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1
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1 <tool id="CSAW" name="CSAW" version="0.1.0">
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2
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2
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3 <requirements>
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4 <requirement type="package" version="1.12.0">bioconductor-csaw</requirement>
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5 <requirement type="package" version="1.20.0">r-getopt</requirement>
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6 <requirement type="package" version="1.10.4">r-data.table</requirement>
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7 <requirement type="package" version="1.2.0">r-stringr</requirement>
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8 <requirement type="package" version="1.12.0">bioconductor-biocparallel</requirement>
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9 <requirement type="package" version="1.8.0">bioconductor-summarizedexperiment</requirement>
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10 <requirement type="package" version="2.38.0">bioconductor-biobase</requirement>
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11 <requirement type="package" version="1.30.0">bioconductor-genomicranges</requirement>
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12 <requirement type="package" version="1.14.0">bioconductor-genomeinfodb</requirement>
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13 <requirement type="package" version="2.12.0">bioconductor-iranges</requirement>
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14 <requirement type="package" version="0.16.0">bioconductor-s4vectors</requirement>
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15 <requirement type="package" version="0.24.0">bioconductor-biocgenerics</requirement>
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4
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16 <requirement type="package" version="1.30.0">bioconductor-rsamtools</requirement>
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17 <requirement type="package" version="2.46.0">bioconductor-biostrings</requirement>
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18 <requirement type="package" version="0.18.0">bioconductor-xvector</requirement>
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2
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19 </requirements>
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20
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1
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21 <command detect_errors="exit_code"><![CDATA[
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22 Rscript $__tool_directory__/csaw.R $inputs $output
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23 ]]></command>
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2
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24
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1
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25 <inputs>
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26 <param type="data" name="inputs" format="bam" multiple="True" />
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27 </inputs>
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8
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28
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1
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29 <outputs>
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8
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30 <data name="output" format="txt"/>
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31 <collection name="countTables" type="list">
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32 <discover_datasets pattern="(?P&1t;name>.+)\.tsv$" format="tabular" visible="false" />
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33 </collection>
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1
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34 </outputs>
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2
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35
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1
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36 <tests>
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37 <test>
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38 <param name="inputs" value="ENCFF027UTM.bam,ENCFF027UTM_1.bam"/>
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39 <output name="output" file="csaw_results"/>
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40 </test>
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41 </tests>
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2
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42
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1
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43 <help><![CDATA[
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44 Write the tool help section here.
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45 ]]></help>
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2
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46
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1
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47 <citations>
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48 <citation type="bibtex">
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49 @misc{github01_mismatch_removal,
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50 author = {LastTODO, FirstTODO},
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51 year = {TODO},
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52 title = {01_mismatch_removal},
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53 publisher = {GitHub},
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54 journal = {GitHub repository},
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55 url = {https://github.com/dktanwar/Galaxy_Tools/tree/master/01_mismatch_removal},
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56 }</citation>
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57 </citations>
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58 </tool>
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