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

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/seal-galaxy-cc1b1911/seal/seqal.xml	Wed Oct 15 09:41:10 2014 -0400
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+
+<!--
+  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_seqal" name="Seqal" version="13986416aa79561bd0102cb7ccc1e0668ac9f0a4">
+  <description>Map reads on 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>
+    hadoop_galaxy
+    --input $input_data
+    --output $output1
+    --executable seal
+    seqal
+    #if $align_only.value:
+      --align-only --num-reducers 0
+    #else
+      --num-reducers $align_only.num_reducers
+    #end if
+    --trimq $trimq
+    ${reference.fields.path}
+  </command>
+
+  <inputs>
+    <param name="input_data" type="data" format="pathset" label="Input data" />
+
+    <param name="reference" type="select" label="Select a built-in reference index archive">
+      <options from_data_table="seqal_indexes">
+      </options>
+    </param>
+
+    <param name="trimq" type="integer" min="0" value="0" label="trim quality, like BWA’s -q argument" />
+
+    <conditional name="align_only">
+      <param name="value" type="boolean" default="false" label="Align only (don't identify duplicates)" />
+      <when value="false">
+        <param name="num_reducers"
+          label="Number of reduce tasks"
+          type="integer"
+          value="90"
+          min="1"
+          />
+      </when>
+    </conditional>
+  </inputs>
+
+  <outputs>
+    <data name="output1" format="pathset" />
+  </outputs>
+
+  <stdio>
+    <exit_code range="1:" level="fatal" />
+  </stdio>
+
+  <help>
+    Seqal is a distributed short read mapping and duplicate removal tool. It
+    implements a distributed version of the BWA aligner, and adds a duplicate
+    read identification feature using the same criteria as the Picard
+    MarkDuplicates command.  For a full description see the `manual
+    &lt;http://biodoop-seal.sourceforge.net/seqal_index.html&gt;`_.
+  </help>
+</tool>