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comparison hicup_deduplicator.xml @ 0:d515a0639f8e draft

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planemo upload for repository https://github.com/joachimwolff/galaxytools/tree/hicup/tools/hicup commit b77cbc104261f8aa1524922f41c2a9a23052f5da
author bgruening
date Thu, 09 Mar 2017 09:30:33 -0500
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children 6cc9a607f899
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-1:000000000000 0:d515a0639f8e
1 <tool id="hicup_deduplicator" name="Hicup Deduplicator" version="0.1.0">
2 <description>removes duplicated di-tags (retaining one copy of each) from the data set.</description>
3 <macros>
4 <import>hicup_macros.xml</import>
5 </macros>
6 <expand macro="requirements_hicup" />
7 <expand macro="stdio" />
8
9 <command><![CDATA[
10 hicup_deduplicator --quiet '$input_file'
11 && mv *.dedup.* dataset.dedup_result
12 && mv hicup_deduplicator_summary*.txt hicup_deduplicator_summary.txt
13 && mv *deduplicator_cis_trans_piechart.svg deduplicator_cis_trans_piechart.svg
14 && mv *deduplicator_uniques_barchart.svg deduplicator_uniques_barchart.svg
15 ]]></command>
16 <inputs>
17 <param name="input_file" type="data" format="bam,sam" label="Input file(s)" help="Input files in bam or sam format."/>
18 </inputs>
19 <outputs>
20 <data name="dedup_result" format="bam,sam" label="Deduplicator Result" from_work_dir="dataset.dedup_result" />
21 <expand macro="deduplicator_output" />
22 </outputs>
23 <tests>
24 <test>
25 <param name="input_file" value="dataset.filt.sam" ftype="sam"/>
26 <output name="dataset_hicup" file="dataset.hicup.sam" lines_diff="5" />
27 <output name="cis_trans_piechart" file="deduplicator_cis_trans_piechart.svg" ftype="svg" lines_diff="1000"/>
28 <output name="uniques_barchart" file="deduplicator_uniques_barchart.svg" ftype="svg" lines_diff="1000"/>
29 <output name="hicup_deduplicator_summary" file="hicup_deduplicator_summary.txt" lines_diff="2"/>
30 </test>
31 </tests>
32 <help><![CDATA[
33
34 For help please consult the documentation of HiCUP: http://www.bioinformatics.babraham.ac.uk/projects/hicup/overview/
35
36 To get more information about the deduplicator visit: http://www.bioinformatics.babraham.ac.uk/projects/hicup/scripts_description/#Deduplicator
37 ]]></help>
38 <expand macro="citation_hicup" />
39 </tool>