Mercurial > repos > bgruening > hicup_deduplicator

comparison hicup_deduplicator.xml @ 4:46e5b4782715 draft

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planemo upload for repository https://github.com/joachimwolff/galaxytools/tree/hicup/tools/hicup commit 22eec1b3b20b788e762837c02488f332f831fab3
author bgruening
date Fri, 25 May 2018 17:51:57 -0400
parents 6cc9a607f899
children a5934ac7c399
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3:6551ad3d75f4 4:46e5b4782715
1 <tool id="hicup_deduplicator" name="Hicup Deduplicator" version="@VERSION@.0"> 1 <tool id="hicup_deduplicator" name="Hicup Deduplicator" version="@VERSION@.0" profile="18.01">
2 <description>removes duplicated di-tags (retaining one copy of each) from the data set.</description> 2 <description>removes duplicated di-tags (retaining one copy of each) from the data set.</description>
3 <macros> 3 <macros>
4 <import>hicup_macros.xml</import> 4 <import>hicup_macros.xml</import>
5 </macros> 5 </macros>
6 <expand macro="requirements_hicup" /> 6 <expand macro="requirements_hicup" />
7 <expand macro="stdio" /> 7 <command detect_errors="exit_code"><![CDATA[
8 8 #if $input_file.ext != 'sam':
9 <command><![CDATA[ 9 ln -s '$input_file' input.bam &&
10 hicup_deduplicator --quiet '$input_file' 10 #end if
11 && mv *.dedup.* dataset.dedup_result 11 hicup_deduplicator --zip --quiet
12 && mv hicup_deduplicator_summary*.txt hicup_deduplicator_summary.txt 12 #if $input_file.ext != 'sam':
13 && mv *deduplicator_cis_trans_piechart.svg deduplicator_cis_trans_piechart.svg 13 input.bam
14 && mv *deduplicator_uniques_barchart.svg deduplicator_uniques_barchart.svg 14 #else
15 '$input_file'
16 #end if
15 ]]></command> 17 ]]></command>
16 <inputs> 18 <inputs>
17 <param name="input_file" type="data" format="bam,sam" label="Input file(s)" help="Input files in bam or sam format."/> 19 <param name="input_file" type="data" format="qname_sorted.bam,sam" label="Input file(s)" help="Input files in BAM or SAM format."/>
18 </inputs> 20 </inputs>
19 <outputs> 21 <outputs>
20 <data name="dedup_result" format="bam,sam" label="Deduplicator Result" from_work_dir="dataset.dedup_result" /> 22 <data name="dedup_result" format="qname_sorted.bam" label="Deduplicator Result" from_work_dir="*dedup*.bam" />
21 <expand macro="deduplicator_output" /> 23 <data name="cis_trans_piechart" format="svg" from_work_dir="*deduplicator_cis_trans_piechart.svg" label="Hicup Deduplicator Cis Trans Piechart.svg"/>
24 <data name="uniques_barchart" format="svg" from_work_dir="*deduplicator_uniques_barchart.svg" label="Hicup Deduplicator Uniques Barchart.svg" />
25 <data name="hicup_deduplicator_summary" format="txt" from_work_dir="hicup_deduplicator_summary*.txt" label="Hicup Deduplicator Summary" />
22 </outputs> 26 </outputs>
23 <tests> 27 <tests>
24 <test> 28 <test>
25 <param name="input_file" value="dataset.filt.sam" ftype="sam"/> 29 <param name="input_file" value="dataset1_2.filt.bam" ftype="qname_sorted.bam"/>
26 <output name="dataset_hicup" file="dataset.hicup.sam" lines_diff="5" /> 30 <output name="dedup_result" file="dataset1_2.hicup.bam" lines_diff="5" ftype="qname_sorted.bam"/>
27 <output name="cis_trans_piechart" file="deduplicator_cis_trans_piechart.svg" ftype="svg" lines_diff="1000"/> 31 <output name="cis_trans_piechart" file="dataset1_2.filt.bam.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"/> 32 <output name="uniques_barchart" file="dataset1_2.filt.bam.deduplicator_uniques_barchart.svg" ftype="svg" lines_diff="1000"/>
29 <output name="hicup_deduplicator_summary" file="hicup_deduplicator_summary.txt" lines_diff="2"/> 33 <output name="hicup_deduplicator_summary" file="hicup_deduplicator_summary.txt" lines_diff="2"/>
30 </test> 34 </test>
31 </tests> 35 </tests>
32 <help><![CDATA[ 36 <help><![CDATA[
33 37