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comparison yac.xml @ 1:7c913274e22a draft

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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/yac_clipper commit 7edb6f8c9744ec9bccee42aecf80207f0984330c
author artbio
date Wed, 26 Jul 2017 17:12:08 -0400
parents ad6b978daa2e
children da08e89abd18
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0:ad6b978daa2e 1:7c913274e22a
1 <tool id="yac" name="Clip adapter" version="2.0.0"> 1 <tool id="yac" name="Clip adapter" version="2.0.1">
2 <description /> 2 <description />
3 <command interpreter="python">yac.py --input $input 3 <command interpreter="python">yac.py --input $input
4 --output $output 4 --output $output
5 --output_format "$out_format" 5 --output_format "$out_format"
6 --adapter_to_clip $clip_source.clip_sequence 6 --adapter_to_clip $clip_source.clip_sequence
12 <param format="fastq" label="Source file" name="input" type="data" /> 12 <param format="fastq" label="Source file" name="input" type="data" />
13 <param label="min size" name="min" size="4" type="integer" value="15" /> 13 <param label="min size" name="min" size="4" type="integer" value="15" />
14 <param label="max size" name="max" size="4" type="integer" value="36" /> 14 <param label="max size" name="max" size="4" type="integer" value="36" />
15 <param label="Select output format" name="out_format" type="select"> 15 <param label="Select output format" name="out_format" type="select">
16 <option selected="true" value="fasta">Fasta format</option> 16 <option selected="true" value="fasta">Fasta format</option>
17 <option value="fastq">Fastq format</option> 17 <option value="fastq">Fastq (Sanger) format</option>
18 </param> 18 </param>
19 <param label="Accept reads containing N?" name="Nmode" type="select"> 19 <param label="Accept reads containing N?" name="Nmode" type="select">
20 <option selected="True" value="accept">accept</option> 20 <option selected="True" value="accept">accept</option>
21 <option value="reject">reject</option> 21 <option value="reject">reject</option>
22 </param> 22 </param>
37 <param label="Enter your Sequence" name="clip_sequence" size="35" type="text" value="GAATCC" /> 37 <param label="Enter your Sequence" name="clip_sequence" size="35" type="text" value="GAATCC" />
38 </when> 38 </when>
39 </conditional> 39 </conditional>
40 </inputs> 40 </inputs>
41 <outputs> 41 <outputs>
42 <data format="fasta" metadata_source="input" name="output" label="Clipping of ${input.name}"> 42 <data format_source="input" metadata_source="input" name="output" label="Clipping of ${input.name}">
43 <change_format> 43 <change_format>
44 <when input="out_format" value="fastq" format="fastq" /> 44 <when input="out_format" value="fasta" format="fasta" />
45 </change_format> 45 </change_format>
46 </data> 46 </data>
47 </outputs> 47 </outputs>
48 <tests> 48 <tests>
49 <test> 49 <test>
90 **Output** 90 **Output**
91 91
92 A fastq or fasta file containing clipped sequences satisfying the selected criteria. 92 A fastq or fasta file containing clipped sequences satisfying the selected criteria.
93 93
94 </help> 94 </help>
95 <citations />
95 </tool> 96 </tool>