Mercurial > repos > iuc > trinity_stats
diff trinityStats.xml @ 0:b2ce45417d9e draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit c6eab3b60743dfa415dc135d657267cc8a0a31ce
author | iuc |
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date | Tue, 08 Aug 2023 09:12:09 +0000 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/trinityStats.xml Tue Aug 08 09:12:09 2023 +0000 @@ -0,0 +1,52 @@ +<tool id="trinity_stats" name="Trinity Stats" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@"> + <description></description> + <macros> + <import>macros.xml</import> + </macros> + <expand macro="bio_tools"/> + <expand macro="requirements" /> + <command detect_errors="aggressive"><![CDATA[ + #if $input.ext.endswith(".gz") + gunzip -c '$input' > input && + #else + ln -s '$input' input && + #end if + TrinityStats.pl input > '$statsfile' + ]]> + </command> + + <inputs> + <param name='input' type="data" format="fasta,fasta.gz" label='Trinity Assembly' help='Trinity Assembled fasta file'/> + </inputs> + + <outputs> + <data name='statsfile' format='txt'/> + </outputs> + + <tests> + <test> + <param name="input" value="count/contig_exn50_statistic/Trinity.fasta"/> + <output name="statsfile" file="count/trinityStats/statsfile.txt"/> + </test> + <test> + <param name="input" value="count/contig_exn50_statistic/Trinity.fasta.gz"/> + <output name="statsfile" file="count/trinityStats/statsfile.txt"/> + </test> + </tests> + <help> +<![CDATA[ +Trinity_ assembles transcript sequences from Illumina RNA-Seq data. +This tool computes basic statistics of the assembly (such as stats for genes, transcripts, reconstruction size and N metrics). + +**Inputs** + +It takes as input a transcriptome assembled with Trinity. + +.. _Trinity: https://github.com/trinityrnaseq/trinityrnaseq/wiki +]]> + </help> + <expand macro="citation" /> + <creator> + <person givenName="Paul" familyName="Zierep" email="zierep@informatik.uni-freiburg.de" /> + </creator> +</tool>