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planemo upload commit 93e677982c3636da455de2f827a87e516c7985ac-dirty
author bioitcore
date Thu, 07 Sep 2017 17:55:18 -0400
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1 <tool id="chimerascan" name="ChimeraScan">
2 <description>A tool for identifying chimeric transcription in sequencing data.</description>
3 <command detect_errors="exit_code" interpreter="python">
4 $__tool_directory__/chimerascan_run.py -p 8 $__tool_directory__/myindex
5 #if $input_type_conditional.chimerascan_input_type == "paired"
6 $input_type_conditional.input_1 $input_type_conditional.input_2
7 #else
8 $input_type_conditional.input.forward $input_type_conditional.input.reverse
9 #end if
10 $galaxy_output
11 </command>
12 <inputs>
13 <conditional name="input_type_conditional">
14 <param name="chimerascan_input_type" type="select" label="Input Type" help="Select between paired and paired collection">
15 <option value="paired" selected="true">Paired</option>
16 <option value="paired_collection">Paired Collection</option>
17 </param>
18 <when value="paired">
19 <param format='fastq' name='input_1' type='data' label='FASTQ file, forward reads' />
20 <param format='fastq' name='input_2' type='data' label='FASTQ file, reverse reads' />
21 </when>
22 <when value="paired_collection">
23 <param format="fastq" name='input' type="data_collection" collection_type="paired" label="Select a paired collection" help="Specify paired dataset collection containing paired reads"/>
24 </when>
25 </conditional>
26 </inputs>
27 <outputs>
28 <data name="galaxy_output" format="bed" />
29 </outputs>
30
31 <tests>
32 <test>
33 <param name="input1" value="input1.fastq"/>
34 <param name="input2" value="input2.fastq"/>
35 <output name="galaxy_output" file="outputfile.bed" ftype="bed"/>
36 </test>
37 <test>
38 <param name="fastq_input">
39 <collection type="paired">
40 <element name="forward" value="input1.fastq" />
41 <element name="reverse" value="input2.fastq" />
42 </collection>
43 </param>
44 <param name="input_type" value="paired_collection" />
45 <output name="galaxy_output" file="outputfile.bed" ftype="bed"/>
46 </test>
47 </tests>
48
49 <help>
50 Bowtie index files must be placed inside 'myindex folder'
51 A tool for identifying chimeric transcription in sequencing data.
52 </help>
53
54 </tool>