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comparison merge_paired_reads.xml @ 0:2e7f0da431e3 draft default tip

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Uploaded version 1.0
author bonsai
date Tue, 30 Apr 2013 13:12:35 -0400
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1 <tool id="merged_paired_reads_wrapper" version="1.0" name="Merge paired reads">
2 <requirements>
3 <requirement type='package' version="1.7">sortmerna</requirement>
4 </requirements>
5 <description>Merges two fastq paired-reads files into one file.</description>
6 <command>
7 merge-paired-reads.sh $input_reads1 $input_reads2 output_file.txt
8 </command>
9 <inputs>
10 <param format="fastq" name="input_reads1" type="data"
11 label="First reads file (fastq)" help=""/>
12 <param format="fastq" name="input_reads2" type="data"
13 label="Second reads file (fastq)" help=""/>
14 </inputs>
15 <outputs>
16 <data format="fastq" name="output" from_work_dir="output_file.txt"
17 label="Merged reads from ${on_string} (fastq)">
18 </data>
19 </outputs>
20 <stdio>
21 <exit_code range="2" level="fatal"
22 description="Too few or two many arguments provided" />
23 </stdio>
24 <tests>
25 <test>
26 <param name="input_reads1" value="sortmerna_wrapper_accept1.fastq" />
27 <param name="input_reads2" value="sortmerna_wrapper_other1.fastq" />
28 <output name="output" file="merged-paired-reads_output.fastq" />
29 </test>
30 </tests>
31 <help>
32 Merges two fastq paired-reads files into one file.
33
34 To run merge-paired-reads::
35
36 bash merge-paired-reads.sh file1.fastq file2.fastq outputfile.fastq
37 </help>
38 </tool>