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comparison seqtk_sample.xml @ 3:bc7d99f46a5d draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 7379d9f8823d3c639c8119b116e141d0a736ca1d
author iuc
date Mon, 05 Jun 2017 13:27:11 -0400
parents f73729b62b51
children ecf1c30da3a2
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2:f73729b62b51 3:bc7d99f46a5d
1 <?xml version="1.0"?> 1 <?xml version="1.0"?>
2 <tool id="seqtk_sample" name="seqtk_sample" version="@WRAPPER_VERSION@.0"> 2 <tool id="seqtk_sample" name="seqtk_sample" version="@WRAPPER_VERSION@.0">
3 <description>random subsample of fasta or fastq sequences</description> 3 <description>random subsample of fasta or fastq sequences</description>
4 <macros> 4 <macros>
5 <import>macros.xml</import> 5 <import>macros.xml</import>
6 </macros> 6 </macros>
7 <expand macro="requirements"/> 7 <expand macro="requirements"/>
8 <expand macro="stdio"/> 8 <expand macro="stdio"/>
9 <command><![CDATA[seqtk sample -s $s 9 <command><![CDATA[
10 $in_file 10 seqtk sample
11 $subsample_size 11 -s $s
12 > $default]]></command> 12 '$in_file'
13 <inputs> 13 $subsample_size
14 <expand macro="in_faq" /> 14 > '$default'
15 <param label="RNG seed" help="(-s)" name="s" type="integer" value="4"/> 15 ]]></command>
16 <param label="Subsample (decimal fraction or number)" name="subsample_size" type="float" value="100"/> 16 <inputs>
17 </inputs> 17 <expand macro="in_faq" />
18 <outputs> 18 <param argument="-s" type="integer" value="4" label="RNG seed" help="The seed used for the random number generator. Manually specifying a number here is useful for reproducing the same subsampling over time" />
19 <data format_source="in_file" hidden="false" name="default" label="Subsample of reads from $in_file.name"/> 19 <param name="subsample_size" type="float" value="100" label="Subsample (decimal fraction or number)" />
20 </outputs> 20 </inputs>
21 <tests> 21 <outputs>
22 <test> 22 <data name="default" format_source="in_file" label="Subsample of reads from $in_file.name"/>
23 <param name="in_file" value="seqtk_sample.fa"/> 23 </outputs>
24 <param name="subsample_size" value="4"/> 24 <tests>
25 <param name="s" value="4"/> 25 <test>
26 <output name="default" file="seqtk_sample.out" ftype="fasta"/> 26 <param name="in_file" value="seqtk_sample.fa"/>
27 </test> 27 <param name="subsample_size" value="4"/>
28 </tests> 28 <param name="s" value="4"/>
29 <help><![CDATA[ 29 <output name="default" file="seqtk_sample.out" ftype="fasta"/>
30 </test>
31 </tests>
32 <help><![CDATA[
30 **What it does** 33 **What it does**
31 34
32 Takes a random subsample of fasta or fastq sequences. The RNG is seedable to allow for reproducible results, and defaults to `4 <http://xkcd.com/221/>`__. 35 Takes a random subsample of FASTA or FASTQ sequences. The RNG is seedable to allow for reproducible results, and defaults to `4 <http://xkcd.com/221/>`__.
33 36
34 The subsample size can be a decimal fraction <=1, where 1 implies 100% of the reads should be used. If a number >1 is provided, that many reads will be taken from the dataset. 37 The subsample size can be a decimal fraction <=1, where 1 implies 100% of the reads should be used. If a number >1 is provided, that many reads will be taken from the dataset.
35 38
36 @ATTRIBUTION@ 39 @ATTRIBUTION@
37 ]]></help> 40 ]]></help>
38 <expand macro="citation" /> 41 <expand macro="citation" />
39 </tool> 42 </tool>