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comparison tools/fastq_paired_unpaired/fastq_paired_unpaired.xml @ 7:2709a0f065c9 draft

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v0.1.4 Internal changes to command line handling
author peterjc
date Tue, 16 May 2017 08:53:57 -0400
parents f396701fbf32
children 8cbc866b72ce
comparison
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6:f396701fbf32 7:2709a0f065c9
1 <tool id="fastq_paired_unpaired" name="Divide FASTQ file into paired and unpaired reads" version="0.1.3"> 1 <tool id="fastq_paired_unpaired" name="Divide FASTQ file into paired and unpaired reads" version="0.1.4">
2 <description>using the read name suffices</description> 2 <description>using the read name suffices</description>
3 <requirements> 3 <requirements>
4 <requirement type="package" version="1.0.1">galaxy_sequence_utils</requirement> 4 <requirement type="package" version="1.0.1">galaxy_sequence_utils</requirement>
5 <requirement type="package" version="1.67">biopython</requirement> 5 <requirement type="package" version="1.67">biopython</requirement>
6 </requirements> 6 </requirements>
7 <stdio> 7 <version_command>
8 <!-- Anything other than zero is an error --> 8 python $__tool_directory__/fastq_paired_unpaired.py --version
9 <exit_code range="1:" /> 9 </version_command>
10 <exit_code range=":-1" /> 10 <command detect_errors="aggressive">
11 </stdio> 11 python $__tool_directory__/fastq_paired_unpaired.py '$input_fastq.extension' '$input_fastq'
12 <version_command interpreter="python">fastq_paired_unpaired.py --version</version_command>
13 <command interpreter="python">
14 fastq_paired_unpaired.py $input_fastq.extension $input_fastq
15 #if $output_choice_cond.output_choice=="separate" 12 #if $output_choice_cond.output_choice=="separate"
16 $output_forward $output_reverse 13 '$output_forward' '$output_reverse'
17 #elif $output_choice_cond.output_choice=="interleaved" 14 #elif $output_choice_cond.output_choice=="interleaved"
18 $output_paired 15 '$output_paired'
19 #end if 16 #end if
20 $output_singles 17 $output_singles
21 </command> 18 </command>
22 <inputs> 19 <inputs>
23 <param name="input_fastq" type="data" format="fastq" label="FASTQ file to divide into paired and unpaired reads"/> 20 <param name="input_fastq" type="data" format="fastq" label="FASTQ file to divide into paired and unpaired reads"/>