Mercurial > repos > davidvanzessen > demultiplex_emc

comparison demultiplex.xml @ 4:146bbd9d58f6 draft default tip

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Added tests
author davidvanzessen
date Mon, 12 Nov 2018 09:33:34 -0500
parents 500c2eee063d
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3:b6d63b9efb8f 4:146bbd9d58f6
1 <tool id="demultiplex-emc" name="Demultiplex" version="1.0.0"> 1 <tool id="demultiplex-emc" name="Demultiplex" version="1.0.0">
2 <description></description>
2 <requirements> 3 <requirements>
3 <requirement type="package" version="3.7.0">python</requirement> 4 <requirement type="package" version="3.7.0">python</requirement>
4 <requirement type="package" version="1.72">biopython</requirement> 5 <requirement type="package" version="1.72">biopython</requirement>
5 </requirements> 6 </requirements>
6 <description></description> 7
7 <command> 8 <command>
8 mkdir outputs; 9 mkdir outputs;
9 python3 $__tool_directory__/demultiplex.py 10 python3 $__tool_directory__/demultiplex.py
10 --input $input 11 --input $input
11 --format auto 12 --format auto
16 <param name="input" type="data" format='fasta,fastq' label="The input fasta/fastq"/> 17 <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 <param name="mapping" type="data" format='tabular' label="The mapping file"/>
18 </inputs> 19 </inputs>
19 <outputs> 20 <outputs>
20 <!--<data name="debug" format="txt" label="debug"/>--> 21 <!--<data name="debug" format="txt" label="debug"/>-->
21 <collection name='demultiplex_out' format_source='input' type='list'> 22 <collection name='demultiplex_out' format_source='input' type="list">
22 <discover_datasets pattern="__name_and_ext__" directory="outputs" format_source='input'/> 23 <discover_datasets pattern="__designation_and_ext__" directory="outputs"/>
24 <!--<discover_datasets pattern="(?P&lt;designation&gt;.+)\.(?P&lt;ext&gt;.+)" directory="outputs"/>-->
23 </collection> 25 </collection>
24 </outputs> 26 </outputs>
25 <tests> 27 <tests>
26 <!--
27 <test> 28 <test>
28 <param name="input1" value="1.bed"/> 29 <param name="input" value="input.fastq"/>
29 <param name="input2" value="2.bed"/> 30 <param name="mapping" value="mapping.txt"/>
30 <output name="out_file1" file="cat_wrapper_out1.bed"/> 31 <output_collection name="demultiplex_out" type="list">
32 <element name="sequence1" file="sequence1.fastq"/>
33 <element name="sequence2" file="sequence2.fastq"/>
34 </output_collection>
31 </test> 35 </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> 36 <test>
35 <param name="input1" value="1.bed"/> 37 <param name="input" value="input.fasta"/>
36 <param name="input2" value="2.bed"/> 38 <param name="mapping" value="mapping.txt"/>
37 <param name="input2" value="3.bed"/> 39 <output_collection name="demultiplex_out" type="list">
38 <output name="out_file1" file="cat_wrapper_out2.bed"/> 40 <element name="sequence1" file="sequence1.fasta"/>
41 <element name="sequence2" file="sequence2.fasta"/>
42 </output_collection>
39 </test> 43 </test>
40 -->
41 </tests> 44 </tests>
42 <help> 45 <help>
43 There is no help 46 There is no help
44 </help> 47 </help>
48 <citations>
49 <citation type="bibtex">@misc{Demultplex-EMC,
50 author = {Erasmus MC},
51 title = {Demultiplex-EMC},
52 year = {2018},
53 howpublished = {https://github.com/ErasmusMC-Bioinformatics/Demultiplex}
54 }</citation>
55 </citations>
45 </tool> 56 </tool>
46 57