Mercurial > repos > iuc > ruvseq
annotate ruvseq.xml @ 5:557362ddaf9e draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit 30117fce22f3771c9c0c13e70c3ad14b694de6e2
| author | iuc |
|---|---|
| date | Fri, 21 Apr 2023 14:08:58 +0000 |
| parents | 6d7a31ff056f |
| children |
| rev | line source |
|---|---|
|
2
a32619eef8b9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit 4daa375d022673d2437d609b1865b78c64b04415"
iuc
parents:
1
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changeset
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1 <tool id="ruvseq" name="Remove Unwanted Variation" version="@TOOL_VERSION@+galaxy@WRAPPER_VERSION@"> |
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0
5f56d460bce3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit b95582cea8320d5488056a9576474f79cec53be8
iuc
parents:
diff
changeset
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2 <description>from RNA-seq data</description> |
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4
6d7a31ff056f
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
3
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changeset
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3 <xrefs> |
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6d7a31ff056f
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
3
diff
changeset
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4 <xref type="bio.tools">ruvseq</xref> |
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5
557362ddaf9e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit 30117fce22f3771c9c0c13e70c3ad14b694de6e2
iuc
parents:
4
diff
changeset
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5 <xref type="bioconductor">ruvseq</xref> |
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4
6d7a31ff056f
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
3
diff
changeset
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6 </xrefs> |
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2
a32619eef8b9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit 4daa375d022673d2437d609b1865b78c64b04415"
iuc
parents:
1
diff
changeset
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7 <macros> |
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3
eec9b8bca012
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit 498fcd4984152eee329802014c7886b9469f97d6"
iuc
parents:
2
diff
changeset
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8 <token name="@TOOL_VERSION@">1.26.0</token> |
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5
557362ddaf9e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit 30117fce22f3771c9c0c13e70c3ad14b694de6e2
iuc
parents:
4
diff
changeset
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9 <token name="@WRAPPER_VERSION@">1</token> |
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2
a32619eef8b9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit 4daa375d022673d2437d609b1865b78c64b04415"
iuc
parents:
1
diff
changeset
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10 </macros> |
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0
5f56d460bce3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit b95582cea8320d5488056a9576474f79cec53be8
iuc
parents:
diff
changeset
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11 <requirements> |
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2
a32619eef8b9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit 4daa375d022673d2437d609b1865b78c64b04415"
iuc
parents:
1
diff
changeset
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12 <requirement type="package" version="@TOOL_VERSION@">bioconductor-ruvseq</requirement> |
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3
eec9b8bca012
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit 498fcd4984152eee329802014c7886b9469f97d6"
iuc
parents:
2
diff
changeset
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13 <requirement type="package" version="1.32.0">bioconductor-deseq2</requirement> |
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eec9b8bca012
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit 498fcd4984152eee329802014c7886b9469f97d6"
iuc
parents:
2
diff
changeset
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14 <requirement type="package" version="1.20.0">bioconductor-tximport</requirement> |
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eec9b8bca012
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit 498fcd4984152eee329802014c7886b9469f97d6"
iuc
parents:
2
diff
changeset
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15 <requirement type="package" version="1.44.0">bioconductor-genomicfeatures</requirement> |
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eec9b8bca012
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit 498fcd4984152eee329802014c7886b9469f97d6"
iuc
parents:
2
diff
changeset
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16 <requirement type="package" version="0.9.1">r-ggrepel</requirement> |
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eec9b8bca012
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit 498fcd4984152eee329802014c7886b9469f97d6"
iuc
parents:
2
diff
changeset
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17 <requirement type="package" version="1.20.3">r-getopt</requirement> |
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eec9b8bca012
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit 498fcd4984152eee329802014c7886b9469f97d6"
iuc
parents:
2
diff
changeset
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18 <requirement type="package" version="1.4.4">r-reshape2</requirement> |
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0
5f56d460bce3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit b95582cea8320d5488056a9576474f79cec53be8
iuc
parents:
diff
changeset
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19 </requirements> |
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5f56d460bce3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit b95582cea8320d5488056a9576474f79cec53be8
iuc
parents:
diff
changeset
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20 <stdio> |
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5f56d460bce3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit b95582cea8320d5488056a9576474f79cec53be8
iuc
parents:
diff
changeset
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21 <regex match="Execution halted" |
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5f56d460bce3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit b95582cea8320d5488056a9576474f79cec53be8
iuc
parents:
diff
changeset
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22 source="both" |
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5f56d460bce3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit b95582cea8320d5488056a9576474f79cec53be8
iuc
parents:
diff
changeset
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23 level="fatal" |
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5f56d460bce3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit b95582cea8320d5488056a9576474f79cec53be8
iuc
parents:
diff
changeset
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24 description="Execution halted." /> |
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5f56d460bce3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit b95582cea8320d5488056a9576474f79cec53be8
iuc
parents:
diff
changeset
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25 <regex match="Error in" |
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5f56d460bce3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit b95582cea8320d5488056a9576474f79cec53be8
iuc
parents:
diff
changeset
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26 source="both" |
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5f56d460bce3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit b95582cea8320d5488056a9576474f79cec53be8
iuc
parents:
diff
changeset
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27 level="fatal" |
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5f56d460bce3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit b95582cea8320d5488056a9576474f79cec53be8
iuc
parents:
diff
changeset
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28 description="An undefined error occurred, please check your input carefully and contact your administrator." /> |
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5f56d460bce3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit b95582cea8320d5488056a9576474f79cec53be8
iuc
parents:
diff
changeset
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29 <regex match="Fatal error" |
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5f56d460bce3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit b95582cea8320d5488056a9576474f79cec53be8
iuc
parents:
diff
changeset
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30 source="both" |
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5f56d460bce3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit b95582cea8320d5488056a9576474f79cec53be8
iuc
parents:
diff
changeset
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31 level="fatal" |
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5f56d460bce3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit b95582cea8320d5488056a9576474f79cec53be8
iuc
parents:
diff
changeset
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32 description="An undefined error occurred, please check your input carefully and contact your administrator." /> |
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5f56d460bce3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit b95582cea8320d5488056a9576474f79cec53be8
iuc
parents:
diff
changeset
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33 </stdio> |
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5f56d460bce3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit b95582cea8320d5488056a9576474f79cec53be8
iuc
parents:
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changeset
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34 <version_command><![CDATA[ |
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5f56d460bce3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit b95582cea8320d5488056a9576474f79cec53be8
iuc
parents:
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changeset
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35 echo $(R --version | grep version | grep -v GNU)", RUVSeq version" $(R --vanilla --slave -e "library(RUVSeq); cat(sessionInfo()\$otherPkgs\$RUVSeq\$Version)" 2> /dev/null | grep -v -i "WARNING: ") |
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5f56d460bce3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit b95582cea8320d5488056a9576474f79cec53be8
iuc
parents:
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changeset
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36 ]]></version_command> |
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5f56d460bce3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit b95582cea8320d5488056a9576474f79cec53be8
iuc
parents:
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changeset
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37 <command><![CDATA[ |
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5f56d460bce3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit b95582cea8320d5488056a9576474f79cec53be8
iuc
parents:
diff
changeset
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38 #if $tximport.tximport_selector == 'tximport': |
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5f56d460bce3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit b95582cea8320d5488056a9576474f79cec53be8
iuc
parents:
diff
changeset
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39 #if $tximport.mapping_format.mapping_format_selector == 'gtf': |
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5f56d460bce3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit b95582cea8320d5488056a9576474f79cec53be8
iuc
parents:
diff
changeset
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40 ln -s '$tximport.mapping_format.gtf_file' mapping.gtf && |
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5f56d460bce3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit b95582cea8320d5488056a9576474f79cec53be8
iuc
parents:
diff
changeset
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41 #else: |
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5f56d460bce3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit b95582cea8320d5488056a9576474f79cec53be8
iuc
parents:
diff
changeset
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42 ln -s '$tximport.mapping_format.tabular_file' mapping.txt && |
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5f56d460bce3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit b95582cea8320d5488056a9576474f79cec53be8
iuc
parents:
diff
changeset
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43 #end if |
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5f56d460bce3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit b95582cea8320d5488056a9576474f79cec53be8
iuc
parents:
diff
changeset
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44 #end if |
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5f56d460bce3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit b95582cea8320d5488056a9576474f79cec53be8
iuc
parents:
diff
changeset
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45 |
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5f56d460bce3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit b95582cea8320d5488056a9576474f79cec53be8
iuc
parents:
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46 Rscript '${__tool_directory__}/ruvseq.R' |
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5f56d460bce3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit b95582cea8320d5488056a9576474f79cec53be8
iuc
parents:
diff
changeset
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47 #if $pdf: |
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5f56d460bce3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit b95582cea8320d5488056a9576474f79cec53be8
iuc
parents:
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48 -p '$plots' |
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5f56d460bce3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit b95582cea8320d5488056a9576474f79cec53be8
iuc
parents:
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changeset
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49 #end if |
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5f56d460bce3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit b95582cea8320d5488056a9576474f79cec53be8
iuc
parents:
diff
changeset
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50 |
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5f56d460bce3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit b95582cea8320d5488056a9576474f79cec53be8
iuc
parents:
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changeset
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51 --sample_json '$sampleTable' |
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5f56d460bce3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit b95582cea8320d5488056a9576474f79cec53be8
iuc
parents:
diff
changeset
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52 |
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5f56d460bce3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit b95582cea8320d5488056a9576474f79cec53be8
iuc
parents:
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changeset
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53 $header |
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5f56d460bce3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit b95582cea8320d5488056a9576474f79cec53be8
iuc
parents:
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54 |
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5f56d460bce3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit b95582cea8320d5488056a9576474f79cec53be8
iuc
parents:
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changeset
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55 --min_k $min_k |
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5f56d460bce3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit b95582cea8320d5488056a9576474f79cec53be8
iuc
parents:
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56 --max_k $max_k |
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1
99e0c629d3a2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit 9ed3d83cc447ee897af867362bf1dd67af8a11c2
iuc
parents:
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57 --min_mean_count $min_mean_count |
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5f56d460bce3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit b95582cea8320d5488056a9576474f79cec53be8
iuc
parents:
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changeset
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58 |
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5f56d460bce3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit b95582cea8320d5488056a9576474f79cec53be8
iuc
parents:
diff
changeset
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59 #if $tximport.tximport_selector == 'tximport': |
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5f56d460bce3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit b95582cea8320d5488056a9576474f79cec53be8
iuc
parents:
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changeset
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60 --txtype $tximport.txtype |
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5f56d460bce3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit b95582cea8320d5488056a9576474f79cec53be8
iuc
parents:
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changeset
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61 #if $tximport.mapping_format.mapping_format_selector == 'gtf': |
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5f56d460bce3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit b95582cea8320d5488056a9576474f79cec53be8
iuc
parents:
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changeset
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62 --tx2gene mapping.gtf |
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5f56d460bce3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit b95582cea8320d5488056a9576474f79cec53be8
iuc
parents:
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63 #else: |
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5f56d460bce3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit b95582cea8320d5488056a9576474f79cec53be8
iuc
parents:
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changeset
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64 --tx2gene mapping.txt |
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5f56d460bce3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit b95582cea8320d5488056a9576474f79cec53be8
iuc
parents:
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65 #end if |
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5f56d460bce3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit b95582cea8320d5488056a9576474f79cec53be8
iuc
parents:
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66 #end if |
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5
557362ddaf9e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit 30117fce22f3771c9c0c13e70c3ad14b694de6e2
iuc
parents:
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67 |
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557362ddaf9e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit 30117fce22f3771c9c0c13e70c3ad14b694de6e2
iuc
parents:
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68 #if $ruv_ncounts == 1: |
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557362ddaf9e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit 30117fce22f3771c9c0c13e70c3ad14b694de6e2
iuc
parents:
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69 --ruv_ncounts |
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557362ddaf9e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit 30117fce22f3771c9c0c13e70c3ad14b694de6e2
iuc
parents:
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70 #end if |
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0
5f56d460bce3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit b95582cea8320d5488056a9576474f79cec53be8
iuc
parents:
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71 ]]></command> |
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5f56d460bce3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit b95582cea8320d5488056a9576474f79cec53be8
iuc
parents:
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changeset
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72 <configfiles> |
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5f56d460bce3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit b95582cea8320d5488056a9576474f79cec53be8
iuc
parents:
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73 <configfile name="sampleTable"> |
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5f56d460bce3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit b95582cea8320d5488056a9576474f79cec53be8
iuc
parents:
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74 #import json |
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5f56d460bce3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit b95582cea8320d5488056a9576474f79cec53be8
iuc
parents:
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75 #set sample_table = [] |
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5f56d460bce3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit b95582cea8320d5488056a9576474f79cec53be8
iuc
parents:
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76 #for $level in $rep_factorLevel: |
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5f56d460bce3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit b95582cea8320d5488056a9576474f79cec53be8
iuc
parents:
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changeset
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77 #for $file in $level.countsFile: |
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5f56d460bce3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit b95582cea8320d5488056a9576474f79cec53be8
iuc
parents:
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78 #silent $sample_table.append({"path": str($file), "label": str($file.element_identifier), "condition": str($level.factorLevel)}) |
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5f56d460bce3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit b95582cea8320d5488056a9576474f79cec53be8
iuc
parents:
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79 #end for |
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5f56d460bce3
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80 #end for |
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81 #echo json.dumps($sample_table) |
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82 </configfile> |
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83 </configfiles> |
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84 <inputs> |
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85 <repeat name="rep_factorLevel" title="Factor level" min="2" default="2"> |
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86 <param name="factorLevel" type="text" value="FactorLevel" label="Specify a factor level, typical values could be 'tumor', 'normal', 'treated' or 'control'" |
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87 help="Only letters, numbers and underscores will be retained in this field"> |
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88 <sanitizer> |
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89 <valid initial="string.letters,string.digits"><add value="_" /></valid> |
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90 </sanitizer> |
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91 </param> |
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92 <param name="countsFile" type="data" format="tabular" multiple="true" label="Counts file(s)"/> |
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93 </repeat> |
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94 <param name="min_k" type="integer" value="1" min="1" label="Try to find at least this many factors of unwanted variation" /> |
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5f56d460bce3
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95 <param name="max_k" type="integer" value="1" min="1" label="Try to find at most this many factors of unwanted variation" /> |
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96 <param name="min_mean_count" type="integer" value="5" min="0" label="Ignore genes with fewer than this many counts on average" /> |
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97 <param name="header" type="boolean" truevalue="-H" falsevalue="" checked="true" label="Files have header?" help="If this option is set to Yes, the tool will assume that the count files have column headers in the first row. Default: Yes" /> |
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98 |
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99 <conditional name="tximport"> |
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100 <param name="tximport_selector" type="select" label="Choice of Input data"> |
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101 <option value="count" selected="True">Count data (e.g. from HTSeq-count, featureCounts or StringTie)</option> |
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102 <option value="tximport">TPM values (e.g. from kallisto, sailfish or salmon)</option> |
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103 </param> |
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104 <when value="tximport"> |
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105 <param name="txtype" type="select" label="Program used to generate TPMs"> |
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106 <option value="kallisto">kallisto</option> |
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107 <option value="sailfish">Sailfish</option> |
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108 <option value="salmon">Salmon</option> |
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109 </param> |
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110 <conditional name="mapping_format"> |
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111 <param name="mapping_format_selector" type="select" label="Gene mapping format"> |
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112 <option value="gtf" selected="True">GTF</option> |
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113 <option value="tabular">Transcript-ID and Gene-ID mapping file</option> |
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114 </param> |
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115 <when value="gtf"> |
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116 <param name="gtf_file" type="data" format="gtf,gff3" label="GTF/GFF3 file with Transcript - Gene mapping"/> |
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117 </when> |
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118 <when value="tabular"> |
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119 <param name="tabular_file" type="data" format="tabular" label="Tabular file with Transcript - Gene mapping"/> |
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120 </when> |
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121 </conditional> |
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122 </when> |
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123 <when value="count" /> |
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124 </conditional> |
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125 <param name="pdf" type="boolean" truevalue="1" falsevalue="0" checked="true" |
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126 label="Visualising the analysis results" |
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127 help="output an additional PDF files" /> |
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5
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128 <param name="ruv_ncounts" type="boolean" truevalue="1" falsevalue="0" checked="false" |
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129 label="Output RUVSeq normalized count tables" |
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130 help="If this option is set to Yes, the tool will generate RUVseq normalized count files. Default: No" /> |
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0
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131 </inputs> |
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132 <outputs> |
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133 <collection name="unwanted_variation" type="list" label="RUVSeq covariate files on ${on_string}"> |
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5
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134 <discover_datasets pattern="uv_(?P<designation>.+)\.tabular" format="tabular" directory="." visible="false"/> |
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135 </collection> |
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136 <collection name="ruv_normcounts" type="list" label="RUVSeq normalized counts on ${on_string}"> |
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137 <filter>ruv_ncounts == True</filter> |
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138 <discover_datasets pattern="ruv_(?P<designation>.+)\.tabular" format="tabular" directory="." visible="false"/> |
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0
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139 </collection> |
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140 <data format="pdf" name="plots" label="RUVSeq diagonstic plots on ${on_string}"> |
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141 <filter>pdf == True</filter> |
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142 </data> |
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143 </outputs> |
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144 <tests> |
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145 <!--Ensure counts files with header works --> |
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146 <test> |
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147 <repeat name="rep_factorLevel"> |
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148 <param name="factorLevel" value="Treated"/> |
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149 <param name="countsFile" value="GSM461179_treat_single.counts,GSM461180_treat_paired.counts,GSM461181_treat_paired.counts"/> |
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150 </repeat> |
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151 <repeat name="rep_factorLevel"> |
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152 <param name="factorLevel" value="Untreated"/> |
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153 <param name="countsFile" value="GSM461176_untreat_single.counts,GSM461177_untreat_paired.counts,GSM461178_untreat_paired.counts,GSM461182_untreat_single.counts"/> |
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154 </repeat> |
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155 <param name="pdf" value="true"/> |
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156 <output name="plots" file="ruvseq_diag.pdf" ftype="pdf" compare="sim_size"/> |
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157 <output_collection name="unwanted_variation" type="list"> |
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158 <element name="batch_effects_control_method_k1"> |
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159 <assert_contents> |
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160 <has_text_matching expression="identifier\tcondition\tW_1"/> |
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161 <has_text_matching expression="GSM461179.*\tTreated\t\-.+"/> |
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0
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162 </assert_contents> |
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163 </element> |
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164 <element name="batch_effects_replicate_method_k1"> |
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165 <assert_contents> |
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166 <has_text_matching expression="identifier\tcondition\tW_1"/> |
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167 <has_text_matching expression="GSM461179.*\tTreated\t\-.+"/> |
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0
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168 </assert_contents> |
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169 </element> |
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170 <element name="batch_effects_residual_method_k1"> |
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171 <assert_contents> |
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172 <has_text_matching expression="identifier\tcondition\tW_1"/> |
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173 <has_text_matching expression="GSM461179.*\tTreated\t\-.+"/> |
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0
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174 </assert_contents> |
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175 </element> |
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176 </output_collection> |
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177 </test> |
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178 <!--Ensure counts files without header works --> |
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179 <test> |
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180 <repeat name="rep_factorLevel"> |
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181 <param name="factorLevel" value="Treated"/> |
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182 <param name="countsFile" value="GSM461179_treat_single.counts.noheader,GSM461180_treat_paired.counts.noheader,GSM461181_treat_paired.counts.noheader"/> |
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183 </repeat> |
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184 <repeat name="rep_factorLevel"> |
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185 <param name="factorLevel" value="Untreated"/> |
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186 <param name="countsFile" value="GSM461176_untreat_single.counts.noheader,GSM461177_untreat_paired.counts.noheader,GSM461178_untreat_paired.counts.noheader,GSM461182_untreat_single.counts.noheader"/> |
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187 </repeat> |
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188 <param name="pdf" value="true"/> |
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189 <param name="header" value="false"/> |
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190 <output name="plots" file="ruvseq_diag.pdf" ftype="pdf" compare="sim_size"/> |
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191 <output_collection name="unwanted_variation" type="list"> |
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192 <element name="batch_effects_control_method_k1"> |
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193 <assert_contents> |
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194 <has_text_matching expression="identifier\tcondition\tW_1"/> |
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195 <has_text_matching expression="GSM461179.*\tTreated\t\-.+"/> |
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0
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196 </assert_contents> |
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197 </element> |
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198 <element name="batch_effects_replicate_method_k1"> |
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199 <assert_contents> |
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200 <has_text_matching expression="identifier\tcondition\tW_1"/> |
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201 <has_text_matching expression="GSM461179.*\tTreated\t\-.+"/> |
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0
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202 </assert_contents> |
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203 </element> |
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204 <element name="batch_effects_residual_method_k1"> |
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205 <assert_contents> |
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206 <has_text_matching expression="identifier\tcondition\tW_1"/> |
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207 <has_text_matching expression="GSM461179.*\tTreated\t\-.+"/> |
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0
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208 </assert_contents> |
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209 </element> |
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210 </output_collection> |
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211 </test> |
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212 <!--Ensure sailfish files work --> |
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213 <test> |
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214 <repeat name="rep_factorLevel"> |
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215 <param name="factorLevel" value="Treated"/> |
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216 <param name="countsFile" value="sailfish/sailfish_quant.sf1.tab,sailfish/sailfish_quant.sf2.tab,sailfish/sailfish_quant.sf3.tab"/> |
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217 </repeat> |
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218 <repeat name="rep_factorLevel"> |
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219 <param name="factorLevel" value="Untreated"/> |
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220 <param name="countsFile" value="sailfish/sailfish_quant.sf4.tab,sailfish/sailfish_quant.sf5.tab,sailfish/sailfish_quant.sf6.tab"/> |
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221 </repeat> |
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222 <param name="pdf" value="true"/> |
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223 <param name="tximport_selector" value="tximport"/> |
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224 <param name="txtype" value="sailfish"/> |
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225 <param name="mapping_format_selector" value="tabular"/> |
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226 <param name="tabular_file" value="tx2gene.tab"/> |
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227 <param name="min_mean_count" value="0"/> |
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228 <output name="plots" file="ruvseq_diag_sailfish.pdf" ftype="pdf" compare="sim_size"/> |
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229 <output_collection name="unwanted_variation" type="list"> |
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230 <element name="batch_effects_control_method_k1"> |
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231 <assert_contents> |
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232 <has_text_matching expression="identifier\tcondition\tW_1"/> |
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233 <has_text_matching expression=".*sailfish_quant.sf1.tab\tTreated\t.+"/> |
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0
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234 </assert_contents> |
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235 </element> |
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236 <element name="batch_effects_replicate_method_k1"> |
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237 <assert_contents> |
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238 <has_text_matching expression="identifier\tcondition\tW_1"/> |
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1
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239 <has_text_matching expression=".*sailfish_quant.sf1.tab\tTreated\t.+"/> |
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0
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240 </assert_contents> |
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241 </element> |
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242 <element name="batch_effects_residual_method_k1"> |
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243 <assert_contents> |
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244 <has_text_matching expression="identifier\tcondition\tW_1"/> |
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1
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245 <has_text_matching expression=".*sailfish_quant.sf1.tab\tTreated\t.+"/> |
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0
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246 </assert_contents> |
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247 </element> |
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248 </output_collection> |
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249 </test> |
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5
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250 <!--Ensure Normalized counts files are generated --> |
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251 <test> |
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252 <repeat name="rep_factorLevel"> |
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253 <param name="factorLevel" value="Treated"/> |
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254 <param name="countsFile" value="GSM461179_treat_single.counts,GSM461180_treat_paired.counts,GSM461181_treat_paired.counts"/> |
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557362ddaf9e
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255 </repeat> |
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256 <repeat name="rep_factorLevel"> |
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257 <param name="factorLevel" value="Untreated"/> |
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258 <param name="countsFile" value="GSM461176_untreat_single.counts,GSM461177_untreat_paired.counts,GSM461178_untreat_paired.counts,GSM461182_untreat_single.counts"/> |
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557362ddaf9e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit 30117fce22f3771c9c0c13e70c3ad14b694de6e2
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259 </repeat> |
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260 <param name="pdf" value="true"/> |
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261 <param name="ruv_ncounts" value="true"/> |
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262 <output name="plots" file="ruvseq_diag.pdf" ftype="pdf" compare="sim_size"/> |
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263 <output_collection name="ruv_normcounts" type="list"> |
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264 <element name="norm_counts_control_method_k1"> |
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265 <assert_contents> |
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266 <has_text_matching expression="geneID\tGSM461179_treat_single.counts\tGSM461180_treat_paired.counts\t.+"/> |
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267 </assert_contents> |
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268 </element> |
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269 <element name="norm_counts_replicate_method_k1"> |
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270 <assert_contents> |
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271 <has_text_matching expression="geneID\tGSM461179_treat_single.counts\tGSM461180_treat_paired.counts\t.+"/> |
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272 </assert_contents> |
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273 </element> |
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274 <element name="norm_counts_residual_method_k1"> |
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275 <assert_contents> |
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276 <has_text_matching expression="geneID\tGSM461179_treat_single.counts\tGSM461180_treat_paired.counts\t.+"/> |
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277 </assert_contents> |
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278 </element> |
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279 </output_collection> |
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280 </test> |
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281 <!--Ensure Normalized counts are generated with sailfish files --> |
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282 <test> |
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283 <repeat name="rep_factorLevel"> |
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284 <param name="factorLevel" value="Treated"/> |
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285 <param name="countsFile" value="sailfish/sailfish_quant.sf1.tab,sailfish/sailfish_quant.sf2.tab,sailfish/sailfish_quant.sf3.tab"/> |
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286 </repeat> |
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287 <repeat name="rep_factorLevel"> |
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288 <param name="factorLevel" value="Untreated"/> |
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289 <param name="countsFile" value="sailfish/sailfish_quant.sf4.tab,sailfish/sailfish_quant.sf5.tab,sailfish/sailfish_quant.sf6.tab"/> |
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290 </repeat> |
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291 <param name="pdf" value="true"/> |
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292 <param name="tximport_selector" value="tximport"/> |
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293 <param name="txtype" value="sailfish"/> |
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294 <param name="mapping_format_selector" value="tabular"/> |
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295 <param name="tabular_file" value="tx2gene.tab"/> |
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296 <param name="min_mean_count" value="0"/> |
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297 <param name="ruv_ncounts" value="true"/> |
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298 <output name="plots" file="ruvseq_diag_sailfish.pdf" ftype="pdf" compare="sim_size"/> |
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299 <output_collection name="ruv_normcounts" type="list"> |
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300 <element name="norm_counts_control_method_k1"> |
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301 <assert_contents> |
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302 <has_text_matching expression="geneID\tsailfish_quant.sf1.tab\tsailfish_quant.sf2.tab\t.+"/> |
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303 </assert_contents> |
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304 </element> |
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305 <element name="norm_counts_replicate_method_k1"> |
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306 <assert_contents> |
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307 <has_text_matching expression="geneID\tsailfish_quant.sf1.tab\tsailfish_quant.sf2.tab\t.+"/> |
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308 </assert_contents> |
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309 </element> |
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310 <element name="norm_counts_residual_method_k1"> |
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311 <assert_contents> |
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312 <has_text_matching expression="geneID\tsailfish_quant.sf1.tab\tsailfish_quant.sf2.tab\t.+"/> |
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313 </assert_contents> |
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314 </element> |
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315 </output_collection> |
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316 </test> |
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317 </tests> |
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318 <help><![CDATA[ |
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319 .. class:: infomark |
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320 |
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321 **What it does** |
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322 |
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323 RUVSeq normalizes RNA-seq data using factor analysis of control genes or samples. RUVSeq has been designed for detecting unwanted variation using replicate sample information. The current RUVSeq Galaxy tool only implements estimating unwanted variation for primary factors. |
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324 RUVSeq implements 3 different methods for the estimation of unwanted variation: |
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325 |
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326 RUVg estimates the factors of unwanted variation using control genes |
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327 |
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328 RUVs estimates the factors of unwanted variation using replicate samples |
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329 |
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330 RUVr estimating the factors of unwanted variation using residuals. |
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331 |
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332 This tool runs all RUV methods and outputs diagnostic plots and tables with covariates that |
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333 may be used for differential expression analsys. |
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334 |
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335 ----- |
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336 |
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337 **Inputs** |
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338 |
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339 **Count Files** |
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340 |
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341 RUVSeq_ takes count tables generated from **featureCounts**, **HTSeq-count** or **StringTie** as input. Count tables must be generated for each sample individually. One header row is assumed, but files with no header (e.g from HTSeq) can be input with the *Files have header?* option set to No. |
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342 |
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343 RUVSeq_ can also take transcript-level counts from quantification tools such as, **kallisto**, **Salmon** and **Sailfish**, and this Galaxy wrapper incorporates the Bioconductor tximport_ package to process the transcript counts for DESeq2. |
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344 |
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345 **Salmon or Sailfish Files** |
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346 |
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347 Salmon or Sailfish ``quant.sf`` files can be imported by setting type to *Salmon* or *Sailfish* respectively above. Note: for previous version of Salmon or Sailfish, in which the quant.sf files start with comment lines you will need to remove the comment lines before inputting here. An example of the format is shown below. |
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348 |
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349 Example: |
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350 |
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351 ============ ========== =============== =========== =========== |
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352 Name Length EffectiveLength TPM NumReads |
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353 ------------ ---------- --------------- ----------- ----------- |
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354 NR_001526 164 20.4518 0 0 |
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355 NR_001526_1 164 20.4518 0 0 |
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356 NR_001526_2 164 20.4518 0 0 |
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5f56d460bce3
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357 NM_130786 1764 1956.04 2.47415 109.165 |
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358 NR_015380 2129 2139.53 1.77331 85.5821 |
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359 NM_001198818 9360 7796.58 2.38616e-07 4.19648e-05 |
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360 NM_001198819 9527 7964.62 0 0 |
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361 NM_001198820 9410 7855.78 0 0 |
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362 NM_014576 9267 7714.88 0.0481114 8.37255 |
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363 ============ ========== =============== =========== =========== |
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364 |
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365 **kallisto Files** |
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366 |
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367 kallisto ``abundance.tsv`` files can be imported by setting type to *kallisto* above. An example of the format is shown below. |
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368 |
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369 Example: |
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370 |
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371 ============ ========== =============== =========== =========== |
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372 target_id length eff_length est_counts tpm |
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373 ------------ ---------- --------------- ----------- ----------- |
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374 NR_001526 164 20.4518 0 0 |
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375 NR_001526_1 164 20.4518 0 0 |
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376 NR_001526_2 164 20.4518 0 0 |
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5f56d460bce3
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377 NM_130786 1764 1956.04 109.165 2.47415 |
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378 NR_015380 2129 2139.53 85.5821 1.77331 |
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379 NM_001198818 9360 7796.58 4.19648e-05 2.38616e-07 |
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380 NM_001198819 9527 7964.62 0 0 |
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381 NM_001198820 9410 7855.78 0 0 |
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382 NM_014576 9267 7714.88 8.37255 0.0481114 |
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383 ============ ========== =============== =========== =========== |
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384 |
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385 ----- |
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386 |
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387 **Output** |
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388 |
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389 RUVSeq_ generates a tabular file for each method and each k of variation as well as a summary PDF. |
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390 |
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5
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391 RUVSeq can also generate RUVSeq normalized count tables. However, *these counts should be used only for exploration. It is important that subsequent DE analysis be done on the original counts, as removing the unwanted factors from the counts can also remove part of a factor of interest*. |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit 30117fce22f3771c9c0c13e70c3ad14b694de6e2
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392 |
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557362ddaf9e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit 30117fce22f3771c9c0c13e70c3ad14b694de6e2
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393 |
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5f56d460bce3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit b95582cea8320d5488056a9576474f79cec53be8
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394 .. _RUVSeq: http://master.bioconductor.org/packages/release/bioc/html/RUVSeq.html |
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5f56d460bce3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit b95582cea8320d5488056a9576474f79cec53be8
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395 .. _tximport: https://bioconductor.org/packages/devel/bioc/vignettes/tximport/inst/doc/tximport.html |
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5f56d460bce3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit b95582cea8320d5488056a9576474f79cec53be8
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396 ]]></help> |
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5f56d460bce3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit b95582cea8320d5488056a9576474f79cec53be8
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397 <citations> |
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5f56d460bce3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit b95582cea8320d5488056a9576474f79cec53be8
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398 <citation type="doi">10.1038/nbt.2931</citation> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit b95582cea8320d5488056a9576474f79cec53be8
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399 </citations> |
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5f56d460bce3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit b95582cea8320d5488056a9576474f79cec53be8
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400 </tool> |