Mercurial > repos > iuc > dexseq
annotate plotdexseq.xml @ 10:df929f257179 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 2ea27822b171dbf519509dc1da150c8ccee2a140
| author | iuc |
|---|---|
| date | Tue, 04 Apr 2023 08:25:51 +0000 |
| parents | b47c006d90c5 |
| children |
| rev | line source |
|---|---|
|
10
df929f257179
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 2ea27822b171dbf519509dc1da150c8ccee2a140
iuc
parents:
9
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1 <tool id="plotdexseq" name="plotDEXSeq" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@"> |
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5
278b189248cd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit c027cb925607cda29bb1e78fe76716af49a276ca
iuc
parents:
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2 <description>Visualization of the per gene DEXSeq results</description> |
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278b189248cd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit c027cb925607cda29bb1e78fe76716af49a276ca
iuc
parents:
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changeset
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3 <macros> |
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278b189248cd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit c027cb925607cda29bb1e78fe76716af49a276ca
iuc
parents:
diff
changeset
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4 <import>macros.xml</import> |
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278b189248cd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit c027cb925607cda29bb1e78fe76716af49a276ca
iuc
parents:
diff
changeset
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5 </macros> |
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10
df929f257179
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 2ea27822b171dbf519509dc1da150c8ccee2a140
iuc
parents:
9
diff
changeset
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6 <expand macro="xrefs"/> |
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df929f257179
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 2ea27822b171dbf519509dc1da150c8ccee2a140
iuc
parents:
9
diff
changeset
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7 <expand macro="requirements"/> |
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5
278b189248cd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit c027cb925607cda29bb1e78fe76716af49a276ca
iuc
parents:
diff
changeset
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8 <version_command><![CDATA[ |
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278b189248cd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit c027cb925607cda29bb1e78fe76716af49a276ca
iuc
parents:
diff
changeset
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9 echo $(R --version | grep version | grep -v GNU)", DEXSeq version" $(R --vanilla --slave -e "library(DEXSeq); cat(sessionInfo()\$otherPkgs\$DEXSeq\$Version)" 2> /dev/null | grep -v -i "WARNING: ")" (depends on DESeq2 "$(R --vanilla --slave -e "library(DESeq2); cat(sessionInfo()\$otherPkgs\$DESeq2\$Version)" 2> /dev/null | grep -v -i "WARNING: ")")" |
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278b189248cd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit c027cb925607cda29bb1e78fe76716af49a276ca
iuc
parents:
diff
changeset
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10 ]]></version_command> |
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278b189248cd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit c027cb925607cda29bb1e78fe76716af49a276ca
iuc
parents:
diff
changeset
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11 <command detect_errors="exit_code"><![CDATA[ |
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278b189248cd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit c027cb925607cda29bb1e78fe76716af49a276ca
iuc
parents:
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changeset
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12 Rscript '$__tool_directory__/plotdexseq.R' |
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278b189248cd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit c027cb925607cda29bb1e78fe76716af49a276ca
iuc
parents:
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changeset
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13 -r '$rdata' |
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278b189248cd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit c027cb925607cda29bb1e78fe76716af49a276ca
iuc
parents:
diff
changeset
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14 -p '$primaryfactor' |
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278b189248cd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit c027cb925607cda29bb1e78fe76716af49a276ca
iuc
parents:
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changeset
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15 #if $genes.genes_select == 'list': |
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278b189248cd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit c027cb925607cda29bb1e78fe76716af49a276ca
iuc
parents:
diff
changeset
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16 -f '$genes.genefile' |
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278b189248cd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit c027cb925607cda29bb1e78fe76716af49a276ca
iuc
parents:
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changeset
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17 #else: |
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278b189248cd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit c027cb925607cda29bb1e78fe76716af49a276ca
iuc
parents:
diff
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18 -g '$genes.geneid' |
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278b189248cd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit c027cb925607cda29bb1e78fe76716af49a276ca
iuc
parents:
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19 #end if |
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278b189248cd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit c027cb925607cda29bb1e78fe76716af49a276ca
iuc
parents:
diff
changeset
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20 -c $fdr_cutoff |
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278b189248cd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit c027cb925607cda29bb1e78fe76716af49a276ca
iuc
parents:
diff
changeset
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21 -t $transcripts |
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278b189248cd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit c027cb925607cda29bb1e78fe76716af49a276ca
iuc
parents:
diff
changeset
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22 -a $names |
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278b189248cd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit c027cb925607cda29bb1e78fe76716af49a276ca
iuc
parents:
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23 -n $normcounts |
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278b189248cd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit c027cb925607cda29bb1e78fe76716af49a276ca
iuc
parents:
diff
changeset
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24 -s $splicing |
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278b189248cd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit c027cb925607cda29bb1e78fe76716af49a276ca
iuc
parents:
diff
changeset
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25 ]]></command> |
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278b189248cd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit c027cb925607cda29bb1e78fe76716af49a276ca
iuc
parents:
diff
changeset
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26 <inputs> |
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278b189248cd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit c027cb925607cda29bb1e78fe76716af49a276ca
iuc
parents:
diff
changeset
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27 <param name="rdata" type="data" format="rdata" label="DEXSeqResults object" help="A DEXSeqResults object in RDS format. This can be output from the DEXSeq tool"/> |
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278b189248cd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit c027cb925607cda29bb1e78fe76716af49a276ca
iuc
parents:
diff
changeset
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28 <param name="primaryfactor" type="text" value="FactorName" label="Specify the primary factor name in the DEXSeqResults object" help="Only letters, numbers and underscores will be retained in this field"> |
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278b189248cd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit c027cb925607cda29bb1e78fe76716af49a276ca
iuc
parents:
diff
changeset
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29 <sanitizer> |
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278b189248cd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit c027cb925607cda29bb1e78fe76716af49a276ca
iuc
parents:
diff
changeset
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30 <valid initial="string.letters,string.digits"><add value="_" /></valid> |
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278b189248cd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit c027cb925607cda29bb1e78fe76716af49a276ca
iuc
parents:
diff
changeset
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31 </sanitizer> |
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278b189248cd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit c027cb925607cda29bb1e78fe76716af49a276ca
iuc
parents:
diff
changeset
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32 </param> |
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278b189248cd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit c027cb925607cda29bb1e78fe76716af49a276ca
iuc
parents:
diff
changeset
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33 <conditional name="genes"> |
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278b189248cd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit c027cb925607cda29bb1e78fe76716af49a276ca
iuc
parents:
diff
changeset
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34 <param name="genes_select" type="select" label="Genes to plot" help="Select to input a single gene ID or a list of IDs. Default: single gene ID"> |
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278b189248cd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit c027cb925607cda29bb1e78fe76716af49a276ca
iuc
parents:
diff
changeset
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35 <option value="single" selected="True">single</option> |
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278b189248cd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit c027cb925607cda29bb1e78fe76716af49a276ca
iuc
parents:
diff
changeset
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36 <option value="list">list</option> |
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278b189248cd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit c027cb925607cda29bb1e78fe76716af49a276ca
iuc
parents:
diff
changeset
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37 </param> |
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278b189248cd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit c027cb925607cda29bb1e78fe76716af49a276ca
iuc
parents:
diff
changeset
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38 <when value="single"> |
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278b189248cd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit c027cb925607cda29bb1e78fe76716af49a276ca
iuc
parents:
diff
changeset
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39 <param name="geneid" type="text" label="Gene identifier" help="Gene identifier to visualize"> |
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278b189248cd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit c027cb925607cda29bb1e78fe76716af49a276ca
iuc
parents:
diff
changeset
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40 <sanitizer> |
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278b189248cd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit c027cb925607cda29bb1e78fe76716af49a276ca
iuc
parents:
diff
changeset
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41 <valid initial="string.letters,string.digits"><add value="_" /></valid> |
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278b189248cd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit c027cb925607cda29bb1e78fe76716af49a276ca
iuc
parents:
diff
changeset
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42 </sanitizer> |
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278b189248cd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit c027cb925607cda29bb1e78fe76716af49a276ca
iuc
parents:
diff
changeset
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43 </param> |
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278b189248cd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit c027cb925607cda29bb1e78fe76716af49a276ca
iuc
parents:
diff
changeset
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44 </when> |
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278b189248cd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit c027cb925607cda29bb1e78fe76716af49a276ca
iuc
parents:
diff
changeset
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45 <when value="list"> |
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278b189248cd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit c027cb925607cda29bb1e78fe76716af49a276ca
iuc
parents:
diff
changeset
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46 <param name="genefile" type="data" format="tabular" label="List of gene IDs" help="This should be a single tabular column with one gene per row and no header." /> |
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278b189248cd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit c027cb925607cda29bb1e78fe76716af49a276ca
iuc
parents:
diff
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47 </when> |
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278b189248cd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit c027cb925607cda29bb1e78fe76716af49a276ca
iuc
parents:
diff
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48 </conditional> |
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278b189248cd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit c027cb925607cda29bb1e78fe76716af49a276ca
iuc
parents:
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49 <param name="fdr_cutoff" type="float" min="0.0" max="1.0" value="0.1" label="False Discovery Rate"/> |
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278b189248cd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit c027cb925607cda29bb1e78fe76716af49a276ca
iuc
parents:
diff
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50 <param name="transcripts" type="boolean" truevalue="True" falsevalue="False" checked="False" label="Display transcripts" help="If Yes, the transcripts are displayed in the plot. Default: No"/> |
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278b189248cd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit c027cb925607cda29bb1e78fe76716af49a276ca
iuc
parents:
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51 <param name="names" type="boolean" truevalue="True" falsevalue="False" checked="False" label="Display transcript names" help="If Yes, the names of the transcripts are shown. Default: No"/> |
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278b189248cd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit c027cb925607cda29bb1e78fe76716af49a276ca
iuc
parents:
diff
changeset
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52 <param name="normcounts" type="boolean" truevalue="True" falsevalue="False" checked="False" label="Plot count values from the individual samples" help="If yes, provides a plot of the counts normalized by the size factors. Default: No"/> |
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278b189248cd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit c027cb925607cda29bb1e78fe76716af49a276ca
iuc
parents:
diff
changeset
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53 <param name="splicing" type="boolean" truevalue="True" falsevalue="False" checked="False" label="Plot exon usage" help="If yes, the samples gene expression effects are averaged out, leaving only exon usage coefficients. Default: No" /> |
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278b189248cd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit c027cb925607cda29bb1e78fe76716af49a276ca
iuc
parents:
diff
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54 </inputs> |
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278b189248cd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit c027cb925607cda29bb1e78fe76716af49a276ca
iuc
parents:
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55 |
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278b189248cd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit c027cb925607cda29bb1e78fe76716af49a276ca
iuc
parents:
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56 <outputs> |
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278b189248cd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit c027cb925607cda29bb1e78fe76716af49a276ca
iuc
parents:
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57 <data name="dexseq_plot" format="pdf" from_work_dir="plot.pdf" label="${tool.name} on ${on_string}" /> |
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278b189248cd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit c027cb925607cda29bb1e78fe76716af49a276ca
iuc
parents:
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58 </outputs> |
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278b189248cd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit c027cb925607cda29bb1e78fe76716af49a276ca
iuc
parents:
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59 <tests> |
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278b189248cd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit c027cb925607cda29bb1e78fe76716af49a276ca
iuc
parents:
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60 <!-- Ensure default output works--> |
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278b189248cd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit c027cb925607cda29bb1e78fe76716af49a276ca
iuc
parents:
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61 <test expect_num_outputs="1"> |
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278b189248cd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit c027cb925607cda29bb1e78fe76716af49a276ca
iuc
parents:
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62 <param name="rdata" ftype="rdata" value="dexseq.rds"/> |
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278b189248cd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit c027cb925607cda29bb1e78fe76716af49a276ca
iuc
parents:
diff
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63 <param name="primaryfactor" value="condition"/> |
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278b189248cd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit c027cb925607cda29bb1e78fe76716af49a276ca
iuc
parents:
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64 <param name="geneid" value="FBgn0000053"/> |
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278b189248cd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit c027cb925607cda29bb1e78fe76716af49a276ca
iuc
parents:
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65 <param name="fdr_cutoff" value="1"/> |
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278b189248cd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit c027cb925607cda29bb1e78fe76716af49a276ca
iuc
parents:
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66 <output name="dexseq_plot" ftype="pdf" file="plotdexseq.pdf" compare="sim_size"/> |
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278b189248cd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit c027cb925607cda29bb1e78fe76716af49a276ca
iuc
parents:
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67 </test> |
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278b189248cd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit c027cb925607cda29bb1e78fe76716af49a276ca
iuc
parents:
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68 <!-- Ensure plotting multiple genes works--> |
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278b189248cd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit c027cb925607cda29bb1e78fe76716af49a276ca
iuc
parents:
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69 <test expect_num_outputs="1"> |
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278b189248cd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit c027cb925607cda29bb1e78fe76716af49a276ca
iuc
parents:
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70 <param name="rdata" ftype="rdata" value="dexseq.rds"/> |
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278b189248cd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit c027cb925607cda29bb1e78fe76716af49a276ca
iuc
parents:
diff
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71 <param name="primaryfactor" value="condition"/> |
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278b189248cd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit c027cb925607cda29bb1e78fe76716af49a276ca
iuc
parents:
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72 <param name="genefile" ftype="tabular" value="plotdexseq_genes.tab"/> |
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278b189248cd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit c027cb925607cda29bb1e78fe76716af49a276ca
iuc
parents:
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73 <param name="fdr_cutoff" value="1"/> |
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278b189248cd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit c027cb925607cda29bb1e78fe76716af49a276ca
iuc
parents:
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74 <output name="dexseq_plot" ftype="pdf" file="plotdexseq_multi.pdf" compare="sim_size"/> |
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278b189248cd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit c027cb925607cda29bb1e78fe76716af49a276ca
iuc
parents:
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75 </test> |
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278b189248cd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit c027cb925607cda29bb1e78fe76716af49a276ca
iuc
parents:
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76 </tests> |
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278b189248cd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit c027cb925607cda29bb1e78fe76716af49a276ca
iuc
parents:
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77 <help><![CDATA[ |
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278b189248cd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit c027cb925607cda29bb1e78fe76716af49a276ca
iuc
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78 .. class:: infomark |
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278b189248cd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit c027cb925607cda29bb1e78fe76716af49a276ca
iuc
parents:
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79 |
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278b189248cd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit c027cb925607cda29bb1e78fe76716af49a276ca
iuc
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80 **What it does** |
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278b189248cd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit c027cb925607cda29bb1e78fe76716af49a276ca
iuc
parents:
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81 |
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278b189248cd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit c027cb925607cda29bb1e78fe76716af49a276ca
iuc
parents:
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82 This tool enables visualization of DEXSeq results for individual genes. The input is a DEXSeqResults rds file, which can be output from the DEXSeq tool, and a single gene ID or list of IDs to plot. |
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83 |
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84 .. _DEXSeq: http://master.bioconductor.org/packages/release/bioc/html/DEXSeq.html |
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85 ]]></help> |
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86 <citations> |
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87 <citation type="doi">10.1101/gr.133744.111</citation> |
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88 </citations> |
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89 </tool> |