Mercurial > repos > jshay > hitsandclusters
comparison countandcluster/countandcluster.xml @ 0:c516cb51d12c draft
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| author | jshay |
|---|---|
| date | Tue, 13 Aug 2019 15:24:15 -0400 |
| parents | |
| children | 1a2a9b1cfd93 |
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| -1:000000000000 | 0:c516cb51d12c |
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| 1 <tool id="hitsandclusters" name="Count hits per gene and cluster" version="0.1.0"> | |
| 2 <requirements> | |
| 3 <requirement type="package" version="3.6.7">python</requirement> | |
| 4 <requirement type="package" version="0.15.2">pysam</requirement> | |
| 5 <requirement type="package" version="0.24.1">pandas</requirement> | |
| 6 <requirement type="package" version="1.15.4">numpy</requirement> | |
| 7 </requirements> | |
| 8 <command detect_errors="exit_code"><![CDATA[ | |
| 9 python '$__tool_directory__/countandcluster.py' -c '$clusters' -b '$bam' -p '$prop' -g '$out1' -i '${bam.metadata.bam_index}' -o '$out2' | |
| 10 ]]></command> | |
| 11 <inputs> | |
| 12 <param type="data" name="clusters" format="tabular" /> | |
| 13 <param type="data" name="bam" format="bam" /> | |
| 14 <param type="float" name="prop" value="0.9" /> | |
| 15 </inputs> | |
| 16 <outputs> | |
| 17 <data name="out1" format="tabular" /> | |
| 18 <data name="out2" format="tabular" /> | |
| 19 </outputs> | |
| 20 <tests> | |
| 21 <test> | |
| 22 <param name="clusters" value="megares_subset.tsv"/> | |
| 23 <param name="bam" value="test.bam"/> | |
| 24 <param name="prop" value="0.5"/> | |
| 25 <output name="out1" file="geneout.tsv"/> | |
| 26 <output name="out2" file="clusterout.tsv"/> | |
| 27 </test> | |
| 28 </tests> | |
| 29 <help><![CDATA[ | |
| 30 usage: countandcluster.py [-h] [-b BAM] [-i INDEX] -c CLUSTERS [-p MINPROP] [-g GENEOUT] [-o CLUSTEROUT] | |
| 31 | |
| 32 optional arguments: | |
| 33 -h, --help show this help message and exit | |
| 34 -b BAM bam alignment file | |
| 35 -i INDEX bam index | |
| 36 -c CLUSTERS Tab-delimited file with genes and clusters | |
| 37 -p MINPROP minimum proportion of cluster covered | |
| 38 -g GENEOUT output file for gene counts | |
| 39 -o CLUSTEROUT output file for cluster counts | |
| 40 | |
| 41 ]]></help> | |
| 42 <citations> | |
| 43 <citation type="bibtex"> | |
| 44 @misc{githubhitsandclusters, | |
| 45 author = {LastTODO, FirstTODO}, | |
| 46 year = {TODO}, | |
| 47 title = {hitsandclusters}, | |
| 48 publisher = {GitHub}, | |
| 49 journal = {GitHub repository}, | |
| 50 url = {https://github.com/jashay90/galaxytools}, | |
| 51 }</citation> | |
| 52 </citations> | |
| 53 </tool> | |
| 54 |