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comparison 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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29:3a2aab18a217 30:5231f398d784
1 <tool id="deeptools_bamPEFragmentSize" name="bamPEFragmentSize" version="@WRAPPER_VERSION@.0"> 1 <tool id="deeptools_bamPEFragmentSize" name="bamPEFragmentSize" version="@WRAPPER_VERSION@.0">
2 <description>Given a BAM file it samples several regions to estimate the paird-end fragment length</description> 2 <description>Given a BAM file it samples several regions to estimate the paired-end fragment length</description>
3 <expand macro="requirements" />
4 <expand macro="stdio" />
5 <macros> 3 <macros>
6 <token name="@BINARY@">bamPEFragmentSize</token> 4 <token name="@BINARY@">bamPEFragmentSize</token>
7 <import>deepTools_macros.xml</import> 5 <import>deepTools_macros.xml</import>
8 </macros> 6 </macros>
7 <expand macro="requirements" />
9 <command> 8 <command>
10 <![CDATA[ 9 <![CDATA[
11 bamPEFragmentSize 10 bamPEFragmentSize
12 11 @THREADS@
13 @THREADS@ 12 -bai ${bamInput.metadata.bam_index}
14 13 #if $histogram:
15 --bam '$bamInput' 14 --histogram ./hist.png
16 --bamIndex ${bamInput.metadata.bam_index} 15 #end if
17 #if $histogram: 16 '$bamInput'
18 --histogram $histogram_outfile 17 > $outfile
19 #end if
20 > $outfile
21
22 ]]> 18 ]]>
23 </command> 19 </command>
24
25 <inputs> 20 <inputs>
26 <param name="bamInput" format="bam" type="data" label="BAM file" 21 <param name="bamInput" format="bam" type="data" label="BAM file"
27 help="The BAM file must be sorted."/> 22 help="The BAM file must be sorted."/>
28 <param name="histogram" type="boolean" truevalue="--histogram" falsevalue="" 23 <param name="histogram" type="boolean" truevalue="--histogram" falsevalue=""
29 label="Get the distribion of fragment length as histogram" 24 label="Get the distribion of fragment length as histogram"
30 help="(--histogram)"/> 25 help="(--histogram)"/>
31 </inputs> 26 </inputs>
32 <outputs> 27 <outputs>
33 <data format="txt" name="outfile" label="${tool.name} on ${on_string}" /> 28 <data name="outfile" format="txt"/>
34 <data name="histogram_outfile" format="tabular" from_work_dir="quant_bias_corrected.sf" label="${tool.name} on ${on_string} (Bias corrected Quantification)"> 29 <data name="histogram_outfile" from_work_dir="hist.png" format="png">
35 <filter>histogram == '--histogram'</filter> 30 <filter>histogram is True</filter>
36 </data> 31 </data>
37 </outputs> 32 </outputs>
33 <tests>
34 <test>
35 <param name="bamInput" value="bowtie2-test1.bam" ftype="bam" />
36 <param name="histogram" value="True" />
37 <output name="outfile" file="bamPEFragmentSize_result1.txt" ftype="txt" />
38 <output name="histogram_outfile" file="bamPEFragmentSize_histogram_result1.png" ftype="png" compare="sim_size" />
39 </test>
40 </tests>
38 <help> 41 <help>
39 42 <![CDATA[
40 **What it does** 43 **What it does**
41 44
42 Given a BAM file it samples several regions to estimate the paird-end fragment length. 45 Given a BAM file it samples several regions to estimate the paird-end fragment length.
43 46
44 ----- 47 -----
45 48
46 @REFERENCES@ 49 @REFERENCES@
47 50 ]]>
48 </help> 51 </help>
49 <expand macro="citations" /> 52 <expand macro="citations" />
50 </tool> 53 </tool>