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planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/get_pairs commit 02689a4f03aff06ce7f56ffd329ad72befdc692c
author genouest
date Mon, 10 Sep 2018 10:16:42 -0400
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1 <tool id="get_pairs" name="Separate paired and unpaired reads" version="0.3" >
2 <!-- author : lecorguille@sb-roscoff.fr -->
3 <!-- date : 20-11-12 -->
4 <!-- adapted by abretaud -->
5
6 <description>from two fastq files</description>
7
8 <requirements>
9 <requirement type="package" version="3.6">python</requirement>
10 </requirements>
11
12 <command><![CDATA[
13 #if $library.type == 'paired':
14 python '$__tool_directory__/get_pairs.py' '$library.input_left' '$library.input_right'
15 #else if $library.type == 'paired_collection'
16 python '$__tool_directory__/get_pairs.py' '$library.input.forward' '$library.input.reverse'
17 #end if
18 ]]></command>
19
20 <inputs>
21 <conditional name="library">
22 <param name="type" type="select" label="Input type">
23 <option value="paired" selected="true">Independent datasets</option>
24 <option value="paired_collection">Paired-end collection</option>
25 </param>
26
27 <when value="paired">
28 <param name="input_left" type="data" format="fastqsanger" label="Forward reads" />
29 <param name="input_right" type="data" format="fastqsanger" label="Reverse reads" />
30 </when>
31
32 <when value="paired_collection">
33 <param name="input" format="fastqsanger" type="data_collection" collection_type="paired" label="Paired collection" />
34 </when>
35
36 </conditional>
37 </inputs>
38
39 <outputs>
40 <data format="fastqsanger" name="left_paired" from_work_dir="left.paired.fastq" label="${tool.name} on ${on_string}: paired forward" />
41 <data format="fastqsanger" name="right_paired" from_work_dir="right.paired.fastq" label="${tool.name} on ${on_string}: paired reverse" />
42 <data format="fastqsanger" name="left_unpaired" from_work_dir="left.unpaired.fastq" label="${tool.name} on ${on_string}: unpaired forward" />
43 <data format="fastqsanger" name="right_unpaired" from_work_dir="right.unpaired.fastq" label="${tool.name} on ${on_string}: unpaired reverse" />
44 </outputs>
45 <tests>
46 <test>
47 <conditional name="library">
48 <param name="input_left" value="r1.fastq" />
49 <param name="input_right" value="r2.fastq" />
50 </conditional>
51 <output name="left_paired" file="r1_paired.fastq" />
52 <output name="right_paired" file="r2_paired.fastq" />
53 <output name="left_unpaired" file="r1_unpaired.fastq" />
54 <output name="right_unpaired" file="r2_unpaired.fastq" />
55 </test>
56 <test>
57 <conditional name="library">
58 <param name="type" value="paired_collection" />
59 <param name="input">
60 <collection type="paired">
61 <element name="forward" ftype="fastq" value="r1.fastq" />
62 <element name="reverse" ftype="fastq" value="r2.fastq" />
63 </collection>
64 </param>
65 </conditional>
66 <output name="left_paired" file="r1_paired.fastq" />
67 <output name="right_paired" file="r2_paired.fastq" />
68 <output name="left_unpaired" file="r1_unpaired.fastq" />
69 <output name="right_unpaired" file="r2_unpaired.fastq" />
70 </test>
71 </tests>
72
73 <help><![CDATA[
74 A tool to separate paired and unpaired reads from fastq datasets.
75 ]]></help>
76 <citations>
77 </citations>
78 </tool>