diff seal-galaxy-cc1b1911/seal/read_sort.xml @ 0:244073d9abc1 draft default tip

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/seal-galaxy-cc1b1911/seal/read_sort.xml	Wed Oct 15 09:41:10 2014 -0400
@@ -0,0 +1,68 @@
+
+<!--
+  Copyright (C) 2011-2014 CRS4.
+
+  This file is part of Seal.
+
+  Seal is free software: you can redistribute it and/or modify it
+  under the terms of the GNU General Public License as published by the Free
+  Software Foundation, either version 3 of the License, or (at your option)
+  any later version.
+
+  Seal is distributed in the hope that it will be useful, but
+  WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY
+  or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU General Public License
+  for more details.
+
+  You should have received a copy of the GNU General Public License along
+  with Seal.  If not, see <http://www.gnu.org/licenses/>.
+-->
+
+
+<tool id="seal_read_sort" name="ReadSort" version="13986416aa79561bd0102cb7ccc1e0668ac9f0a4">
+  <description>Sort reads with Hadoop</description>
+  <requirements>
+    <requirement type="package" version="13986416aa79561bd0102cb7ccc1e0668ac9f0a4">seal</requirement>
+    <requirement type="package" version="0.11">pydoop</requirement>
+    <requirement type="package" version="0.1.3">hadoop-galaxy</requirement>
+  </requirements>
+  <command>
+    #set $ref_path = 'file://' + $reference.fields.path if $reference.fields.path.startswith('/') else $reference.fields.path
+    hadoop_galaxy
+    --input $input_data
+    --output $output
+    --executable seal
+    read_sort
+    --annotations ${ref_path}.ann
+    --num-reducers $num_reducers
+  </command>
+
+  <inputs>
+    <param name="input_data" type="data" format="pathset" label="Input data" />
+
+    <param name="reference" type="select" label="Reference (should be the same one used for alignment)">
+      <options from_data_table="bwa_0510_indexes" />
+    </param>
+
+    <param name="num_reducers"
+      label="Number of reduce tasks"
+      type="integer"
+      value="90"
+      min="1"
+      />
+  </inputs>
+
+  <outputs>
+    <data name="output" format="pathset" />
+  </outputs>
+
+  <stdio>
+    <exit_code range="1:" level="fatal" />
+  </stdio>
+
+  <help>
+ReadSort is a Hadoop-based program for sorting reads by alignment position.
+For the full help see the `manual &lt;http://biodoop-seal.sourceforge.net/read_sort_index.html&gt;`_.
+  </help>
+
+</tool>