Mercurial > repos > gga > apollo_feat_from_gff3

diff create_features_from_gff3.xml @ 0:5aa3bc8d0253 draft

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planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
author gga
date Mon, 11 Sep 2017 05:45:37 -0400
parents
children 7c4a3e737e08
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/create_features_from_gff3.xml	Mon Sep 11 05:45:37 2017 -0400
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+<?xml version="1.0"?>
+<tool id="feat_from_gff3" name="GFF3 to Apollo Annotations" version="0.9">
+  <description></description>
+  <macros>
+    <import>macros.xml</import>
+  </macros>
+  <expand macro="requirements"/>
+  <code file="webapollo.py"/>
+  <command detect_errors="aggressive"><![CDATA[
+python $__tool_directory__/create_features_from_gff3.py
+@ADMIN_AUTH@
+@ORG_OR_GUESS@
+
+"$__user_email__"
+'$gff3_data'
+--source "${__app__.config.galaxy_infrastructure_url}history/view/${__app__.security.encode_id($gff3_data.history_id)}"
+
+> $output]]></command>
+  <inputs>
+    <expand macro="org_or_guess" />
+    <expand macro="gff3_input" />
+  </inputs>
+  <outputs>
+	<data format="tabular" name="output" label="Process and Error Log"/>
+  </outputs>
+  <tests>
+      <test expect_failure="true">
+          <conditional name="org_source">
+              <param name="source_select" value="direct"/>
+              <param name="org_raw" value="Test org" />
+          </conditional>
+          <param name="gff3_data" value="good-model.gff3"/>
+          <expand macro="test_result" />
+      </test>
+  </tests>
+  <help><![CDATA[
+**NOTA BENE**
+
+This is **incredibly, highly experimental**
+
+DO NOT:
+
+-  Run on gff3 referencing multiple reference sequences/contigs
+-  Expect it to work well
+-  Expect it to work at all
+
+@REFERENCES@
+]]></help>
+  <expand macro="citations"/>
+</tool>