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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
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13 @THREADS@
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14
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15 --bam '$bamInput'
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16 --bamIndex ${bamInput.metadata.bam_index}
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17 #if $histogram:
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18 --histogram $histogram_outfile
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19 #end if
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20 > $outfile
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21
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22 ]]>
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23 </command>
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24
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25 <inputs>
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26 <param name="bamInput" format="bam" type="data" label="BAM file"
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27 help="The BAM file must be sorted."/>
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28 <param name="histogram" type="boolean" truevalue="--histogram" falsevalue=""
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29 label="Get the distribion of fragment length as histogram"
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30 help="(--histogram)"/>
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31 </inputs>
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32 <outputs>
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33 <data format="txt" name="outfile" label="${tool.name} on ${on_string}" />
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34 <data name="histogram_outfile" format="tabular" from_work_dir="quant_bias_corrected.sf" label="${tool.name} on ${on_string} (Bias corrected Quantification)">
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35 <filter>histogram == '--histogram'</filter>
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36 </data>
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37 </outputs>
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38 <help>
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39
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40 **What it does**
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41
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42 Given a BAM file it samples several regions to estimate the paird-end fragment length.
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43
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44 -----
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45
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46 @REFERENCES@
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47
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48 </help>
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49 <expand macro="citations" />
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50 </tool>
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