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comparison obisort.xml @ 0:aca6a8c9cf83 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
author iuc
date Wed, 12 Apr 2017 17:38:00 -0400
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-1:000000000000 0:aca6a8c9cf83
1 <tool id="obi_sort" name="obisort" version="@WRAPPER_VERSION@">
2 <description>sorts sequence records according to the value of a given attribute, which can be either numeric or alphanumeric</description>
3 <macros>
4 <import>macros.xml</import>
5 </macros>
6 <expand macro="requirements"/>
7 <expand macro="stdio"/>
8
9 <command>
10
11 <![CDATA[
12 obisort
13 -k '$key'
14 ${reverse}
15 '$input' > '$output'
16 ]]>
17
18 </command>
19
20 <inputs>
21 <param name="input" type="data" format="fastq,fasta,txt,tabular" label="Input sequences file" />
22 <param name="key" type="text" label="key" />
23 <param name="reverse" type="boolean" checked="false" truevalue="-r" falsevalue="" label="sorts in reverse order?" />
24 <param name="out_format" type="select" label="Output data type">
25 <option value="fasta">fasta</option>
26 <option value="fastq">fastq</option>
27 </param>
28
29 </inputs>
30 <outputs>
31 <data format="fastq" name="output" label="output with ${tool.name} on ${on_string}" >
32 <change_format>
33 <when input="out_format" value="fasta" format="fasta" />
34 </change_format>
35 </data>
36 </outputs>
37 <tests>
38 <test>
39 <param name="input" value="output_obiclean_advanced.fasta" />
40 <param name="key" value="count"/>
41 <param name="reverse" value="False"/>
42 <param name="out_format" value="fasta"/>
43 <output name="output" file="output_obisort.fasta" ftype="fasta"/>
44 </test>
45 <test>
46 <param name="input" value="output_obiclean_advanced.fasta" />
47 <param name="key" value="count"/>
48 <param name="reverse" value="True"/>
49 <param name="out_format" value="fastq"/>
50 <output name="output" file="output_obisort.fastq" ftype="fastq"/>
51 </test>
52 </tests>
53 <help><![CDATA[
54
55 .. class:: infomark
56
57 **What it does**
58
59 obisort sorts sequence records according to the value of a given attribute, which can be either numeric or alphanumeric.
60
61 @OBITOOLS_LINK@
62
63 ]]>
64
65 </help>
66 <expand macro="citation" />
67 </tool>