Mercurial > repos > peterjc > fastq_paired_unpaired
comparison tools/fastq/fastq_paired_unpaired.xml @ 2:95a632a71951 draft
Uploaded v0.0.6, adds unit test
author | peterjc |
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date | Tue, 30 Apr 2013 14:08:37 -0400 |
parents | 7ed81e36fc1c |
children | 528ba9c896e0 |
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1:7ed81e36fc1c | 2:95a632a71951 |
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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 |