Mercurial > repos > peterjc > fastq_paired_unpaired
comparison tools/fastq_paired_unpaired/fastq_paired_unpaired.xml @ 7:2709a0f065c9 draft
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
equal
deleted
inserted
replaced
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"/> |