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annotate bamPEFragmentSize.xml @ 30:5231f398d784 draft

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planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 3bc1d1c6f4e28ac7ff8df79fe4e3f00a195938e6-dirty
author bgruening
date Tue, 20 Oct 2015 14:43:12 -0400
parents 3a2aab18a217
children
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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 paired-end fragment length</description>
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3 <macros>
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4 <token name="@BINARY@">bamPEFragmentSize</token>
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5 <import>deepTools_macros.xml</import>
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6 </macros>
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7 <expand macro="requirements" />
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8 <command>
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9 <![CDATA[
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10 bamPEFragmentSize
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11 @THREADS@
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12 -bai ${bamInput.metadata.bam_index}
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13 #if $histogram:
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14 --histogram ./hist.png
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15 #end if
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16 '$bamInput'
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17 > $outfile
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18 ]]>
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19 </command>
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20 <inputs>
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21 <param name="bamInput" format="bam" type="data" label="BAM file"
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22 help="The BAM file must be sorted."/>
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23 <param name="histogram" type="boolean" truevalue="--histogram" falsevalue=""
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24 label="Get the distribion of fragment length as histogram"
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25 help="(--histogram)"/>
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26 </inputs>
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27 <outputs>
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28 <data name="outfile" format="txt"/>
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29 <data name="histogram_outfile" from_work_dir="hist.png" format="png">
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30 <filter>histogram is True</filter>
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31 </data>
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32 </outputs>
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33 <tests>
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34 <test>
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35 <param name="bamInput" value="bowtie2-test1.bam" ftype="bam" />
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36 <param name="histogram" value="True" />
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37 <output name="outfile" file="bamPEFragmentSize_result1.txt" ftype="txt" />
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38 <output name="histogram_outfile" file="bamPEFragmentSize_histogram_result1.png" ftype="png" compare="sim_size" />
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39 </test>
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40 </tests>
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41 <help>
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42 <![CDATA[
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43 **What it does**
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44
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45 Given a BAM file it samples several regions to estimate the paird-end fragment length.
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46
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47 -----
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49 @REFERENCES@
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50 ]]>
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51 </help>
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52 <expand macro="citations" />
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53 </tool>