Mercurial > repos > bioitcore > chimerascan

comparison chimerascan.xml @ 7:37a16ff93dd9 draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload
author bioitcore
date Thu, 12 Oct 2017 16:26:36 -0400
parents 6d54abd510d7
children
comparison
equal deleted inserted replaced
6:6d54abd510d7 7:37a16ff93dd9
1 <tool id="chimerascan" name="ChimeraScan">
2 <description>A tool for identifying chimeric transcription in sequencing data.</description>
3 <command detect_errors="exit_code"><![CDATA[
4 bash $__tool_directory__/run.sh $__tool_directory__ &&
5 python $__tool_directory__/chimerascan_run.py -p 8 $__tool_directory__/myindex
6 #if $input_type_conditional.chimerascan_input_type == "paired"
7 $input_type_conditional.input_1 $input_type_conditional.input_2
8 #else
9 $input_type_conditional.input.forward $input_type_conditional.input.reverse
10 #end if
11 $galaxy_output
12 ]]>
13 </command>
14 <inputs>
15 <conditional name="input_type_conditional">
16 <param name="chimerascan_input_type" type="select" label="Input Type" help="Select between paired and paired collection">
17 <option value="paired" selected="true">Paired</option>
18 <option value="paired_collection">Paired Collection</option>
19 </param>
20 <when value="paired">
21 <param format='fastq' name='input_1' type='data' label='FASTQ file, forward reads' />
22 <param format='fastq' name='input_2' type='data' label='FASTQ file, reverse reads' />
23 </when>
24 <when value="paired_collection">
25 <param format="fastq" name='input' type="data_collection" collection_type="paired" label="Select a paired collection" help="Specify paired dataset collection containing paired reads"/>
26 </when>
27 </conditional>
28 </inputs>
29 <outputs>
30 <data name="galaxy_output" format="bed" />
31 </outputs>
32
33 <tests>
34 <test>
35 <param name="input1" value="input1.fastq"/>
36 <param name="input2" value="input2.fastq"/>
37 <output name="galaxy_output" file="outputfile.bed" ftype="bed"/>
38 </test>
39 <test>
40 <param name="fastq_input">
41 <collection type="paired">
42 <element name="forward" value="input1.fastq" />
43 <element name="reverse" value="input2.fastq" />
44 </collection>
45 </param>
46 <param name="input_type" value="paired_collection" />
47 <output name="galaxy_output" file="outputfile.bed" ftype="bed"/>
48 </test>
49 </tests>
50
51 <help>
52 Bowtie index files must be placed inside 'myindex folder'
53 A tool for identifying chimeric transcription in sequencing data.
54 </help>
55
56 </tool>