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comparison contig_exn50_statistic.xml @ 0:1e8a2c87461a draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit ed037d83415937b11a45a4611584e71e99ad1da0
author iuc
date Thu, 23 Mar 2017 10:18:11 -0400
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1 <tool id="trinity_contig_exn50_statistic" name="Compute contig Ex90N50 statistic and Ex90 transcript count" version="@WRAPPER_VERSION@.0">
2 <description>from a Trinity assembly</description>
3 <macros>
4 <import>macros.xml</import>
5 </macros>
6 <expand macro="requirements">
7 </expand>
8 <expand macro="stdio"/>
9 <command><![CDATA[
10
11 contig_ExN50_statistic.pl
12 '$matrix'
13 '$transcripts'
14 > '$output'
15
16 ]]></command>
17 <inputs>
18 <param format="tabular" name="matrix" type="data" label="Expression matrix" help="Matrix of normalized expression values produced by 'Build expression matrix for a de novo assembly of RNA-Seq data by Trinity' tool"/>
19 <param format="fasta" name="transcripts" type="data" label="Transcripts" help="De novo assembly of RNA-Seq data"/>
20 </inputs>
21 <outputs>
22 <data format="tabular" name="output" label="${tool.name} on ${on_string}: ExN50 statistics"/>
23 </outputs>
24 <tests>
25 <test>
26 <param name="matrix" value="count/contig_exn50_statistic/matrix.TMM.EXPR.matrix"/>
27 <param name="transcripts" value="count/contig_exn50_statistic/Trinity.fasta"/>
28 <output name="output" file="count/contig_exn50_statistic/ExN50.stats"/>
29 </test>
30 </tests>
31 <help>
32 <![CDATA[
33 Trinity_ assembles transcript sequences from Illumina RNA-Seq data.
34 This tool computes the N50 statistic limited to the top most highly expressed transcripts that represent x% of the total normalized expression data. This requires that you have first performed transcript abundance estimation with 'Align reads and estimate abundance for a de novo assembly of RNA-Seq data by Trinity' tool and that you have built the expression matrix with 'Build expression matrix for a de novo assembly of RNA-Seq data by Trinity' tool.
35
36 **Inputs**
37
38 It takes as input a transcriptome assembled with Trinity and the matrix of normalized expression values produced by 'Build expression matrix for a de novo assembly of RNA-Seq data by Trinity' tool.
39
40 .. _Trinity: http://trinityrnaseq.github.io
41 ]]>
42 </help>
43 <expand macro="citation" />
44 </tool>