diff create_or_update_organism.xml @ 0:6002cc0df04e draft

planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 4e5a5af7689f1713c34a6ad9a9594c205e762fdd

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/create_or_update_organism.xml	Tue May 03 13:38:55 2016 -0400
@@ -0,0 +1,58 @@
+<?xml version="1.0"?>
+<tool id="edu.tamu.cpt2.webapollo.create_or_update" name="WA2: Create or Update Organism" version="1.5">
+  <description>will create the organism if it doesn't exist, and update otherwise</description>
+  <macros>
+    <import>macros.xml</import>
+  </macros>
+  <expand macro="requirements"/>
+  <command detect_errors="aggressive"><![CDATA[
+cp -R ${jbrowse.extra_files_path}/data/ /opt/apollo/data/galaxy/${jbrowse.id};
+
+python $__tool_directory__/create_or_update_organism.py
+
+@AUTH@
+
+#if str($blatdb) != "None":
+    --blatdb "$blatdb"
+#end if
+
+--genus "$genus"
+--species "$species"
+$public
+
+@CN_OR_GUESS@
+
+"/opt/apollo/data/galaxy/${jbrowse.id}"
+
+$__user_email__
+
+> $output]]></command>
+  <inputs>
+    <param name="jbrowse" type="data" format="html" label="JBrowse HTML Output" />
+    <param name="blatdb" type="data" label="Blat DB" optional="True" />
+
+    <expand macro="cn_or_guess" />
+    <param name="genus" type="text" label="Host Bacteria" optional="True" />
+    <param name="species" type="text" label="Phage Name" optional="True" />
+    <param name="public" type="boolean" truevalue="--public" falsevalue="" label="Is Organism Public" />
+  </inputs>
+  <outputs>
+    <data format="json" name="output"/>
+  </outputs>
+  <help><![CDATA[
+**NOTA BENE**
+
+All organism data is currently shared. By using this tool your annotation data will be visible to your fellow lab members.
+This will be fixed at a later date.
+
+This only works with JBrowse v0.4 and above!
+
+**What it does**
+
+Adds an organism to the Apollo database. The tool takes the output of a
+JBrowse run as that contains all of the necessary information for which
+tracks are appropriate for a given analysis.
+
+@REFERENCES@
+      ]]></help>
+</tool>