diff cpt_rem_annotes/remove_annotations.xml @ 0:03d27abd1dfd draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/cpt_rem_annotes/remove_annotations.xml	Fri May 13 05:26:10 2022 +0000
@@ -0,0 +1,48 @@
+<?xml version="1.0"?>
+<tool id="edu.tamu.cpt.gff3.remove_annots" name="Remove Annotation Feature" version="19.1.0.1" profile="16.04">
+  <description>that's unused in our GFF tools</description>
+  <macros>
+    <import>macros.xml</import>
+		<import>cpt-macros.xml</import>
+  </macros>
+  <expand macro="requirements"/>
+  <command detect_errors="aggressive"><![CDATA[
+python $__tool_directory__/remove_annotations.py
+$gff3_data
+$remark
+$region
+> $default]]></command>
+  <inputs>
+      <expand macro="gff3_input" />
+      <param checked="true" label="Remove 'remark' features" name="remark" type="boolean" truevalue="--remark" falsevalue="" />
+      <param checked="true" label="Remove 'region' features" name="region" type="boolean" truevalue="--region" falsevalue="" />
+  </inputs>
+  <outputs>
+    <data format="gff3" name="default"/>
+  </outputs>
+  <tests>
+		<test>
+			<param name="gff3_data" value="RemoveAnnote_In.gff3" />
+			<param name="remark" value="--remark" />
+                        <param name="region" value= "--region" />
+			<output name="default" file="RemoveAnnote_Out.gff3" />
+		</test>
+  </tests>
+  <help><![CDATA[
+**What it does**
+
+For an input GFF3, this tool specifically removes the feature entry with remark and/or region type (column 3) as needed for compatibility 
+with certain tools. These feature typically encompasses the entire length of the sequence upon which the GFF3 is based.
+
+Example input:
+    Miro	annotation	remark	1	167935	.	.	.	gff-version=3;sequence-region=%28%27Miro%27%2C 0%2C 172788%29
+
+    Miro	cpt		gene	1231	5436	.	.	.	ID=CDS1;
+
+Example output:
+    Miro	cpt		gene	1231	5436	.	.	.	ID=CDS1;
+
+
+      ]]></help>
+		<expand macro="citations" />
+</tool>