Mercurial > repos > iuc > limma_voom
comparison limma_voom.xml @ 23:e827f9aae031 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 38cf93fd693c810b4150c5d8aa3763aebc988b07"
| author | iuc |
|---|---|
| date | Mon, 29 Nov 2021 11:05:15 +0000 |
| parents | 708348a17fa1 |
| children | 32511f586472 |
comparison
equal
deleted
inserted
replaced
| 22:708348a17fa1 | 23:e827f9aae031 |
|---|---|
| 1 <tool id="limma_voom" name="limma" version="3.48.0+galaxy1"> | 1 <tool id="limma_voom" name="limma" version="@TOOL_VERSION@+galaxy2"> |
| 2 <description> | 2 <description> |
| 3 Perform differential expression with limma-voom or limma-trend | 3 Perform differential expression with limma-voom or limma-trend |
| 4 </description> | 4 </description> |
| 5 <macros> | |
| 6 <token name="@TOOL_VERSION@">3.48.0</token> | |
| 7 </macros> | |
| 5 <xrefs> | 8 <xrefs> |
| 6 <xref type="bio.tools">limma</xref> | 9 <xref type="bio.tools">limma</xref> |
| 7 </xrefs> | 10 </xrefs> |
| 8 <edam_topics> | 11 <edam_topics> |
| 9 <edam_topic>topic_3308</edam_topic> | 12 <edam_topic>topic_3308</edam_topic> |
| 12 <edam_operation>operation_3563</edam_operation> | 15 <edam_operation>operation_3563</edam_operation> |
| 13 <edam_operation>operation_3223</edam_operation> | 16 <edam_operation>operation_3223</edam_operation> |
| 14 </edam_operations> | 17 </edam_operations> |
| 15 | 18 |
| 16 <requirements> | 19 <requirements> |
| 17 <requirement type="package" version="3.48.0">bioconductor-limma</requirement> | 20 <requirement type="package" version="@TOOL_VERSION@">bioconductor-limma</requirement> |
| 18 <requirement type="package" version="3.34.0">bioconductor-edger</requirement> | 21 <requirement type="package" version="3.34.0">bioconductor-edger</requirement> |
| 19 <requirement type="package" version="1.4.36">r-statmod</requirement> | 22 <requirement type="package" version="1.4.36">r-statmod</requirement> |
| 20 <requirement type="package" version="1.1.1">r-scales</requirement> | 23 <requirement type="package" version="1.1.1">r-scales</requirement> |
| 21 <requirement type="package" version="0.2.20">r-rjson</requirement> | 24 <requirement type="package" version="0.2.20">r-rjson</requirement> |
| 22 <requirement type="package" version="1.20.3">r-getopt</requirement> | 25 <requirement type="package" version="1.20.3">r-getopt</requirement> |
| 269 <option value="cpm">CPM</option> | 272 <option value="cpm">CPM</option> |
| 270 <option value="counts">Counts</option> | 273 <option value="counts">Counts</option> |
| 271 </param> | 274 </param> |
| 272 <when value="cpm"> | 275 <when value="cpm"> |
| 273 <param name="cpmReq" type="float" value="1" min="0" label="Minimum CPM" help="Treat genes with CPM below this value as unexpressed and filter out. See the Filter Low Counts section below for more information."/> | 276 <param name="cpmReq" type="float" value="1" min="0" label="Minimum CPM" help="Treat genes with CPM below this value as unexpressed and filter out. See the Filter Low Counts section below for more information."/> |
| 274 <param name="cpmSampleReq" type="integer" value="0" min="0" label="Minimum Samples" | 277 <param name="cpmSampleReq" type="integer" value="0" min="0" label="Minimum Samples" |
| 275 help="Filter out all genes that do not meet the Minimum CPM in at least this many samples. See the Filter Low Counts section below for more information."/> | 278 help="Filter out all genes that do not meet the Minimum CPM in at least this many samples. See the Filter Low Counts section below for more information."/> |
| 276 </when> | 279 </when> |
| 277 <when value="counts"> | 280 <when value="counts"> |
| 278 <param name="cntReq" type="integer" value="0" min="0" label="Minimum Count" help="Filter out all genes that do not meet this minimum count. You can choose below to apply this filter to the total count for all samples or specify the number of samples under Minimum Samples. See the Filter Low Counts section below for more information." /> | 281 <param name="cntReq" type="integer" value="0" min="0" label="Minimum Count" help="Filter out all genes that do not meet this minimum count. You can choose below to apply this filter to the total count for all samples or specify the number of samples under Minimum Samples. See the Filter Low Counts section below for more information." /> |
| 279 <conditional name="samples"> | 282 <conditional name="samples"> |
| 280 <param name="count_select" type="select" label="Filter on Total Count or per Sample Count values?" > | 283 <param name="count_select" type="select" label="Filter on Total Count or per Sample Count values?" > |
| 281 <option value="total">Total</option> | 284 <option value="total">Total</option> |
| 282 <option value="sample">Sample</option> | 285 <option value="sample">Sample</option> |
| 283 </param> | 286 </param> |
| 284 <when value="total"> | 287 <when value="total"/> |
| 285 <param name="totReq" type="boolean" truevalue="1" falsevalue="0" checked="false" label="Filter on Total Count" help="Apply the Minimum Count filter to genes after summing counts for all samples. See the Filter Low Counts section below for more information." /> | |
| 286 </when> | |
| 287 <when value="sample"> | 288 <when value="sample"> |
| 288 <param name="cntSampleReq" type="integer" value="0" min="0" label="Minimum Samples" | 289 <param name="cntSampleReq" type="integer" value="0" min="0" label="Minimum Samples" |
| 289 help="Filter out all genes that do not meet the Minimum Count in at least this many samples. See the Filter Low Counts section below for more information."/> | 290 help="Filter out all genes that do not meet the Minimum Count in at least this many samples. See the Filter Low Counts section below for more information."/> |
| 290 </when> | 291 </when> |
| 291 </conditional> | 292 </conditional> |
| 726 <repeat name="rep_factor"> | 727 <repeat name="rep_factor"> |
| 727 <param name="factorName" value="Genotype"/> | 728 <param name="factorName" value="Genotype"/> |
| 728 <param name="groupNames" value="Mut,Mut,Mut,WT,WT,WT" /> | 729 <param name="groupNames" value="Mut,Mut,Mut,WT,WT,WT" /> |
| 729 </repeat> | 730 </repeat> |
| 730 <param name="cfile" value="yes" /> | 731 <param name="cfile" value="yes" /> |
| 731 <param name="cinfo" value="contrasts.txt" /> | 732 <param name="cinfo" value="contrasts.txt" ftype="tabular" /> |
| 732 <param name="normalisationOption" value="TMM" /> | 733 <param name="normalisationOption" value="TMM" /> |
| 733 <param name="topgenes" value="6" /> | 734 <param name="topgenes" value="6" /> |
| 734 <output_collection name="outTables" count="3"> | 735 <output_collection name="outTables" count="3"> |
| 735 <element name="limma-voom_Mut-WT" ftype="tabular" > | 736 <element name="limma-voom_Mut-WT" ftype="tabular" > |
| 736 <assert_contents> | 737 <assert_contents> |