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