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1 <tool id="deeptools_bamPEFragmentSize" name="bamPEFragmentSize" version="@WRAPPER_VERSION@.0">
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2 <description>Given a BAM file it samples several regions to estimate the paird-end fragment length</description>
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3 <expand macro="requirements" />
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4 <expand macro="stdio" />
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5 <macros>
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6 <token name="@BINARY@">bamPEFragmentSize</token>
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7 <import>deepTools_macros.xml</import>
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8 </macros>
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9 <command>
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10 <![CDATA[
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11 bamPEFragmentSize
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12 @THREADS@
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13 -bai ${bamInput.metadata.bam_index}
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14 #if $histogram:
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15 --histogram ./hist.png
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16 #end if
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17 '$bamInput'
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18 > $outfile
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19 &&
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20 mv ./hist.png $histogram_outfile
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21 ]]>
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22 </command>
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23 <inputs>
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24 <param name="bamInput" format="bam" type="data" label="BAM file"
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25 help="The BAM file must be sorted."/>
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26 <param name="histogram" type="boolean" truevalue="--histogram" falsevalue=""
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27 label="Get the distribion of fragment length as histogram"
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28 help="(--histogram)"/>
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29 </inputs>
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30 <outputs>
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31 <data name="outfile" format="txt"/>
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32 <data name="histogram_outfile" format="png">
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33 <filter>histogram is True</filter>
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34 </data>
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35 </outputs>
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36 <tests>
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37 <test>
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38 <param name="bamInput" value="bowtie2-test1.bam" ftype="bam" />
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39 <param name="histogram" value="True" />
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40 <output name="outfile" file="bamPEFragmentSize_result1.txt" ftype="txt" />
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41 <output name="histogram_outfile" file="bamPEFragmentSize_histogram_result1.png" ftype="png" />
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42 </test>
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43 </tests>
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44 <help>
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45 <![CDATA[
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46 **What it does**
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47
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48 Given a BAM file it samples several regions to estimate the paird-end fragment length.
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49
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50 -----
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51
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52 @REFERENCES@
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53 ]]>
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54 </help>
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55 <expand macro="citations" />
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56 </tool>
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