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comparison csaw.xml @ 2:ed929b85b051 draft

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author dktanwar
date Mon, 18 Dec 2017 10:58:39 -0500
parents 63fdbd0a8fc3
children 609b5a2ae0e8
comparison
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1:63fdbd0a8fc3 2:ed929b85b051
1 <tool id="CSAW" name="CSAW" version="0.1.0"> 1 <tool id="CSAW" name="CSAW" version="0.1.0">
2
3 <requirements>
4 <requirement type="package" version="1.12.0">bioconductor-csaw</requirement>
5 <requirement type="package" version="1.20.0">r-getopt</requirement>
6 <requirement type="package" version="1.10.4">r-data.table</requirement>
7 <requirement type="package" version="1.2.0">r-stringr</requirement>
8 <requirement type="package" version="1.12.0">bioconductor-biocparallel</requirement>
9 <requirement type="package" version="1.8.0">bioconductor-summarizedexperiment</requirement>
10 <requirement type="package" version="2.38.0">bioconductor-biobase</requirement>
11 <requirement type="package" version="1.30.0">bioconductor-genomicranges</requirement>
12 <requirement type="package" version="1.14.0">bioconductor-genomeinfodb</requirement>
13 <requirement type="package" version="2.12.0">bioconductor-iranges</requirement>
14 <requirement type="package" version="0.16.0">bioconductor-s4vectors</requirement>
15 <requirement type="package" version="0.24.0">bioconductor-biocgenerics</requirement>
16 </requirements>
17
2 <command detect_errors="exit_code"><![CDATA[ 18 <command detect_errors="exit_code"><![CDATA[
3 Rscript $__tool_directory__/csaw.R $inputs $output 19 Rscript $__tool_directory__/csaw.R $inputs $output
4 ]]></command> 20 ]]></command>
21
5 <inputs> 22 <inputs>
6 <param type="data" name="inputs" format="bam" multiple="True" /> 23 <param type="data" name="inputs" format="bam" multiple="True" />
7 </inputs> 24 </inputs>
25
8 <outputs> 26 <outputs>
9 <data name="output" format="txt" /> 27 <data name="output" format="txt" />
10 </outputs> 28 </outputs>
29
11 <tests> 30 <tests>
12 <test> 31 <test>
13 <param name="inputs" value="ENCFF027UTM.bam,ENCFF027UTM_1.bam"/> 32 <param name="inputs" value="ENCFF027UTM.bam,ENCFF027UTM_1.bam"/>
14 <output name="output" file="csaw_results"/> 33 <output name="output" file="csaw_results"/>
15 </test> 34 </test>
16 </tests> 35 </tests>
36
17 <help><![CDATA[ 37 <help><![CDATA[
18 Write the tool help section here. 38 Write the tool help section here.
19 ]]></help> 39 ]]></help>
40
20 <citations> 41 <citations>
21 <citation type="bibtex"> 42 <citation type="bibtex">
22 @misc{github01_mismatch_removal, 43 @misc{github01_mismatch_removal,
23 author = {LastTODO, FirstTODO}, 44 author = {LastTODO, FirstTODO},
24 year = {TODO}, 45 year = {TODO},