Mercurial > repos > gga > chado_phylogeny_gene_order

diff phylogeny_gene_order.xml @ 0:4854abe5473b draft

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planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 81a83f06b49db32928ba0cd44e5b6d0431868d27
author gga
date Thu, 21 Jun 2018 08:41:53 -0400
parents
children 9bd557c70bcb
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/phylogeny_gene_order.xml	Thu Jun 21 08:41:53 2018 -0400
@@ -0,0 +1,33 @@
+<?xml version="1.0"?>
+<tool id="phylogeny_gene_order" name="Chado gene ordering" version="@WRAPPER_VERSION@.0">
+ 	<description>for phylogeny module</description>
+	<macros>
+		<import>macros.xml</import>
+	</macros>
+	<expand macro="requirements"/>
+	<command detect_errors="aggressive"><![CDATA[
+@AUTH@
+
+chakin phylogeny gene_order
+
+#if $nuke:
+  $nuke
+#end if
+
+ > $results
+    ]]></command>
+	<inputs>
+    <!-- options -->
+		<param name="nuke" label="Nuke" argument="nuke" type="boolean" truevalue="--nuke" falsevalue="" help="Removes all previous gene ordering data" />
+	    <expand macro="wait_for"/>
+
+	</inputs>
+	<outputs>
+		<data format="txt" name="results"/>
+	</outputs>
+	<help>
+Orders all the genes in the database by their order on their respective chromosomes in the gene_order table (for use in https://github.com/legumeinfo/lis_context_viewer/).
+
+@HELP@
+	</help>
+</tool>