diff trinityStats.xml @ 0:b2ce45417d9e draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit c6eab3b60743dfa415dc135d657267cc8a0a31ce

--- /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="[e-mail]" />
+    </creator>
+</tool>