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comparison demultiplex.xml @ 0:36c79869620b draft

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author davidvanzessen
date Fri, 09 Nov 2018 05:37:11 -0500
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children 9cb2a61a5a1e
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1 <tool id="demultiplex-emc" name="Demultiplex" version="1.0.0">
2 <requirements>
3 <requirement type="package" version="3.7.0">python</requirement>
4 <requirement type="package" version="1.7.2">biopython</requirement>
5 </requirements>
6 <description></description>
7 <command>
8 mkdir outputs;
9 python3 $__tool_directory__/demultiplex.py
10 --input $input
11 --format auto
12 --output-dir ./outputs
13 --mapping-file $mapping
14 </command>
15 <inputs>
16 <param name="input" type="data" format='fasta,fastq' label="The input fasta/fastq"/>
17 <param name="mapping" type="data" format='tabular' label="The mapping file"/>
18 </inputs>
19 <outputs>
20 <data name="debug" format="txt" label="debug"/>
21 <collection name='demultiplex_out' format_source='input' type='list'>
22 <discover_datasets pattern="__name_and_ext__" directory="outputs" format_source='input'/>
23 </collection>
24 </outputs>
25 <tests>
26 <!--
27 <test>
28 <param name="input1" value="1.bed"/>
29 <param name="input2" value="2.bed"/>
30 <output name="out_file1" file="cat_wrapper_out1.bed"/>
31 </test>
32 TODO: if possible, enhance the underlying test code to handle this test
33 the problem is multiple params with the same name "input2"
34 <test>
35 <param name="input1" value="1.bed"/>
36 <param name="input2" value="2.bed"/>
37 <param name="input2" value="3.bed"/>
38 <output name="out_file1" file="cat_wrapper_out2.bed"/>
39 </test>
40 -->
41 </tests>
42 <help>
43 There is no help
44 </help>
45 </tool>
46