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1 <tool id="hitsandclusters" name="Count hits per gene and cluster" version="0.1.1">
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2 <description> given a bam file and list with clusters.</description>
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0
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3 <requirements>
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4 <requirement type="package" version="3.6.7">python</requirement>
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5 <requirement type="package" version="0.15.2">pysam</requirement>
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6 <requirement type="package" version="0.24.1">pandas</requirement>
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7 <requirement type="package" version="1.15.4">numpy</requirement>
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8 </requirements>
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9 <command detect_errors="exit_code"><![CDATA[
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10 python '$__tool_directory__/countandcluster.py' -c '$clusters' -b '$bam' -p '$prop' -g '$out1' -i '${bam.metadata.bam_index}' -o '$out2'
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11 ]]></command>
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12 <inputs>
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13 <param type="data" name="clusters" format="tabular" />
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14 <param type="data" name="bam" format="bam" />
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15 <param type="float" name="prop" value="0.9" />
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16 </inputs>
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17 <outputs>
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18 <data name="out1" format="tabular" />
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19 <data name="out2" format="tabular" />
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20 </outputs>
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21 <tests>
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22 <test>
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23 <param name="clusters" value="megares_subset.tsv"/>
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24 <param name="bam" value="test.bam"/>
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25 <param name="prop" value="0.5"/>
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26 <output name="out1" file="geneout.tsv"/>
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27 <output name="out2" file="clusterout.tsv"/>
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28 </test>
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29 </tests>
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30 <help><![CDATA[
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31 usage: countandcluster.py [-h] [-b BAM] [-i INDEX] -c CLUSTERS [-p MINPROP] [-g GENEOUT] [-o CLUSTEROUT]
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32
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33 optional arguments:
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34 -h, --help show this help message and exit
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35 -b BAM bam alignment file
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36 -i INDEX bam index
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37 -c CLUSTERS Tab-delimited file with genes and clusters
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38 -p MINPROP minimum proportion of cluster covered
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39 -g GENEOUT output file for gene counts
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40 -o CLUSTEROUT output file for cluster counts
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41
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42 ]]></help>
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43 <citations>
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44 <citation type="bibtex">
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45 @misc{githubhitsandclusters,
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46 author = {Shay, Julie},
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47 year = {2019},
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48 title = {hitsandclusters},
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49 publisher = {GitHub},
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50 journal = {GitHub repository},
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51 url = {https://github.com/jashay90/galaxytools},
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52 }</citation>
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53 </citations>
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54 </tool>
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55
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