Mercurial > repos > cpt_testbed > functionalworkflow

diff gff3_reformat.xml @ 0:f678e282b320 draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload"
author cpt_testbed
date Fri, 06 May 2022 07:07:23 +0000
parents
children
line wrap: on
line diff
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/gff3_reformat.xml	Fri May 06 07:07:23 2022 +0000
@@ -0,0 +1,38 @@
+<?xml version="1.0"?>
+<tool id="edu.tamu.cpt.gff3.reformat" name="Reformat GFF3 File" version="19.1.0.0">
+  <description>by passing it through biopython</description>
+  <macros>
+    <import>macros.xml</import>
+		<import>cpt-macros.xml</import>
+  </macros>
+  <expand macro="requirements"/>
+  <command detect_errors="aggressive"><![CDATA[
+$__tool_directory__/gff3_reformat.py
+@INPUT_GFF@
+> $default]]></command>
+  <inputs>
+    <expand macro="gff3_input" />
+  </inputs>
+  <outputs>
+    <data format="gff3" hidden="false" name="default"/>
+  </outputs>
+  <tests>
+                <test>
+			<param name="gff3_data" value="T7_ReformatIn.gff3" />
+			<output name="output" file="T7_ReformatOut.gff3" />
+		</test>
+		<test>
+			<param name="gff3_data" value="Miro_ReformatIn.gff3" />
+			<output name="output" file="Miro_ReformatOut.gff3" />
+		</test>
+	</tests>
+  <help><![CDATA[
+**What it does**
+
+Uses the biopython tools to clean up poorly formatted input GFF3 or GFF2 data. 
+This includes reformatting the GFF3 file header and properly displaying special 
+characters.      
+	
+	]]></help>
+		<expand macro="citations" />
+</tool>