Mercurial > repos > artbio > sequence_format_converter

comparison sequence_format_converter.xml @ 1:9ce7ccd468aa draft

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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sequence_format_converter commit dfecfb40f245a3cdb09dd1cfe37be4cb164ad2eb
author artbio
date Fri, 16 Feb 2018 04:55:44 -0500
parents a8aacccd79a3
children f1d59113125a
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0:a8aacccd79a3 1:9ce7ccd468aa
1 <tool id="sequence_format_converter" name="sequence_format_converter" version="2.0.0"> 1 <tool id="sequence_format_converter" name="sequence_format_converter" version="2.1.0">
2 <description></description> 2 <description></description>
3 <command><![CDATA[ 3 <command><![CDATA[
4 #if $input.is_of_type('fastq.gz'):
5 gzip -dc $input > '${input}.tmp';
6 python '$__tool_directory__'/sequence_format_converter.py
7 --input '${input}.tmp'
8 --output '$output'
9 --format '$output_format';
10 rm '${input}.tmp';
11 #else:
4 python '$__tool_directory__'/sequence_format_converter.py 12 python '$__tool_directory__'/sequence_format_converter.py
5 --input '$input' 13 --input '$input'
6 --output '$output' 14 --output '$output'
7 --format '$output_format' 15 --format '$output_format'
16 #end if
8 ]]></command> 17 ]]></command>
9 18
10 <inputs> 19 <inputs>
11 <param name="input" type="data" format="fasta, fastq, tabular" label="file to convert to tabular (input format is automatically detected)"/> 20 <param name="input" type="data" format="fasta, fastq, tabular" label="file to convert to tabular (input format is automatically detected)"/>
12 <param name="output_format" type="select" label="conversion options"> 21 <param name="output_format" type="select" label="conversion options">
75 </test> 84 </test>
76 <test> 85 <test>
77 <!-- convertion fastq to fastaw --> 86 <!-- convertion fastq to fastaw -->
78 <param name="output_format" value="fastaw" /> 87 <param name="output_format" value="fastaw" />
79 <param ftype="fasta" name="input" value="input.fastqsanger" /> 88 <param ftype="fasta" name="input" value="input.fastqsanger" />
89 <output file="fastqTofastaw.sorted.faw" name="output" sort="True" />
90 </test>
91 <test>
92 <!-- convertion fastq.gz to tabular -->
93 <param name="output_format" value="tabular" />
94 <param ftype="fastq.gz" name="input" value="input.fastqsanger.gz" />
95 <output file="fastqTotabular.sorted.tab" name="output" sort="True" />
96 </test>
97 <test>
98 <!-- convertion fastq.gz to fasta -->
99 <param name="output_format" value="fasta" />
100 <param ftype="fastq.gz" name="input" value="input.fastqsanger.gz" />
101 <output file="fastqTofasta.sorted.fa" name="output" sort="True" />
102 </test>
103 <test>
104 <!-- convertion fastq.gz to fastaw -->
105 <param name="output_format" value="fastaw" />
106 <param ftype="fastq.gz" name="input" value="input.fastqsanger.gz" />
80 <output file="fastqTofastaw.sorted.faw" name="output" sort="True" /> 107 <output file="fastqTofastaw.sorted.faw" name="output" sort="True" />
81 </test> 108 </test>
82 </tests> 109 </tests>
83 110
84 111