Mercurial > repos > iuc > deeptools_bam_pe_fragmentsize

annotate bamPEFragmentSize.xml @ 0:870935826b58 draft default tip

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planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
author iuc
date Mon, 25 Jan 2016 20:10:51 -0500
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0
870935826b58 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
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1 <tool id="deeptools_bam_pe_fragmentsize" name="bamPEFragmentSize" version="@WRAPPER_VERSION@.0">
870935826b58 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
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2 <description>Estimate the paired-end fragment length in a BAM file</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 ln -s $bamInput one.bam &&
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11 ln -s '${bamInput.metadata.bam_index}' one.bam.bai &&
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12
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13 @BINARY@
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14 @THREADS@
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15 #if $histogram:
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16 --histogram ./hist.png
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17 #end if
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18 --plotTitle "$plotTitle"
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19 one.bam
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20 > $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 argument="--histogram" type="boolean" truevalue="--histogram" falsevalue=""
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27 label="Get the distribution of fragment lengths as a histogram"
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28 help=""/>
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29 <expand macro="plotTitle" />
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30 </inputs>
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31 <outputs>
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32 <data name="outfile" format="txt"/>
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33 <data name="histogram_outfile" from_work_dir="hist.png" format="png">
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34 <filter>histogram is True</filter>
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35 </data>
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36 </outputs>
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37 <tests>
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38 <test>
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39 <param name="bamInput" value="bowtie2-test1.bam" ftype="bam" />
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40 <param name="histogram" value="True" />
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41 <param name="plotTitle" value="Test Plot" />
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42 <output name="outfile" file="bamPEFragmentSize_result1.txt" ftype="txt" />
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43 <output name="histogram_outfile" file="bamPEFragmentSize_histogram_result1.png" ftype="png" compare="sim_size" />
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44 </test>
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45 </tests>
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46 <help>
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47 <![CDATA[
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48 **What it does**
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49
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50 This tool samples a BAM file containing paired-end data to estimate the fragment length distribution.
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51 Properly paired reads are preferred for computation. The output can be obtained as a histogram.
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52
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53 -----
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54
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55 @REFERENCES@
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56 ]]>
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57 </help>
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58 <expand macro="citations" />
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59 </tool>