Mercurial > repos > iracooke > protk_proteogenomics

diff gff3_to_fasta.xml @ 0:956bfab63005 draft default tip

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planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/protk-proteogenomics/.shed.yml commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
author iracooke
date Tue, 20 Oct 2015 20:36:03 -0400
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/gff3_to_fasta.xml	Tue Oct 20 20:36:03 2015 -0400
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+<tool id="gff3_to_fasta" name="Extract proteins from gff3" version="1.1.1">
+    <description>Extract proteins from gff3 and encode genomic coordinates in the fasta header</description>
+    <requirements>
+        <container type="docker">iracooke/protk-1.4.3</container>
+        <requirement type="package" version="1.4.3">protk</requirement>
+   </requirements>
+    <stdio>
+        <exit_code range="1:"   level="fatal"   description="Failure" />
+    </stdio>
+    <command>
+        augustus_to_proteindb.rb $gff_file -o $output $coords
+    </command>
+    <inputs>
+        <param name="gff_file" type="data" format="gff3" label="Augustus Generated gff3 File" />
+        <param name="coords" type="boolean" label="Write genomic coordinates" help="" truevalue="--info" falsevalue="" />
+    </inputs>
+    <outputs>
+        <data format="fasta" name="output" />
+    </outputs>
+    <tests>
+      <!-- Just test that the tool runs and produces vaguely correct output -->
+      <test>
+          <param name="gff_file" value="augustus_sample.gff" format="gff3"/>
+          <output name="output" file="augustus_sample.fasta" format="fasta"/>
+      </test>
+    </tests>
+  <help>
+
+**What it does**
+
+Extract proteins from gff3 and encode genomic coordinates in the fasta header.
+Currently this only works with gff3 generated using the Augustus gene finder
+
+  </help>
+</tool>