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comparison trinityStats.xml @ 0:b2ce45417d9e draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit c6eab3b60743dfa415dc135d657267cc8a0a31ce
author iuc
date Tue, 08 Aug 2023 09:12:09 +0000
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-1:000000000000 0:b2ce45417d9e
1 <tool id="trinity_stats" name="Trinity Stats" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
2 <description></description>
3 <macros>
4 <import>macros.xml</import>
5 </macros>
6 <expand macro="bio_tools"/>
7 <expand macro="requirements" />
8 <command detect_errors="aggressive"><![CDATA[
9 #if $input.ext.endswith(".gz")
10 gunzip -c '$input' > input &&
11 #else
12 ln -s '$input' input &&
13 #end if
14 TrinityStats.pl input > '$statsfile'
15 ]]>
16 </command>
17
18 <inputs>
19 <param name='input' type="data" format="fasta,fasta.gz" label='Trinity Assembly' help='Trinity Assembled fasta file'/>
20 </inputs>
21
22 <outputs>
23 <data name='statsfile' format='txt'/>
24 </outputs>
25
26 <tests>
27 <test>
28 <param name="input" value="count/contig_exn50_statistic/Trinity.fasta"/>
29 <output name="statsfile" file="count/trinityStats/statsfile.txt"/>
30 </test>
31 <test>
32 <param name="input" value="count/contig_exn50_statistic/Trinity.fasta.gz"/>
33 <output name="statsfile" file="count/trinityStats/statsfile.txt"/>
34 </test>
35 </tests>
36 <help>
37 <![CDATA[
38 Trinity_ assembles transcript sequences from Illumina RNA-Seq data.
39 This tool computes basic statistics of the assembly (such as stats for genes, transcripts, reconstruction size and N metrics).
40
41 **Inputs**
42
43 It takes as input a transcriptome assembled with Trinity.
44
45 .. _Trinity: https://github.com/trinityrnaseq/trinityrnaseq/wiki
46 ]]>
47 </help>
48 <expand macro="citation" />
49 <creator>
50 <person givenName="Paul" familyName="Zierep" email="zierep@informatik.uni-freiburg.de" />
51 </creator>
52 </tool>