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comparison tools/fastq/fastq_paired_unpaired.xml @ 2:95a632a71951 draft

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Uploaded v0.0.6, adds unit test
author peterjc
date Tue, 30 Apr 2013 14:08:37 -0400
parents 7ed81e36fc1c
children 528ba9c896e0
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1:7ed81e36fc1c 2:95a632a71951
1 <tool id="fastq_paired_unpaired" name="Divide FASTQ file into paired and unpaired reads" version="0.0.5"> 1 <tool id="fastq_paired_unpaired" name="Divide FASTQ file into paired and unpaired reads" version="0.0.6">
2 <description>using the read name suffices</description> 2 <description>using the read name suffices</description>
3 <version_command interpreter="python">fastq_paired_unpaired.py --version</version_command>
3 <command interpreter="python"> 4 <command interpreter="python">
4 fastq_paired_unpaired.py $input_fastq.extension $input_fastq 5 fastq_paired_unpaired.py $input_fastq.extension $input_fastq
5 #if $output_choice_cond.output_choice=="separate" 6 #if $output_choice_cond.output_choice=="separate"
6 $output_forward $output_reverse 7 $output_forward $output_reverse
7 #elif $output_choice_cond.output_choice=="interleaved" 8 #elif $output_choice_cond.output_choice=="interleaved"
8 $output_paired 9 $output_paired
9 #end if 10 #end if
10 $output_singles 11 $output_singles
11 </command> 12 </command>
13 <stdio>
14 <!-- Anything other than zero is an error -->
15 <exit_code range="1:" />
16 <exit_code range=":-1" />
17 </stdio>
12 <inputs> 18 <inputs>
13 <param name="input_fastq" type="data" format="fastq" label="FASTQ file to divide into paired and unpaired reads"/> 19 <param name="input_fastq" type="data" format="fastq" label="FASTQ file to divide into paired and unpaired reads"/>
14 <conditional name="output_choice_cond"> 20 <conditional name="output_choice_cond">
15 <param name="output_choice" type="select" label="How to output paired reads?"> 21 <param name="output_choice" type="select" label="How to output paired reads?">
16 <option value="separate">Separate (two FASTQ files, for the forward and reverse reads, in matching order).</option> 22 <option value="separate">Separate (two FASTQ files, for the forward and reverse reads, in matching order).</option>
32 <data name="output_paired" format="input" label="Interleaved paired reads"> 38 <data name="output_paired" format="input" label="Interleaved paired reads">
33 <filter>output_choice_cond["output_choice"] == "interleaved"</filter> 39 <filter>output_choice_cond["output_choice"] == "interleaved"</filter>
34 </data> 40 </data>
35 </outputs> 41 </outputs>
36 <tests> 42 <tests>
43 <test>
44 <param name="input_fastq" value="sanger-pairs-mixed.fastq" ftype="fastq"/>
45 <param name="output_choice" value="separate"/>
46 <output name="output_singles" file="sanger-pairs-singles.fastq" ftype="fastq"/>
47 <output name="output_forward" file="sanger-pairs-forward.fastq" ftype="fastq"/>
48 <output name="output_reverse" file="sanger-pairs-reverse.fastq" ftype="fastq"/>
49 </test>
50 <test>
51 <param name="input_fastq" value="sanger-pairs-mixed.fastq" ftype="fastq"/>
52 <param name="output_choice" value="interleaved"/>
53 <output name="output_singles" file="sanger-pairs-singles.fastq" ftype="fastq"/>
54 <output name="output_paired" file="sanger-pairs-interleaved.fastq" ftype="fastq"/>
55 </test>
37 </tests> 56 </tests>
38 <requirements>
39 <requirement type="python-module">Bio</requirement>
40 </requirements>
41 <help> 57 <help>
42 58
43 **What it does** 59 **What it does**
44 60
45 Using the common read name suffix conventions, it divides a FASTQ file into 61 Using the common read name suffix conventions, it divides a FASTQ file into