Mercurial > repos > iuc > featurecounts
comparison featurecounts.xml @ 18:d60b1c4e0347 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit b467fdf3fabeed440dcb596108fc792d44e7d8d9
| author | iuc |
|---|---|
| date | Wed, 04 Jul 2018 17:32:47 -0400 |
| parents | 8ce1e2c7ee72 |
| children | f3a5f075498f |
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| 17:8ce1e2c7ee72 | 18:d60b1c4e0347 |
|---|---|
| 1 <tool id="featurecounts" name="featureCounts" version="1.6.0.7" profile="16.04"> | 1 <tool id="featurecounts" name="featureCounts" version="1.6.1.0" profile="16.04"> |
| 2 <description>Measure gene expression in RNA-Seq experiments from SAM or BAM files.</description> | 2 <description>Measure gene expression in RNA-Seq experiments from SAM or BAM files.</description> |
| 3 <requirements> | 3 <requirements> |
| 4 <requirement type="package" version="1.6.0">subread</requirement> | 4 <requirement type="package" version="1.6.1">subread</requirement> |
| 5 <requirement type="package" version="1.7">samtools</requirement> | 5 <requirement type="package" version="1.7">samtools</requirement> |
| 6 </requirements> | 6 </requirements> |
| 7 | 7 |
| 8 <version_command>featureCounts -v 2>&1 | grep .</version_command> | 8 <version_command>featureCounts -v 2>&1 | grep .</version_command> |
| 9 <command detect_errors="exit_code"><![CDATA[ | 9 <command detect_errors="exit_code"><![CDATA[ |
| 543 </output> | 543 </output> |
| 544 <output name="output_summary" file="output_1_summary.tab"> | 544 <output name="output_summary" file="output_1_summary.tab"> |
| 545 <metadata name="column_names" value="Status,featureCounts_input1.bam"/> | 545 <metadata name="column_names" value="Status,featureCounts_input1.bam"/> |
| 546 </output> | 546 </output> |
| 547 </test> | 547 </test> |
| 548 <!-- Ensure BAM output works --> | |
| 549 <test> | |
| 550 <param name="alignment" value="subset.sorted.bam" ftype="bam" /> | |
| 551 <param name="anno_select" value="history" /> | |
| 552 <param name="reference_gene_sets" value="small.gtf" ftype="gtf" /> | |
| 553 <section name="extended_parameters" > | |
| 554 <param name="R" value="true" /> | |
| 555 </section> | |
| 556 <output name="output_bam" value="subset.sorted.featurecounts.bam" /> | |
| 557 </test> | |
| 548 </tests> | 558 </tests> |
| 549 | 559 |
| 550 <help><![CDATA[ | 560 <help><![CDATA[ |
| 551 featureCounts | 561 featureCounts |
| 552 ############# | 562 ############# |