuc
parents:
11
diff
changeset
|
100 #if $out.filtCounts: |
|
81796eb60bd0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 33651907e4d5d6672537b80142c022d2b4951e8c
iuc
parents:
11
diff
changeset
|
101 -F |
|
81796eb60bd0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 33651907e4d5d6672537b80142c022d2b4951e8c
iuc
parents:
11
diff
changeset
|
102 #end if |
|
81796eb60bd0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 33651907e4d5d6672537b80142c022d2b4951e8c
iuc
parents:
11
diff
changeset
|
103 |
|
3
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents:
2
diff
changeset
|
104 #if $out.normCounts: |
|
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents:
2
diff
changeset
|
105 -x |
|
1
76d01fe0ec36
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 58c05c0ce9334f8b9c800283cfd1f40573546edd
iuc
parents:
0
diff
changeset
|
106 #end if |
|
0
bdebdea5f6a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff
changeset
|
107 |
|
11
7e8af58c8052
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 4bcbd83574ecf7194f3370aa883a9573563afdbc
iuc
parents:
10
diff
changeset
|
108 #if $out.libinfo: |
|
7e8af58c8052
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 4bcbd83574ecf7194f3370aa883a9573563afdbc
iuc
parents:
10
diff
changeset
|
109 -L |
|
7e8af58c8052
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 4bcbd83574ecf7194f3370aa883a9573563afdbc
iuc
parents:
10
diff
changeset
|
110 #end if |
|
7e8af58c8052
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 4bcbd83574ecf7194f3370aa883a9573563afdbc
iuc
parents:
10
diff
changeset
|
111 |
|
3
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents:
2
diff
changeset
|
112 #if $out.rdaOption: |
|
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents:
2
diff
changeset
|
113 -r |
|
1
76d01fe0ec36
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 58c05c0ce9334f8b9c800283cfd1f40573546edd
iuc
parents:
0
diff
changeset
|
114 #end if |
|
76d01fe0ec36
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 58c05c0ce9334f8b9c800283cfd1f40573546edd
iuc
parents:
0
diff
changeset
|
115 |
|
11
7e8af58c8052
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 4bcbd83574ecf7194f3370aa883a9573563afdbc
iuc
parents:
10
diff
changeset
|
116 |
|
3
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents:
2
diff
changeset
|
117 -l '$adv.lfc' |
|
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents:
2
diff
changeset
|
118 -p '$adv.pVal' |
|
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents:
2
diff
changeset
|
119 -d '$adv.pAdjust' |
|
7
e6a4ff41af6b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit cf399638ebca4250bcc15f468238a9964de97b33
iuc
parents:
6
diff
changeset
|
120 -G '$adv.topgenes' |
|
6
39fa12a6d885
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 60cae222b10f43f830936c19298bd723ac47e43d
iuc
parents:
5
diff
changeset
|
121 #if $adv.treat: |
|
39fa12a6d885
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 60cae222b10f43f830936c19298bd723ac47e43d
iuc
parents:
5
diff
changeset
|
122 -T |
|
39fa12a6d885
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 60cae222b10f43f830936c19298bd723ac47e43d
iuc
parents:
5
diff
changeset
|
123 #end if |
|
0
bdebdea5f6a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff
changeset
|
124 |
|
3
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents:
2
diff
changeset
|
125 #if $deMethod.de_select == 'voom': |
|
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents:
2
diff
changeset
|
126 #if $deMethod.weightOption: |
|
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents:
2
diff
changeset
|
127 -w |
|
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents:
2
diff
changeset
|
128 #end if |
|
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents:
2
diff
changeset
|
129 #elif $deMethod.de_select == 'trend': |
|
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents:
2
diff
changeset
|
130 -t $deMethod.prior_count |
|
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents:
2
diff
changeset
|
131 #end if |
|
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents:
2
diff
changeset
|
132 |
|
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents:
2
diff
changeset
|
133 -n '$adv.normalisationOption' |
|
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents:
2
diff
changeset
|
134 |
|
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents:
2
diff
changeset
|
135 #if $adv.robOption: |
|
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents:
2
diff
changeset
|
136 -b |
|
1
76d01fe0ec36
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 58c05c0ce9334f8b9c800283cfd1f40573546edd
iuc
parents:
0
diff
changeset
|
137 #end if |
|
0
bdebdea5f6a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff
changeset
|
138 |
|
1
76d01fe0ec36
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 58c05c0ce9334f8b9c800283cfd1f40573546edd
iuc
parents:
0
diff
changeset
|
139 && |
|
76d01fe0ec36
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 58c05c0ce9334f8b9c800283cfd1f40573546edd
iuc
parents:
0
diff
changeset
|
140 mkdir ./output_dir |
|
76d01fe0ec36
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 58c05c0ce9334f8b9c800283cfd1f40573546edd
iuc
parents:
0
diff
changeset
|
141 |
|
76d01fe0ec36
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 58c05c0ce9334f8b9c800283cfd1f40573546edd
iuc
parents:
0
diff
changeset
|
142 && |
|
14
3133e833b3ce
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit c915bd7e68cb3a2944397aaf184c2b1db97cb3a5
iuc
parents:
13
diff
changeset
|
143 cp '$outReport.files_path'/*tsv output_dir/ |
|
3133e833b3ce
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit c915bd7e68cb3a2944397aaf184c2b1db97cb3a5
iuc
parents:
13
diff
changeset
|
144 |
|
3133e833b3ce
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit c915bd7e68cb3a2944397aaf184c2b1db97cb3a5
iuc
parents:
13
diff
changeset
|
145 #if 'i' in str($out.plots).split( "," ): |
|
3133e833b3ce
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit c915bd7e68cb3a2944397aaf184c2b1db97cb3a5
iuc
parents:
13
diff
changeset
|
146 && cp -r ./glimma* '$outReport.files_path' |
|
9
4255881bebb1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 5f8052ab47b789da5ea47feb48e1b8e08b5fc1e0
iuc
parents:
8
diff
changeset
|
147 #end if |
|
13
d5a940112511
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 8560b34a261fde200bd77dc2e817d55d386ac811
iuc
parents:
12
diff
changeset
|
148 |
|
d5a940112511
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 8560b34a261fde200bd77dc2e817d55d386ac811
iuc
parents:
12
diff
changeset
|
149 #if $out.filtCounts or $out.normCounts: |
|
d5a940112511
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 8560b34a261fde200bd77dc2e817d55d386ac811
iuc
parents:
12
diff
changeset
|
150 && cp '$outReport.files_path'/*counts output_dir/ |
|
d5a940112511
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 8560b34a261fde200bd77dc2e817d55d386ac811
iuc
parents:
12
diff
changeset
|
151 #end if |
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d5a940112511
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 8560b34a261fde200bd77dc2e817d55d386ac811
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152 |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
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153 #if $out.rscript: |
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154 && cp '$__tool_directory__/limma_voom.R' '$rscript' |
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155 #end if |
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156 ]]></command> |
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157 |
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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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158 <inputs> |
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159 |
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160 <!-- DE Method Option --> |
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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 <conditional name="deMethod"> |
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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 <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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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
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163 <option value="voom" selected="True">limma-voom</option> |
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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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164 <option value="trend">limma-trend</option> |
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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> |
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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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166 <when value="voom"> |
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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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167 <param name="weightOption" type="boolean" truevalue="1" falsevalue="0" checked="false" label="Apply voom with sample quality 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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168 help="Apply weights if outliers are present (voomWithQualityWeights). Default: False."> |
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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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169 </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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170 </when> |
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171 <when value="trend"> |
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172 <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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173 </when> |
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174 </conditional> |
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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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175 <!-- Counts and Factors --> |
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176 <conditional name="input"> |
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177 <param name="format" type="select" label="Count Files or Matrix?" |
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178 help="You can choose to input either separate count files (one per sample) or a single count 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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179 <option value="files">Separate Count Files</option> |
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180 <option value="matrix">Single Count Matrix</option> |
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181 </param> |
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182 |
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183 <when value="files"> |
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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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184 <repeat name="rep_factor" title="Factor" min="1"> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 42b1160a549a85c87ed5226a83b55c4e44648597
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185 <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."> |
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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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186 <sanitizer> |
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187 <valid initial="string.letters,string.digits"><add value="_" /></valid> |
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188 </sanitizer> |
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189 </param> |
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190 <repeat name="rep_group" title="Group" min="2" default="2"> |
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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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191 <param name="groupName" type="text" label="Name" |
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192 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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193 <sanitizer> |
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194 <valid initial="string.letters,string.digits"><add value="_" /></valid> |
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195 </sanitizer> |
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196 </param> |
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197 <param name="countsFile" type="data" format="tabular" multiple="true" label="Counts files"/> |
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198 </repeat> |
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199 </repeat> |
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200 </when> |
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201 |
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202 <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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203 <param name="counts" type="data" format="tabular" label="Count Matrix"/> |
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204 |
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205 <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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206 <param name="ffile" type="select" label="Input factor information from file?" |
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207 help="You can choose to input the factor and group information for the samples from a file or manually enter below. NOTE: Please only use letters, numbers or underscores (case sensitive), the group names MUST not contain hyphens."> |
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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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208 <option value="no">No</option> |
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209 <option value="yes">Yes</option> |
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210 </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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211 <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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212 <param name="finfo" type="data" format="tabular" label="Factor File"/> |
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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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213 </when> |
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214 <when value="no" > |
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215 <repeat name="rep_factor" title="Factor" min="1"> |
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216 <param name="factorName" type="text" label="Factor Name" |
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17
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217 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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3
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
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218 <validator type="empty_field" /> |
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219 <validator type="regex" message="Please only use letters, numbers or underscores">^[\w]+$</validator> |
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220 </param> |
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221 <param name="groupNames" type="text" label="Groups" |
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17
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222 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), the group names MUST not contain hyphens."> |
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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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223 <validator type="empty_field" /> |
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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 <validator type="regex" message="Please only use letters, numbers or underscores, and separate levels by commas">^[\w,]+$</validator> |
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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 </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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226 </repeat> |
|
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
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227 </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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228 </conditional> |
|
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
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229 </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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230 </conditional> |
|
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
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231 |
|
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
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232 <!-- Gene Annotations --> |
|
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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233 <conditional name="anno"> |
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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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234 <param name="annoOpt" type="select" label="Use Gene Annotations?" |
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14
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit c915bd7e68cb3a2944397aaf184c2b1db97cb3a5
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235 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. Interactive Glimma Volcano and MD plots will also be generated. See Help section below."> |
|
0
bdebdea5f6a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
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236 <option value="no">No</option> |
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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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237 <option value="yes">Yes</option> |
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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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238 </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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239 <when value="yes"> |
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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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240 <param name="geneanno" type="data" format="tabular" label="Gene Annotations"/> |
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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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241 </when> |
|
bdebdea5f6a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
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242 <when value="no" /> |
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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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243 </conditional> |
|
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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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244 |
|
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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245 <!-- Contrasts --> |
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19
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 4c0406815cb76175d7d90b2874310635694126f5
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246 <conditional name="cont"> |
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c9c6427edfe9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 4c0406815cb76175d7d90b2874310635694126f5
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247 <param name="cfile" type="select" label="Input Contrast information from file?" |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 4c0406815cb76175d7d90b2874310635694126f5
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248 help="You can choose to input the contrast information for the samples from a file or manually enter below. NOTE: Please only use letters, numbers or underscores (case sensitive), the group names MUST not contain hyphens. Use a hyphen to separate the groups you want to compare, as shown in the Help section below."> |
|
c9c6427edfe9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 4c0406815cb76175d7d90b2874310635694126f5
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249 <option value="no">No</option> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 4c0406815cb76175d7d90b2874310635694126f5
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250 <option value="yes">Yes</option> |
|
0
bdebdea5f6a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
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251 </param> |
|
19
c9c6427edfe9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 4c0406815cb76175d7d90b2874310635694126f5
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252 <when value="yes"> |
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c9c6427edfe9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 4c0406815cb76175d7d90b2874310635694126f5
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253 <param name="cinfo" type="data" format="tabular" label="Contrasts File"/> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 4c0406815cb76175d7d90b2874310635694126f5
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254 </when> |
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c9c6427edfe9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 4c0406815cb76175d7d90b2874310635694126f5
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255 <when value="no" > |
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c9c6427edfe9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 4c0406815cb76175d7d90b2874310635694126f5
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256 <repeat name="rep_contrast" title="Contrast" min="1" default="1"> |
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c9c6427edfe9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 4c0406815cb76175d7d90b2874310635694126f5
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257 <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-Ctrl1)-(Mut2-Ctrl2). 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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c9c6427edfe9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 4c0406815cb76175d7d90b2874310635694126f5
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258 <validator type="empty_field" /> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 4c0406815cb76175d7d90b2874310635694126f5
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259 <validator type="regex" message="Please only use letters, numbers or underscores">^[\(\w\)-]+$</validator> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 4c0406815cb76175d7d90b2874310635694126f5
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260 </param> |
|
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 4c0406815cb76175d7d90b2874310635694126f5
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261 </repeat> |
|
c9c6427edfe9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 4c0406815cb76175d7d90b2874310635694126f5
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262 </when> |
|
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 4c0406815cb76175d7d90b2874310635694126f5
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263 </conditional> |
|
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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264 |
|
3
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
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265 <!-- Filter Options --> |
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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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266 <section name="f" expanded="false" title="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
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267 <conditional name="filt"> |
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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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268 <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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38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
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269 <option value="no" selected="true">No</option> |
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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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270 <option value="yes">Yes</option> |
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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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271 </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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272 <when value="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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273 <conditional name="cformat"> |
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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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274 <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. "> |
|
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
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275 <option value="cpm">CPM</option> |
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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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276 <option value="counts">Counts</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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277 </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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278 <when value="cpm"> |
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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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279 <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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23
e827f9aae031
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 38cf93fd693c810b4150c5d8aa3763aebc988b07"
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280 <param name="cpmSampleReq" type="integer" value="0" min="0" label="Minimum Samples" |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 38cf93fd693c810b4150c5d8aa3763aebc988b07"
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281 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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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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282 </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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283 <when value="counts"> |
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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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284 <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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38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
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285 <conditional name="samples"> |
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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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286 <param name="count_select" type="select" label="Filter on Total Count or per Sample Count values?" > |
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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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287 <option value="total">Total</option> |
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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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288 <option value="sample">Sample</option> |
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289 </param> |
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23
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 38cf93fd693c810b4150c5d8aa3763aebc988b07"
iuc
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290 <when value="total"/> |
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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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291 <when value="sample"> |
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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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292 <param name="cntSampleReq" type="integer" value="0" min="0" label="Minimum Samples" |
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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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293 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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38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
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294 </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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295 </conditional> |
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296 </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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297 </conditional> |
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298 </when> |
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299 <when value="no" /> |
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iuc
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300 </conditional> |
|
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301 </section> |
|
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302 |
|
3
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303 <!-- Output Options --> |
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304 <section name="out" expanded="false" title="Output Options"> |
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305 <param name="plots" type="select" display="checkboxes" multiple="True" optional="True" label="Additional Plots" help="Select additional plots to output in the report"> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit c915bd7e68cb3a2944397aaf184c2b1db97cb3a5
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306 <option value="i" selected="True">Glimma Interactive Plots</option> |
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8
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307 <option value="d">Density Plots (if filtering)</option> |
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308 <option value="c">CpmsVsCounts Plots (if filtering on cpms)</option> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
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309 <option value="b">Box Plots (if normalising)</option> |
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310 <option value="x">MDS Extra (Dims 2vs3 and 3vs4)</option> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
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311 <option value="m">MD Plots for individual samples</option> |
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00a42b66e522
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312 <option value="h">Heatmaps (top DE genes) </option> |
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313 <option value="s">Stripcharts (top DE genes)</option> |
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314 </param> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 33651907e4d5d6672537b80142c022d2b4951e8c
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315 <param name="filtCounts" type="boolean" truevalue="1" falsevalue="0" checked="false" |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 33651907e4d5d6672537b80142c022d2b4951e8c
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316 label="Output Filtered Counts Table?" |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 33651907e4d5d6672537b80142c022d2b4951e8c
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317 help="Output a file containing the raw filtered counts if Filter Low Counts is selected. Default: No"> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 33651907e4d5d6672537b80142c022d2b4951e8c
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318 </param> |
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3
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319 <param name="normCounts" type="boolean" truevalue="1" falsevalue="0" checked="false" |
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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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320 label="Output Normalised Counts Table?" |
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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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321 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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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 58c05c0ce9334f8b9c800283cfd1f40573546edd
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322 </param> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 4bcbd83574ecf7194f3370aa883a9573563afdbc
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323 <param name="libinfo" type="boolean" truevalue="1" falsevalue="0" checked="false" |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 4bcbd83574ecf7194f3370aa883a9573563afdbc
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324 label="Output Library information file?" |
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325 help="Output a tabular file showing the library sizes, normalisation factors and effective library sizes for the samples. Default: No"> |
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7e8af58c8052
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 4bcbd83574ecf7194f3370aa883a9573563afdbc
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326 </param> |
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4
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
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327 <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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3
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
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328 <param name="rdaOption" type="boolean" truevalue="1" falsevalue="0" checked="false" |
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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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329 label="Output RData file?" |
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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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330 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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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
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331 </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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332 </section> |
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333 |
|
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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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334 <!-- Advanced Options --> |
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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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335 <section name="adv" expanded="false" title="Advanced Options"> |
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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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336 <param name="lfc" type="float" value="0" min="0" |
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337 label="Minimum Log2 Fold Change" |
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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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338 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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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
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339 <param name="pVal" type="float" value="0.05" min="0" max="1" |
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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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340 label="P-Value Adjusted Threshold" |
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341 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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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
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342 <param name="pAdjust" type="select" label="P-Value Adjustment Method" help="Default: BH"> |
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343 <option value="BH" selected="true">Benjamini and Hochberg (1995)</option> |
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344 <option value="BY">Benjamini and Yekutieli (2001)</option> |
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345 <option value="holm">Holm (1979)</option> |
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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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346 <option value="none">None</option> |
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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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347 </param> |
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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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348 <param name="treat" type="boolean" truevalue="1" falsevalue="0" checked="False" |
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349 label="Test significance relative to a fold-change threshold (TREAT)" |
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350 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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8
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351 <param name="topgenes" type="integer" value="10" min="0" max="100" |
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352 label="Number of genes to highlight in Volcano plot, Heatmap and Stripcharts" |
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353 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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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
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354 <param name="normalisationOption" type="select" label="Normalisation Method" help="Default: TMM"> |
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355 <option value="TMM" selected="true">TMM</option> |
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356 <option value="RLE">RLE</option> |
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357 <option value="upperquartile">Upperquartile</option> |
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358 <option value="none">None (Don't normalise)</option> |
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359 </param> |
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360 <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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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
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361 </section> |
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0
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362 |
|
bdebdea5f6a7
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363 </inputs> |
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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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364 |
|
0
bdebdea5f6a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
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365 <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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366 <data name="outReport" format="html" label="${tool.name} on ${on_string}: Report" /> |
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13
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367 <collection name="outTables" type="list" label="${tool.name} on ${on_string}: DE tables"> |
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0
bdebdea5f6a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
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368 <discover_datasets pattern="(?P<name>.+)\.tsv$" format="tabular" directory="output_dir" visible="false" /> |
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369 </collection> |
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13
d5a940112511
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 8560b34a261fde200bd77dc2e817d55d386ac811
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370 <data name="outFilt" format="tabular" from_work_dir="output_dir/*_filtcounts" label="${tool.name} on ${on_string}: Filtered counts"> |
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371 <filter>out['filtCounts']</filter> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 8560b34a261fde200bd77dc2e817d55d386ac811
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372 </data> |
|
d5a940112511
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 8560b34a261fde200bd77dc2e817d55d386ac811
iuc
parents:
12
diff
changeset
|
373 <data name="outNorm" format="tabular" from_work_dir="output_dir/*_normcounts" label="${tool.name} on ${on_string}: Normalised counts"> |
|
d5a940112511
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 8560b34a261fde200bd77dc2e817d55d386ac811
iuc
parents:
12
diff
changeset
|
374 <filter>out['normCounts']</filter> |
|
d5a940112511
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 8560b34a261fde200bd77dc2e817d55d386ac811
iuc
parents:
12
diff
changeset
|
375 </data> |
|
4
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
3
diff
changeset
|
376 <data name="rscript" format="txt" label="${tool.name} on ${on_string}: Rscript"> |
|
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
3
diff
changeset
|
377 <filter>out['rscript']</filter> |
|
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
3
diff
changeset
|
378 </data> |
|
11
7e8af58c8052
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 4bcbd83574ecf7194f3370aa883a9573563afdbc
iuc
parents:
10
diff
changeset
|
379 <data name="libinfo" format="tabular" from_work_dir="libsizeinfo" label="${tool.name} on ${on_string}: Library information"> |
|
7e8af58c8052
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 4bcbd83574ecf7194f3370aa883a9573563afdbc
iuc
parents:
10
diff
changeset
|
380 <filter>out['libinfo']</filter> |
|
7e8af58c8052
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 4bcbd83574ecf7194f3370aa883a9573563afdbc
iuc
parents:
10
diff
changeset
|
381 </data> |
|
0
bdebdea5f6a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff
changeset
|
382 </outputs> |
|
bdebdea5f6a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff
changeset
|
383 |
|
bdebdea5f6a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff
changeset
|
384 <tests> |
|
3
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents:
2
diff
changeset
|
385 <!-- Ensure report is output --> |
|
17
86b3df7db58b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 42b1160a549a85c87ed5226a83b55c4e44648597
iuc
parents:
16
diff
changeset
|
386 <test expect_num_outputs="2"> |
|
3
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="format" value="matrix" /> |
|
0
bdebdea5f6a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff
changeset
|
388 <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
|
389 <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
|
390 <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
|
391 <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
|
392 </repeat> |
|
19
c9c6427edfe9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 4c0406815cb76175d7d90b2874310635694126f5
iuc
parents:
18
diff
changeset
|
393 <param name="cfile" value="no" /> |
|
3
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents:
2
diff
changeset
|
394 <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
|
395 <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
|
396 </repeat> |
|
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents:
2
diff
changeset
|
397 <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
|
398 <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
|
399 </repeat> |
|
0
bdebdea5f6a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff
changeset
|
400 <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
|
401 <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
|
402 <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
|
403 <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
|
404 <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
|
405 <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
|
406 <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
|
407 </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
|
408 </element> |
|
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
3
diff
changeset
|
409 <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
|
410 <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
|
411 <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
|
412 <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
|
413 </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
|
414 </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
|
415 </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
|
416 <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
|
417 <assert_contents> |
|
3
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents:
2
diff
changeset
|
418 <has_text text="Limma Analysis Output" /> |
|
14
3133e833b3ce
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit c915bd7e68cb3a2944397aaf184c2b1db97cb3a5
iuc
parents:
13
diff
changeset
|
419 <has_text text="Glimma Interactive Results" /> |
|
0
bdebdea5f6a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff
changeset
|
420 <not_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
|
421 </assert_contents> |
|
1
76d01fe0ec36
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 58c05c0ce9334f8b9c800283cfd1f40573546edd
iuc
parents:
0
diff
changeset
|
422 </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
|
423 </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
|
424 <!-- Ensure annotation file input works --> |
|
17
86b3df7db58b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 42b1160a549a85c87ed5226a83b55c4e44648597
iuc
parents:
16
diff
changeset
|
425 <test expect_num_outputs="2"> |
|
3
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents:
2
diff
changeset
|
426 <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
parents:
diff
changeset
|
427 <param name="annoOpt" value="yes" /> |
|
bdebdea5f6a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff
changeset
|
428 <param name="geneanno" value="anno.txt" /> |
|
bdebdea5f6a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff
changeset
|
429 <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
|
430 <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
|
431 <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
|
432 <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
|
433 </repeat> |
|
19
c9c6427edfe9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 4c0406815cb76175d7d90b2874310635694126f5
iuc
parents:
18
diff
changeset
|
434 <param name="cfile" value="no" /> |
|
3
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents:
2
diff
changeset
|
435 <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
|
436 <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
|
437 </repeat> |
|
0
bdebdea5f6a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff
changeset
|
438 <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
|
439 <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
|
440 <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
|
441 <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
|
442 <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
|
443 <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
|
444 <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
|
445 </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
|
446 </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
|
447 </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
|
448 </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
|
449 <!-- Ensure Rscript and RData file can be output --> |
|
17
86b3df7db58b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 42b1160a549a85c87ed5226a83b55c4e44648597
iuc
parents:
16
diff
changeset
|
450 <test expect_num_outputs="3"> |
|
3
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="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
|
452 <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
|
453 <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
|
454 <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
|
455 <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
|
456 <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
|
457 <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
|
458 </repeat> |
|
19
c9c6427edfe9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 4c0406815cb76175d7d90b2874310635694126f5
iuc
parents:
18
diff
changeset
|
459 <param name="cfile" value="no" /> |
|
3
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents:
2
diff
changeset
|
460 <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
|
461 <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
|
462 </repeat> |
|
0
bdebdea5f6a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff
changeset
|
463 <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
|
464 <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
|
465 <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
|
466 <assert_contents> |
|
bdebdea5f6a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff
changeset
|
467 <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
|
468 </assert_contents> |
|
bdebdea5f6a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff
changeset
|
469 </output> |
|
9
4255881bebb1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 5f8052ab47b789da5ea47feb48e1b8e08b5fc1e0
iuc
parents:
8
diff
changeset
|
470 <output name="rscript"> |
|
4255881bebb1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 5f8052ab47b789da5ea47feb48e1b8e08b5fc1e0
iuc
parents:
8
diff
changeset
|
471 <assert_contents> |
|
4255881bebb1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 5f8052ab47b789da5ea47feb48e1b8e08b5fc1e0
iuc
parents:
8
diff
changeset
|
472 <has_text_matching expression="Task run time" /> |
|
4255881bebb1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 5f8052ab47b789da5ea47feb48e1b8e08b5fc1e0
iuc
parents:
8
diff
changeset
|
473 </assert_contents> |
|
4255881bebb1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 5f8052ab47b789da5ea47feb48e1b8e08b5fc1e0
iuc
parents:
8
diff
changeset
|
474 </output> |
|
0
bdebdea5f6a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff
changeset
|
475 </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
|
476 <!-- Ensure secondary factors work --> |
|
17
86b3df7db58b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 42b1160a549a85c87ed5226a83b55c4e44648597
iuc
parents:
16
diff
changeset
|
477 <test expect_num_outputs="2"> |
|
3
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents:
2
diff
changeset
|
478 <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
|
479 <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
|
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 <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
|
483 </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
|
484 <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
|
485 <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
|
486 <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
|
487 </repeat> |
|
19
c9c6427edfe9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 4c0406815cb76175d7d90b2874310635694126f5
iuc
parents:
18
diff
changeset
|
488 <param name="cfile" value="no" /> |
|
3
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 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
|
490 <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
|
491 </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
|
492 <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
|
493 <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
|
494 <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
|
495 <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
|
496 <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
|
497 <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
|
498 <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
|
499 </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
|
500 </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
|
501 </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
|
502 </test> |
|
14
3133e833b3ce
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit c915bd7e68cb3a2944397aaf184c2b1db97cb3a5
iuc
parents:
13
diff
changeset
|
503 <!-- Ensure factors file with unordered samples works --> |
|
17
86b3df7db58b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 42b1160a549a85c87ed5226a83b55c4e44648597
iuc
parents:
16
diff
changeset
|
504 <test expect_num_outputs="2"> |
|
3
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents:
2
diff
changeset
|
505 <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
|
506 <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
|
507 <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
|
508 <param name="counts" value="matrix.txt" /> |
|
19
c9c6427edfe9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 4c0406815cb76175d7d90b2874310635694126f5
iuc
parents:
18
diff
changeset
|
509 <param name="cfile" value="no" /> |
|
3
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 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
|
511 <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
|
512 </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
|
513 <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
|
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 <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
|
516 <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
|
517 <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
|
518 <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
|
519 <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
|
520 </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
|
521 </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
|
522 </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
|
523 </test> |
|
12
81796eb60bd0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 33651907e4d5d6672537b80142c022d2b4951e8c
iuc
parents:
11
diff
changeset
|
524 <!-- Ensure filtered and normalised count outputs works--> |
|
17
86b3df7db58b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 42b1160a549a85c87ed5226a83b55c4e44648597
iuc
parents:
16
diff
changeset
|
525 <test expect_num_outputs="4"> |
|
3
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents:
2
diff
changeset
|
526 <param name="format" value="matrix" /> |
|
12
81796eb60bd0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 33651907e4d5d6672537b80142c022d2b4951e8c
iuc
parents:
11
diff
changeset
|
527 <param name="filtCounts" 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
|
528 <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
|
529 <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
|
530 <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
|
531 <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
|
532 <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
|
533 </repeat> |
|
19
c9c6427edfe9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 4c0406815cb76175d7d90b2874310635694126f5
iuc
parents:
18
diff
changeset
|
534 <param name="cfile" value="no" /> |
|
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 <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
|
536 <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
|
537 </repeat> |
|
12
81796eb60bd0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 33651907e4d5d6672537b80142c022d2b4951e8c
iuc
parents:
11
diff
changeset
|
538 <param name="filt_select" value="yes" /> |
|
81796eb60bd0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 33651907e4d5d6672537b80142c022d2b4951e8c
iuc
parents:
11
diff
changeset
|
539 <param name="format_select" value="counts"/> |
|
81796eb60bd0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 33651907e4d5d6672537b80142c022d2b4951e8c
iuc
parents:
11
diff
changeset
|
540 <param name="cntReq" value="10"/> |
|
81796eb60bd0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 33651907e4d5d6672537b80142c022d2b4951e8c
iuc
parents:
11
diff
changeset
|
541 <param name="count_select" value="sample"/> |
|
81796eb60bd0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 33651907e4d5d6672537b80142c022d2b4951e8c
iuc
parents:
11
diff
changeset
|
542 <param name="cntSampleReq" value="3"/> |
|
1
76d01fe0ec36
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 58c05c0ce9334f8b9c800283cfd1f40573546edd
iuc
parents:
0
diff
changeset
|
543 <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
|
544 <param name="topgenes" value="6" /> |
|
13
d5a940112511
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 8560b34a261fde200bd77dc2e817d55d386ac811
iuc
parents:
12
diff
changeset
|
545 <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
|
546 <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
|
547 <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
|
548 <has_text_matching expression="GeneID.*logFC.*AveExpr.*t.*P.Value.*adj.P.Val.*B" /> |
|
12
81796eb60bd0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 33651907e4d5d6672537b80142c022d2b4951e8c
iuc
parents:
11
diff
changeset
|
549 <has_text_matching expression="11304.*0.45.*15.52.*4.94.*7.74.*0.0001.*5.27" /> |
|
4
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
3
diff
changeset
|
550 </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
|
551 </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
|
552 </output_collection> |
|
13
d5a940112511
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 8560b34a261fde200bd77dc2e817d55d386ac811
iuc
parents:
12
diff
changeset
|
553 <output name="outNorm" ftype="tabular" > |
|
d5a940112511
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 8560b34a261fde200bd77dc2e817d55d386ac811
iuc
parents:
12
diff
changeset
|
554 <assert_contents> |
|
d5a940112511
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 8560b34a261fde200bd77dc2e817d55d386ac811
iuc
parents:
12
diff
changeset
|
555 <has_text_matching expression="GeneID.*Mut1.*Mut2.*Mut3.*WT1.*WT2.*WT3" /> |
|
d5a940112511
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 8560b34a261fde200bd77dc2e817d55d386ac811
iuc
parents:
12
diff
changeset
|
556 <has_text_matching expression="11304.*15.7.*15.8.*15.6.*15.3.*15.2.*15.2" /> |
|
d5a940112511
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 8560b34a261fde200bd77dc2e817d55d386ac811
iuc
parents:
12
diff
changeset
|
557 </assert_contents> |
|
d5a940112511
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 8560b34a261fde200bd77dc2e817d55d386ac811
iuc
parents:
12
diff
changeset
|
558 </output> |
|
d5a940112511
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 8560b34a261fde200bd77dc2e817d55d386ac811
iuc
parents:
12
diff
changeset
|
559 <output name="outFilt" ftype="tabular" > |
|
d5a940112511
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 8560b34a261fde200bd77dc2e817d55d386ac811
iuc
parents:
12
diff
changeset
|
560 <assert_contents> |
|
d5a940112511
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 8560b34a261fde200bd77dc2e817d55d386ac811
iuc
parents:
12
diff
changeset
|
561 <has_text_matching expression="GeneID.*Mut1.*Mut2.*Mut3.*WT1.*WT2.*WT3" /> |
|
d5a940112511
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 8560b34a261fde200bd77dc2e817d55d386ac811
iuc
parents:
12
diff
changeset
|
562 <has_text_matching expression="11304.*361.*397.*346.*356.*312.*337" /> |
|
d5a940112511
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 8560b34a261fde200bd77dc2e817d55d386ac811
iuc
parents:
12
diff
changeset
|
563 <not_has_text text="11302"/> |
|
d5a940112511
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 8560b34a261fde200bd77dc2e817d55d386ac811
iuc
parents:
12
diff
changeset
|
564 </assert_contents> |
|
d5a940112511
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 8560b34a261fde200bd77dc2e817d55d386ac811
iuc
parents:
12
diff
changeset
|
565 </output> |
|
1
76d01fe0ec36
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 58c05c0ce9334f8b9c800283cfd1f40573546edd
iuc
parents:
0
diff
changeset
|
566 </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
|
567 <!-- Ensure multiple counts files input works --> |
|
17
86b3df7db58b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 42b1160a549a85c87ed5226a83b55c4e44648597
iuc
parents:
16
diff
changeset
|
568 <test expect_num_outputs="3"> |
|
3
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents:
2
diff
changeset
|
569 <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
|
570 <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
|
571 <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
|
572 <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
|
573 <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
|
574 <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
|
575 </repeat> |
|
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents:
2
diff
changeset
|
576 <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
|
577 <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
|
578 <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
|
579 </repeat> |
|
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents:
2
diff
changeset
|
580 </repeat> |
|
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents:
2
diff
changeset
|
581 <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
|
582 <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
|
583 <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
|
584 <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
|
585 <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
|
586 </repeat> |
|
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents:
2
diff
changeset
|
587 <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
|
588 <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
|
589 <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
|
590 </repeat> |
|
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents:
2
diff
changeset
|
591 <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
|
592 <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
|
593 <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
|
594 </repeat> |
|
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents:
2
diff
changeset
|
595 </repeat> |
|
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents:
2
diff
changeset
|
596 <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
|
597 <param name="geneanno" value="anno.txt" /> |
|
19
c9c6427edfe9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 4c0406815cb76175d7d90b2874310635694126f5
iuc
parents:
18
diff
changeset
|
598 <param name="cfile" value="no" /> |
|
3
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents:
2
diff
changeset
|
599 <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
|
600 <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
|
601 </repeat> |
|
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents:
2
diff
changeset
|
602 <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
|
603 <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
|
604 </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
|
605 <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
|
606 <param name="normCounts" value="true" /> |
|
13
d5a940112511
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 8560b34a261fde200bd77dc2e817d55d386ac811
iuc
parents:
12
diff
changeset
|
607 <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
|
608 <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
|
609 <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
|
610 <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
|
611 <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
|
612 </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
|
613 </element> |
|
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
3
diff
changeset
|
614 <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
|
615 <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
|
616 <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
|
617 <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
|
618 </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
|
619 </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
|
620 </output_collection> |
|
13
d5a940112511
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 8560b34a261fde200bd77dc2e817d55d386ac811
iuc
parents:
12
diff
changeset
|
621 <output name="outNorm" ftype="tabular" > |
|
d5a940112511
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 8560b34a261fde200bd77dc2e817d55d386ac811
iuc
parents:
12
diff
changeset
|
622 <assert_contents> |
|
d5a940112511
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 8560b34a261fde200bd77dc2e817d55d386ac811
iuc
parents:
12
diff
changeset
|
623 <has_text_matching expression="EntrezID.*Symbol.*Mut1.*Mut2.*Mut3.*WT1.*WT2.*WT3" /> |
|
d5a940112511
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 8560b34a261fde200bd77dc2e817d55d386ac811
iuc
parents:
12
diff
changeset
|
624 <has_text_matching expression="11304.*Abca4.*15.7545" /> |
|
d5a940112511
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 8560b34a261fde200bd77dc2e817d55d386ac811
iuc
parents:
12
diff
changeset
|
625 </assert_contents> |
|
d5a940112511
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 8560b34a261fde200bd77dc2e817d55d386ac811
iuc
parents:
12
diff
changeset
|
626 </output> |
|
3
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents:
2
diff
changeset
|
627 </test> |
|
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents:
2
diff
changeset
|
628 <!-- Ensure limma-trend option works --> |
|
17
86b3df7db58b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 42b1160a549a85c87ed5226a83b55c4e44648597
iuc
parents:
16
diff
changeset
|
629 <test expect_num_outputs="2"> |
|
3
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents:
2
diff
changeset
|
630 <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
|
631 <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
|
632 <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
|
633 <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
|
634 <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
|
635 </repeat> |
|
19
c9c6427edfe9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 4c0406815cb76175d7d90b2874310635694126f5
iuc
parents:
18
diff
changeset
|
636 <param name="cfile" value="no" /> |
|
3
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents:
2
diff
changeset
|
637 <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
|
638 <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
|
639 </repeat> |
|
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents:
2
diff
changeset
|
640 <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
|
641 <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
|
642 <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
|
643 <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
|
644 <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
|
645 <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
|
646 </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
|
647 </output> |
|
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents:
2
diff
changeset
|
648 <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
|
649 <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
|
650 <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
|
651 <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
|
652 <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
|
653 </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
|
654 </element> |
|
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
3
diff
changeset
|
655 </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
|
656 </test> |
|
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
3
diff
changeset
|
657 <!-- Ensure limma-trend option with annotation works --> |
|
17
86b3df7db58b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 42b1160a549a85c87ed5226a83b55c4e44648597
iuc
parents:
16
diff
changeset
|
658 <test expect_num_outputs="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
|
659 <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
|
660 <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
|
661 <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
|
662 <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
|
663 <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
|
664 <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
|
665 <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
|
666 </repeat> |
|
19
c9c6427edfe9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 4c0406815cb76175d7d90b2874310635694126f5
iuc
parents:
18
diff
changeset
|
667 <param name="cfile" value="no" /> |
|
4
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
3
diff
changeset
|
668 <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
|
669 <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
|
670 </repeat> |
|
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
3
diff
changeset
|
671 <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
|
672 <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
|
673 <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
|
674 <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
|
675 <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
|
676 <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
|
677 </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
|
678 </output> |
|
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
3
diff
changeset
|
679 <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
|
680 <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
|
681 <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
|
682 <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
|
683 <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
|
684 </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
|
685 </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
|
686 </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
|
687 </test> |
|
17
86b3df7db58b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 42b1160a549a85c87ed5226a83b55c4e44648597
iuc
parents:
16
diff
changeset
|
688 <!-- Ensure samples and groups beginning with numbers can be handled --> |
|
86b3df7db58b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 42b1160a549a85c87ed5226a83b55c4e44648597
iuc
parents:
16
diff
changeset
|
689 <test expect_num_outputs="3"> |
|
86b3df7db58b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 42b1160a549a85c87ed5226a83b55c4e44648597
iuc
parents:
16
diff
changeset
|
690 <param name="format" value="matrix" /> |
|
86b3df7db58b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 42b1160a549a85c87ed5226a83b55c4e44648597
iuc
parents:
16
diff
changeset
|
691 <param name="counts" value="matrix_num.txt" /> |
|
86b3df7db58b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 42b1160a549a85c87ed5226a83b55c4e44648597
iuc
parents:
16
diff
changeset
|
692 <param name="annoOpt" value="yes" /> |
|
86b3df7db58b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 42b1160a549a85c87ed5226a83b55c4e44648597
iuc
parents:
16
diff
changeset
|
693 <param name="geneanno" value="anno.txt" /> |
|
86b3df7db58b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 42b1160a549a85c87ed5226a83b55c4e44648597
iuc
parents:
16
diff
changeset
|
694 <repeat name="rep_factor"> |
|
86b3df7db58b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 42b1160a549a85c87ed5226a83b55c4e44648597
iuc
parents:
16
diff
changeset
|
695 <param name="factorName" value="Group"/> |
|
86b3df7db58b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 42b1160a549a85c87ed5226a83b55c4e44648597
iuc
parents:
16
diff
changeset
|
696 <param name="groupNames" value="2,2,2,1,1,1" /> |
|
86b3df7db58b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 42b1160a549a85c87ed5226a83b55c4e44648597
iuc
parents:
16
diff
changeset
|
697 </repeat> |
|
19
c9c6427edfe9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 4c0406815cb76175d7d90b2874310635694126f5
iuc
parents:
18
diff
changeset
|
698 <param name="cfile" value="no" /> |
|
17
86b3df7db58b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 42b1160a549a85c87ed5226a83b55c4e44648597
iuc
parents:
16
diff
changeset
|
699 <repeat name="rep_contrast"> |
|
86b3df7db58b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 42b1160a549a85c87ed5226a83b55c4e44648597
iuc
parents:
16
diff
changeset
|
700 <param name="contrast" value="2-1" /> |
|
86b3df7db58b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 42b1160a549a85c87ed5226a83b55c4e44648597
iuc
parents:
16
diff
changeset
|
701 </repeat> |
|
86b3df7db58b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 42b1160a549a85c87ed5226a83b55c4e44648597
iuc
parents:
16
diff
changeset
|
702 <param name="filt_select" value="yes" /> |
|
86b3df7db58b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 42b1160a549a85c87ed5226a83b55c4e44648597
iuc
parents:
16
diff
changeset
|
703 <param name="format_select" value="counts"/> |
|
86b3df7db58b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 42b1160a549a85c87ed5226a83b55c4e44648597
iuc
parents:
16
diff
changeset
|
704 <param name="cntReq" value="10"/> |
|
86b3df7db58b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 42b1160a549a85c87ed5226a83b55c4e44648597
iuc
parents:
16
diff
changeset
|
705 <param name="count_select" value="sample"/> |
|
86b3df7db58b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 42b1160a549a85c87ed5226a83b55c4e44648597
iuc
parents:
16
diff
changeset
|
706 <param name="cntSampleReq" value="3"/> |
|
86b3df7db58b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 42b1160a549a85c87ed5226a83b55c4e44648597
iuc
parents:
16
diff
changeset
|
707 <param name="normalisationOption" value="TMM" /> |
|
86b3df7db58b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 42b1160a549a85c87ed5226a83b55c4e44648597
iuc
parents:
16
diff
changeset
|
708 <param name="normCounts" value="true" /> |
|
86b3df7db58b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 42b1160a549a85c87ed5226a83b55c4e44648597
iuc
parents:
16
diff
changeset
|
709 <param name="topgenes" value="6" /> |
|
86b3df7db58b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 42b1160a549a85c87ed5226a83b55c4e44648597
iuc
parents:
16
diff
changeset
|
710 <param name="de_select" value="voom" /> |
|
86b3df7db58b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 42b1160a549a85c87ed5226a83b55c4e44648597
iuc
parents:
16
diff
changeset
|
711 <output_collection name="outTables" count="1"> |
|
86b3df7db58b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 42b1160a549a85c87ed5226a83b55c4e44648597
iuc
parents:
16
diff
changeset
|
712 <element name="limma-voom_X2-X1" ftype="tabular" > |
|
86b3df7db58b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 42b1160a549a85c87ed5226a83b55c4e44648597
iuc
parents:
16
diff
changeset
|
713 <assert_contents> |
|
86b3df7db58b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 42b1160a549a85c87ed5226a83b55c4e44648597
iuc
parents:
16
diff
changeset
|
714 <has_text_matching expression="EntrezID.*logFC.*AveExpr.*t.*P.Value.*adj.P.Val.*B" /> |
|
86b3df7db58b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 42b1160a549a85c87ed5226a83b55c4e44648597
iuc
parents:
16
diff
changeset
|
715 <has_text_matching expression="11304.*0.45.*15.52.*4.94.*7.74.*0.0001.*5.27" /> |
|
86b3df7db58b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 42b1160a549a85c87ed5226a83b55c4e44648597
iuc
parents:
16
diff
changeset
|
716 </assert_contents> |
|
86b3df7db58b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 42b1160a549a85c87ed5226a83b55c4e44648597
iuc
parents:
16
diff
changeset
|
717 </element> |
|
86b3df7db58b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 42b1160a549a85c87ed5226a83b55c4e44648597
iuc
parents:
16
diff
changeset
|
718 </output_collection> |
|
86b3df7db58b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 42b1160a549a85c87ed5226a83b55c4e44648597
iuc
parents:
16
diff
changeset
|
719 <output name="outNorm" ftype="tabular" > |
|
86b3df7db58b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 42b1160a549a85c87ed5226a83b55c4e44648597
iuc
parents:
16
diff
changeset
|
720 <assert_contents> |
|
86b3df7db58b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 42b1160a549a85c87ed5226a83b55c4e44648597
iuc
parents:
16
diff
changeset
|
721 <has_text_matching expression="EntrezID.*2-1.*2-2.*2-3.*1-1.*1-2.*1-3" /> |
|
86b3df7db58b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 42b1160a549a85c87ed5226a83b55c4e44648597
iuc
parents:
16
diff
changeset
|
722 <has_text_matching expression="11304.*15.7.*15.8.*15.6.*15.3.*15.2.*15.2" /> |
|
86b3df7db58b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 42b1160a549a85c87ed5226a83b55c4e44648597
iuc
parents:
16
diff
changeset
|
723 </assert_contents> |
|
86b3df7db58b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 42b1160a549a85c87ed5226a83b55c4e44648597
iuc
parents:
16
diff
changeset
|
724 </output> |
|
86b3df7db58b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 42b1160a549a85c87ed5226a83b55c4e44648597
iuc
parents:
16
diff
changeset
|
725 </test> |
|
19
c9c6427edfe9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 4c0406815cb76175d7d90b2874310635694126f5
iuc
parents:
18
diff
changeset
|
726 <!-- Ensure contrasts file works --> |
|
c9c6427edfe9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 4c0406815cb76175d7d90b2874310635694126f5
iuc
parents:
18
diff
changeset
|
727 <test expect_num_outputs="2"> |
|
c9c6427edfe9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 4c0406815cb76175d7d90b2874310635694126f5
iuc
parents:
18
diff
changeset
|
728 <param name="format" value="matrix" /> |
|
c9c6427edfe9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 4c0406815cb76175d7d90b2874310635694126f5
iuc
parents:
18
diff
changeset
|
729 <param name="counts" value="matrix.txt" /> |
|
c9c6427edfe9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 4c0406815cb76175d7d90b2874310635694126f5
iuc
parents:
18
diff
changeset
|
730 <repeat name="rep_factor"> |
|
c9c6427edfe9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 4c0406815cb76175d7d90b2874310635694126f5
iuc
parents:
18
diff
changeset
|
731 <param name="factorName" value="Genotype"/> |
|
c9c6427edfe9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 4c0406815cb76175d7d90b2874310635694126f5
iuc
parents:
18
diff
changeset
|
732 <param name="groupNames" value="Mut,Mut,Mut,WT,WT,WT" /> |
|
c9c6427edfe9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 4c0406815cb76175d7d90b2874310635694126f5
iuc
parents:
18
diff
changeset
|
733 </repeat> |
|
c9c6427edfe9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 4c0406815cb76175d7d90b2874310635694126f5
iuc
parents:
18
diff
changeset
|
734 <param name="cfile" value="yes" /> |
|
23
e827f9aae031
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 38cf93fd693c810b4150c5d8aa3763aebc988b07"
iuc
parents:
22
diff
changeset
|
735 <param name="cinfo" value="contrasts.txt" ftype="tabular" /> |
|
19
c9c6427edfe9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 4c0406815cb76175d7d90b2874310635694126f5
iuc
parents:
18
diff
changeset
|
736 <param name="normalisationOption" value="TMM" /> |
|
c9c6427edfe9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 4c0406815cb76175d7d90b2874310635694126f5
iuc
parents:
18
diff
changeset
|
737 <param name="topgenes" value="6" /> |
|
20
0921444c832d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 0cc16fe170b5c8d3b9441177bf2749aa7bddca7b
iuc
parents:
19
diff
changeset
|
738 <output_collection name="outTables" count="3"> |
|
26
119b069fc845
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit b4d788c0f159d507159117a063b1f867b243c738
iuc
parents:
25
diff
changeset
|
739 <element name="limma-voom_Mut-WT-WT-Mut" ftype="tabular" > |
|
119b069fc845
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit b4d788c0f159d507159117a063b1f867b243c738
iuc
parents:
25
diff
changeset
|
740 <assert_contents> |
|
119b069fc845
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit b4d788c0f159d507159117a063b1f867b243c738
iuc
parents:
25
diff
changeset
|
741 <has_text_matching expression="GeneID.*logFC.*AveExpr.*t.*P.Value.*adj.P.Val.*B" /> |
|
119b069fc845
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit b4d788c0f159d507159117a063b1f867b243c738
iuc
parents:
25
diff
changeset
|
742 <has_text_matching expression="11304.*0.9146" /> |
|
119b069fc845
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit b4d788c0f159d507159117a063b1f867b243c738
iuc
parents:
25
diff
changeset
|
743 </assert_contents> |
|
119b069fc845
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit b4d788c0f159d507159117a063b1f867b243c738
iuc
parents:
25
diff
changeset
|
744 </element> |
|
19
c9c6427edfe9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 4c0406815cb76175d7d90b2874310635694126f5
iuc
parents:
18
diff
changeset
|
745 <element name="limma-voom_Mut-WT" ftype="tabular" > |
|
c9c6427edfe9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 4c0406815cb76175d7d90b2874310635694126f5
iuc
parents:
18
diff
changeset
|
746 <assert_contents> |
|
c9c6427edfe9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 4c0406815cb76175d7d90b2874310635694126f5
iuc
parents:
18
diff
changeset
|
747 <has_text_matching expression="GeneID.*logFC.*AveExpr.*t.*P.Value.*adj.P.Val.*B" /> |
|
c9c6427edfe9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 4c0406815cb76175d7d90b2874310635694126f5
iuc
parents:
18
diff
changeset
|
748 <has_text_matching expression="11304.*0.4573" /> |
|
c9c6427edfe9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 4c0406815cb76175d7d90b2874310635694126f5
iuc
parents:
18
diff
changeset
|
749 </assert_contents> |
|
c9c6427edfe9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 4c0406815cb76175d7d90b2874310635694126f5
iuc
parents:
18
diff
changeset
|
750 </element> |
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c9c6427edfe9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 4c0406815cb76175d7d90b2874310635694126f5
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|
751 <element name="limma-voom_WT-Mut" ftype="tabular" > |
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c9c6427edfe9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 4c0406815cb76175d7d90b2874310635694126f5
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|
752 <assert_contents> |
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c9c6427edfe9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 4c0406815cb76175d7d90b2874310635694126f5
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|
753 <has_text_matching expression="GeneID.*logFC.*AveExpr.*t.*P.Value.*adj.P.Val.*B" /> |
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c9c6427edfe9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 4c0406815cb76175d7d90b2874310635694126f5
iuc
parents:
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changeset
|
754 <has_text_matching expression="11304.*-0.4573" /> |
|
c9c6427edfe9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 4c0406815cb76175d7d90b2874310635694126f5
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changeset
|
755 </assert_contents> |
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c9c6427edfe9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 4c0406815cb76175d7d90b2874310635694126f5
iuc
parents:
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changeset
|
756 </element> |
|
c9c6427edfe9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 4c0406815cb76175d7d90b2874310635694126f5
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changeset
|
757 </output_collection> |
|
c9c6427edfe9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 4c0406815cb76175d7d90b2874310635694126f5
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|
758 </test> |
|
0
bdebdea5f6a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
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|
759 </tests> |
|
1
76d01fe0ec36
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 58c05c0ce9334f8b9c800283cfd1f40573546edd
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parents:
0
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|
760 |
|
76d01fe0ec36
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 58c05c0ce9334f8b9c800283cfd1f40573546edd
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0
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|
761 <help><![CDATA[ |
|
0
bdebdea5f6a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
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changeset
|
762 .. class:: infomark |
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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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parents:
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changeset
|
763 |
|
bdebdea5f6a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
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parents:
diff
changeset
|
764 **What it does** |
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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
|
765 |
|
14
3133e833b3ce
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit c915bd7e68cb3a2944397aaf184c2b1db97cb3a5
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|
766 Given a matrix of counts (e.g. from featureCounts) and optional information about the genes, this tool performs differential expression (DE) using the limma_ Bioconductor package and produces plots and tables useful in DE analysis. Interactive Glimma_ plots and tables can also be generated and links to the Glimma plots will be provided in the report. See an example workflow here_. |
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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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changeset
|
767 |
|
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
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768 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
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changeset
|
769 |
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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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parents:
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changeset
|
770 ----- |
|
bdebdea5f6a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
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parents:
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changeset
|
771 |
|
bdebdea5f6a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
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parents:
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changeset
|
772 **Inputs** |
|
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
|
773 |
|
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
|
774 **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
|
775 Option to use the limma-voom or limma-trend approach for differential expression. The default is limma-voom. |
|
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
|
776 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
|
777 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:
2
diff
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778 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:
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diff
changeset
|
779 |
|
0
bdebdea5f6a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff
changeset
|
780 **Counts Data:** |
|
16
5d903d528193
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 349e35a66009449851b21e2810bc5aaa58225fca
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781 The counts data can either be input as separate counts files (one sample per file) or a single count matrix (one sample per column). The rows correspond to genes, and columns correspond to the counts for the samples. Values must be tab separated, with the first row containing the sample/column labels and the first column containing the row/gene labels. The sample labels must start with a letter. Gene identifiers can be of any type but must be unique and not repeated within a counts file. |
|
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
|
782 |
|
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
|
783 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
|
784 |
|
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
|
785 ========== ======= |
|
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
|
786 **GeneID** **WT1** |
|
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
|
787 ---------- ------- |
|
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
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diff
changeset
|
788 11287 1699 |
|
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
|
789 11298 1905 |
|
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
|
790 11302 6 |
|
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
|
791 11303 2099 |
|
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
|
792 11304 356 |
|
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
|
793 11305 2528 |
|
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
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|
794 ========== ======= |
|
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
|
795 |
|
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
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changeset
|
796 Example - **Single Count 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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changeset
|
797 |
|
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
|
798 ========== ======= ======= ======= ======== ======== ======== |
|
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
|
799 **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
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changeset
|
800 ---------- ------- ------- ------- -------- -------- -------- |
|
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
|
801 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
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changeset
|
802 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
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changeset
|
803 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
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changeset
|
804 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
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changeset
|
805 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
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0
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changeset
|
806 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
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changeset
|
807 ========== ======= ======= ======= ======== ======== ======== |
|
bdebdea5f6a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
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changeset
|
808 |
|
bdebdea5f6a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
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changeset
|
809 **Gene Annotations:** |
|
bdebdea5f6a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
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changeset
|
810 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
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changeset
|
811 information about the genes than just an ID number. The annotations will |
|
14
3133e833b3ce
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit c915bd7e68cb3a2944397aaf184c2b1db97cb3a5
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|
812 be available in the differential expression results table and the optional normalised counts table. They will also be used to generate interactive Glimma_ Volcano, MD plots and tables of differential expression. The input annotation 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 and interactive Glimma plots, additional columns will be available in the Glimma interactive table. 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
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changeset
|
813 |
|
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
|
814 Example: |
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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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changeset
|
815 |
|
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
|
816 ========== ========== =================================================== |
|
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
|
817 **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
|
818 ---------- ---------- --------------------------------------------------- |
|
4
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
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changeset
|
819 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
|
820 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
|
821 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
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822 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
|
823 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
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diff
changeset
|
824 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:
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changeset
|
825 ========== ========== =================================================== |
|
bdebdea5f6a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff
changeset
|
826 |
|
1
76d01fe0ec36
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 58c05c0ce9334f8b9c800283cfd1f40573546edd
iuc
parents:
0
diff
changeset
|
827 **Factor Information:** |
|
14
3133e833b3ce
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit c915bd7e68cb3a2944397aaf184c2b1db97cb3a5
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parents:
13
diff
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828 Enter factor names and groups in the tool form, or provide a tab-separated file that has the names of the samples in the first column and one header row. The sample names must be the same as the names in the columns of the count matrix. The second column should contain the primary factor levels (e.g. WT, Mut) with optional additional columns for any secondary factors. |
|
1
76d01fe0ec36
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 58c05c0ce9334f8b9c800283cfd1f40573546edd
iuc
parents:
0
diff
changeset
|
829 |
|
76d01fe0ec36
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 58c05c0ce9334f8b9c800283cfd1f40573546edd
iuc
parents:
0
diff
changeset
|
830 Example: |
|
0
bdebdea5f6a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff
changeset
|
831 |
|
1
76d01fe0ec36
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 58c05c0ce9334f8b9c800283cfd1f40573546edd
iuc
parents:
0
diff
changeset
|
832 ========== ============ ========= |
|
76d01fe0ec36
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 58c05c0ce9334f8b9c800283cfd1f40573546edd
iuc
parents:
0
diff
changeset
|
833 **Sample** **Genotype** **Batch** |
|
76d01fe0ec36
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 58c05c0ce9334f8b9c800283cfd1f40573546edd
iuc
parents:
0
diff
changeset
|
834 ---------- ------------ --------- |
|
76d01fe0ec36
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 58c05c0ce9334f8b9c800283cfd1f40573546edd
iuc
parents:
0
diff
changeset
|
835 WT1 WT b1 |
|
76d01fe0ec36
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 58c05c0ce9334f8b9c800283cfd1f40573546edd
iuc
parents:
0
diff
changeset
|
836 WT2 WT b2 |
|
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
|
837 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
|
838 Mut1 Mut b1 |
|
76d01fe0ec36
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 58c05c0ce9334f8b9c800283cfd1f40573546edd
iuc
parents:
0
diff
changeset
|
839 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
|
840 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
|
841 ========== ============ ========= |
|
0
bdebdea5f6a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff
changeset
|
842 |
|
17
86b3df7db58b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 42b1160a549a85c87ed5226a83b55c4e44648597
iuc
parents:
16
diff
changeset
|
843 *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, an additive linear model will be used. |
|
3
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents:
2
diff
changeset
|
844 |
|
17
86b3df7db58b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 42b1160a549a85c87ed5226a83b55c4e44648597
iuc
parents:
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diff
changeset
|
845 *Groups:* The names of the groups for the factor. The names should only contain letters, numbers and underscores, other characters such as spaces and hyphens MUST not be used. If entered into the tool form above, the order must be the same as the samples (to which the groups correspond) are listed in the columns of the counts matrix, with the values separated by commas. If the group names begin with a number an X will be added as a prefix. |
|
1
76d01fe0ec36
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 58c05c0ce9334f8b9c800283cfd1f40573546edd
iuc
parents:
0
diff
changeset
|
846 |
|
0
bdebdea5f6a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff
changeset
|
847 **Contrasts of Interest:** |
|
19
c9c6427edfe9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 4c0406815cb76175d7d90b2874310635694126f5
iuc
parents:
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diff
changeset
|
848 The contrasts you wish to make between levels. A common contrast would be a simple difference between two levels: "Mut-WT" |
|
c9c6427edfe9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 4c0406815cb76175d7d90b2874310635694126f5
iuc
parents:
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diff
changeset
|
849 represents the difference between the mutant and wild type genotypes. Multiple contrasts must be entered separately using the Insert Contrast button, spaces must not be used. Alternatively, a tab-separated file can be input that has the names of the comparisons in the first column and one header row, as shown below. |
|
c9c6427edfe9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 4c0406815cb76175d7d90b2874310635694126f5
iuc
parents:
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diff
changeset
|
850 |
|
c9c6427edfe9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 4c0406815cb76175d7d90b2874310635694126f5
iuc
parents:
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diff
changeset
|
851 Example: |
|
c9c6427edfe9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 4c0406815cb76175d7d90b2874310635694126f5
iuc
parents:
18
diff
changeset
|
852 |
|
c9c6427edfe9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 4c0406815cb76175d7d90b2874310635694126f5
iuc
parents:
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diff
changeset
|
853 ============= = |
|
c9c6427edfe9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 4c0406815cb76175d7d90b2874310635694126f5
iuc
parents:
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diff
changeset
|
854 **Contrasts** |
|
c9c6427edfe9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 4c0406815cb76175d7d90b2874310635694126f5
iuc
parents:
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diff
changeset
|
855 ------------- - |
|
c9c6427edfe9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 4c0406815cb76175d7d90b2874310635694126f5
iuc
parents:
18
diff
changeset
|
856 Mut-WT |
|
c9c6427edfe9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 4c0406815cb76175d7d90b2874310635694126f5
iuc
parents:
18
diff
changeset
|
857 WT-Mut |
|
c9c6427edfe9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 4c0406815cb76175d7d90b2874310635694126f5
iuc
parents:
18
diff
changeset
|
858 ============= = |
|
0
bdebdea5f6a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff
changeset
|
859 |
|
3
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents:
2
diff
changeset
|
860 **Filter Low Counts:** |
|
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents:
2
diff
changeset
|
861 Genes with very low counts across all libraries provide little evidence for differential expression. |
|
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents:
2
diff
changeset
|
862 In the biological point of view, a gene must be expressed at some minimal level before |
|
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents:
2
diff
changeset
|
863 it is likely to be translated into a protein or to be biologically important. In addition, the |
|
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents:
2
diff
changeset
|
864 pronounced discreteness of these counts interferes with some of the statistical approximations |
|
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents:
2
diff
changeset
|
865 that are used later in the pipeline. These genes should be filtered out prior to further |
|
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
|
866 analysis. |
|
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents:
2
diff
changeset
|
867 As a rule of thumb, genes are dropped if they can’t possibly be expressed in all the samples |
|
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents:
2
diff
changeset
|
868 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:
2
diff
changeset
|
869 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
|
870 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:
2
diff
changeset
|
871 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
|
872 |
|
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
|
873 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:
2
diff
changeset
|
874 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
|
875 |
|
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents:
2
diff
changeset
|
876 * **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:
2
diff
changeset
|
877 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
|
878 |
|
3
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents:
2
diff
changeset
|
879 * **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:
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changeset
|
880 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
|
881 |
|
3
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents:
2
diff
changeset
|
882 * **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
|
883 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
|
884 |
|
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents:
2
diff
changeset
|
885 * **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
|
886 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
|
887 |
|
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
|
888 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
|
889 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
|
890 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
|
891 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
|
892 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
|
893 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
|
894 |
|
3
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents:
2
diff
changeset
|
895 **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
|
896 |
|
bdebdea5f6a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff
changeset
|
897 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
|
898 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
|
899 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
|
900 |
|
3
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
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|
901 * **Minimum log2-fold-change Required:** |
|
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
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902 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
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|
903 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
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changeset
|
904 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
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parents:
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changeset
|
905 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
|
906 |
|
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
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|
907 * **Adjusted Threshold:** |
|
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
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parents:
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|
908 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
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|
909 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
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|
910 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
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parents:
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|
911 |
|
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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changeset
|
912 * **P-Value Adjustment Method:** |
|
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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parents:
0
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changeset
|
913 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
|
914 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
|
915 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
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|
916 |
|
6
39fa12a6d885
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 60cae222b10f43f830936c19298bd723ac47e43d
iuc
parents:
5
diff
changeset
|
917 **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:
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diff
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|
918 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`_). |
|
39fa12a6d885
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 60cae222b10f43f830936c19298bd723ac47e43d
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diff
changeset
|
919 |
|
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
|
920 **Normalisation 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
|
921 The most obvious technical factor that affects the read counts, other than gene expression |
|
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents:
2
diff
changeset
|
922 levels, is the sequencing depth of each RNA sample. edgeR adjusts any differential expression |
|
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
|
923 analysis for varying sequencing depths as represented by differing library sizes. This is |
|
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
|
924 part of the basic modeling procedure and flows automatically into fold-change or p-value |
|
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
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parents:
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changeset
|
925 calculations. It is always present, and doesn’t require any user intervention. |
|
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents:
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|
926 The second most important technical influence on differential expression is one that is less |
|
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
|
927 obvious. RNA-seq provides a measure of the relative abundance of each gene in each RNA |
|
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
|
928 sample, but does not provide any measure of the total RNA output on a per-cell basis. |
|
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents:
2
diff
changeset
|
929 This commonly becomes important when a small number of genes are very highly expressed |
|
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents:
2
diff
changeset
|
930 in one sample, but not in another. The highly expressed genes can consume a substantial |
|
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents:
2
diff
changeset
|
931 proportion of the total library size, causing the remaining genes to be under-sampled 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
|
932 sample. Unless this RNA composition effect is adjusted for, the remaining genes may falsely |
|
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents:
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|
933 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`_. |
|
1
76d01fe0ec36
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 58c05c0ce9334f8b9c800283cfd1f40573546edd
iuc
parents:
0
diff
changeset
|
934 |
|
3
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents:
2
diff
changeset
|
935 **Robust Settings** |
|
6
39fa12a6d885
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 60cae222b10f43f830936c19298bd723ac47e43d
iuc
parents:
5
diff
changeset
|
936 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. |
|
3
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
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parents:
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diff
changeset
|
937 |
|
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
|
938 **Prior Count:** |
|
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
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parents:
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diff
changeset
|
939 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`_. |
|
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents:
2
diff
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|
940 |
|
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents:
2
diff
changeset
|
941 **Apply Sample Weights:** |
|
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents:
2
diff
changeset
|
942 If the limma-voom method is used, an option is available to downweight outlier samples, such that their information is still |
|
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
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|
943 used in the statistical analysis but their impact is reduced. Use this |
|
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
|
944 whenever significant outliers are present. The MDS plotting tool in this package |
|
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
|
945 is useful for identifying outliers. For more information on this option see Liu et al. (2015). |
|
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
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|
946 |
|
0
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
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changeset
|
947 |
|
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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diff
changeset
|
948 **Outputs** |
|
76d01fe0ec36
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 58c05c0ce9334f8b9c800283cfd1f40573546edd
iuc
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|
949 |
|
3
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
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diff
changeset
|
950 This tool outputs |
|
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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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|
951 |
|
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
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diff
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|
952 * 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
iuc
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|
953 * 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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|
954 |
|
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents:
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|
955 Optionally, under **Output Options** you can choose to output |
|
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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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|
956 |
|
14
3133e833b3ce
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit c915bd7e68cb3a2944397aaf184c2b1db97cb3a5
iuc
parents:
13
diff
changeset
|
957 * interactive Glimma plots and tables: MDS plot, and (if annotation file is input) Volcano plot and MD plot (default: Yes) |
|
3133e833b3ce
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit c915bd7e68cb3a2944397aaf184c2b1db97cb3a5
iuc
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diff
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|
958 * additional plots in the report and as PDFs |
|
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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|
959 * a normalised counts table |
|
11
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 4bcbd83574ecf7194f3370aa883a9573563afdbc
iuc
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changeset
|
960 * a library size information file |
|
4
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
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|
961 * the R script used by this tool |
|
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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|
962 * an RData file |
|
1
76d01fe0ec36
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 58c05c0ce9334f8b9c800283cfd1f40573546edd
iuc
parents:
0
diff
changeset
|
963 |
|
0
bdebdea5f6a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff
changeset
|
964 ----- |
|
bdebdea5f6a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff
changeset
|
965 |
|
bdebdea5f6a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff
changeset
|
966 **Citations:** |
|
bdebdea5f6a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
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parents:
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|
967 |
|
3
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents:
2
diff
changeset
|
968 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. |
|
0
bdebdea5f6a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff
changeset
|
969 |
|
bdebdea5f6a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff
changeset
|
970 limma |
|
bdebdea5f6a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff
changeset
|
971 |
|
1
76d01fe0ec36
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 58c05c0ce9334f8b9c800283cfd1f40573546edd
iuc
parents:
0
diff
changeset
|
972 Please cite the paper below for the limma software itself. Please also try |
|
0
bdebdea5f6a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff
changeset
|
973 to cite the appropriate methodology articles that describe the statistical |
|
bdebdea5f6a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff
changeset
|
974 methods implemented in limma, depending on which limma functions you are |
|
3
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975 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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976 User's Guide`_. |
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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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977 |
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1
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978 * 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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979 '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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980 Bioconductor'. R. Gentleman, V. Carey, S. Dudoit, R. Irizarry, |
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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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981 W. Huber (eds), Springer, New York, pages 397-420. |
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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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982 |
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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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983 * 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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984 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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985 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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986 |
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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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987 * 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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988 |
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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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989 * Ritchie, M. E., Diyagama, D., Neilson, J., van Laar, R., Dobrovic, |
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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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990 A., Holloway, A., and Smyth, G. K. (2006). Empirical array quality weights |
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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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991 for microarray data. BMC Bioinformatics 7, Article 261. |
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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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992 |
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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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993 |
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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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994 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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995 |
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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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996 Please cite the first paper for the software itself and the other papers for |
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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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997 the various original statistical methods implemented in edgeR. See |
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998 Section 1.2 in the `edgeR User's Guide`_ for more detail. |
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999 |
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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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1000 * 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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1001 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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1002 data. Bioinformatics 26, 139-140 |
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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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1003 |
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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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1004 * Robinson MD and Smyth GK (2007). Moderated statistical tests for assessing |
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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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1005 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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1006 |
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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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1007 * Robinson MD and Smyth GK (2008). Small-sample estimation of negative |
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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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1008 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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1009 Biostatistics, 9, 321-332 |
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1010 |
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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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1011 * McCarthy DJ, Chen Y and Smyth GK (2012). Differential expression analysis |
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1012 of multifactor RNA-Seq experiments with respect to biological variation. |
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1013 Nucleic Acids Research 40, 4288-4297 |
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1014 |
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1015 Please report problems or suggestions to: su.s@wehi.edu.au |
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1016 |
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1017 .. _limma: http://www.bioconductor.org/packages/release/bioc/html/limma.html |
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9
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1018 .. _Glimma: https://bioconductor.org/packages/release/bioc/html/Glimma.html |
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14
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1019 .. _here: https://f1000research.com/articles/5-1408/v3 |
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1020 .. _limma approach: https://www.ncbi.nlm.nih.gov/pubmed/25605792 |
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1021 .. _limma User's Guide: http://bioconductor.org/packages/release/bioc/vignettes/limma/inst/doc/usersguide.pdf |
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0
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1022 .. _edgeR: http://www.bioconductor.org/packages/release/bioc/html/edgeR.html |
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3
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1023 .. _edgeR User's Guide: https://bioconductor.org/packages/release/bioc/vignettes/edgeR/inst/doc/edgeRUsersGuide.pdf |
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6
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1024 .. _McCarthy and Smyth, 2009: https://www.ncbi.nlm.nih.gov/pubmed/19176553 |
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1025 .. _Phipson et al. 2016: https://www.ncbi.nlm.nih.gov/pubmed/28367255 |
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1026 ]]></help> |
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1027 <citations> |
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1028 <citation type="doi">10.1186/gb-2014-15-2-r29</citation> |
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1029 <citation type="doi">10.1093/nar/gkv412</citation> |
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1030 </citations> |
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15
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1031 </tool> |