Mercurial > repos > iuc > jbrowse

diff jbrowse.xml @ 0:c77c1d5baadb draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 25797deb85d5b7582b8ee11076998622bc282fd8
author: iuc
date: Mon, 04 May 2015 11:58:52 -0400
children: 3b7938dfd6f9
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/jbrowse.xml	Mon May 04 11:58:52 2015 -0400
@@ -0,0 +1,39 @@
+<tool id="jbrowse" name="JBrowse" version="1.0">
+  <description>genome browser</description>
+  <macros>
+    <import>macros.xml</import>
+  </macros>
+  <expand macro="requirements"/>
+  <expand macro="stdio"/>
+  <version_command>python jbrowse.py --version</version_command>
+  <command interpreter="python"><![CDATA[jbrowse.py
+$positional_1
+
+#set repeat_var_2 = '" "'.join([ str($var.gff3) for $var in $repeat_2 ])
+#set repeat_var_3 = '" "'.join([ str($var.gff3.ext) for $var in $repeat_2 ])
+#set repeat_var_4 = '" "'.join([ str($var.gff3_label) for $var in $repeat_2 ])
+
+--gff3 "$repeat_var_2"
+--gff3_format "$repeat_var_3"
+--gff3_label "$repeat_var_4"
+
+
+--jbrowse \${JBROWSE_SOURCE_DIR}
+--outdir $default.files_path
+> $default]]></command>
+  <inputs>
+    <param label="Genome" name="positional_1" type="data"/>
+    <repeat name="repeat_2" title="Annotation Track">
+      <param label="GFF3/BED" format="gff,gff3,bed" name="gff3"
+          type="data"/>
+      <param label="Dataset Label" name="gff3_label" type="text"/>
+    </repeat>
+  </inputs>
+  <outputs>
+    <data format="html" name="default" label="JBrowse on $positional_1.name"/>
+  </outputs>
+  <help><![CDATA[
+Deploy a static JBrowse visualization of a genome and some associated datasets
+]]></help>
+</tool>
+