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

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/seal-galaxy-cc1b1911/seal/prq.xml	Wed Oct 15 09:41:10 2014 -0400
@@ -0,0 +1,118 @@
+
+<!--
+  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_prq" name="Prq" version="13986416aa79561bd0102cb7ccc1e0668ac9f0a4">
+  <description>Convert qseq or fastq files to prq 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
+    --input-format $input_format.type
+    --output $output1
+    --executable seal
+    prq
+    --input-format $input_format.type
+    --num-reducers $num_reducers
+    -D hbam.qseq-input.base-quality-encoding=$input_format.bq_encoding
+    -D hbam.fastq-input.base-quality-encoding=$input_format.bq_encoding
+
+    #if $bpr
+      -D seal.prq.min-bases-per-read=$bpr
+    #end if
+    #if $drop_failed
+      -D seal.prq.drop-failed-filter=$drop_failed
+    #end if
+    #if $warn_unpaired
+      -D seal.prq.warning-only-if-unpaired=$warn_unpaired
+    #end if
+  </command>
+
+  <inputs>
+    <param name="input_data" type="data" format="pathset" label="Input data" />
+    <conditional name="input_format">
+      <!-- We use a conditional for the input_format since we want a different
+           default base quality encoding value for each of the respective
+           supported formats, qseq and fastq.-->
+      <param name="type" type="select" label="Input format" default="qseq">
+        <option value="qseq" />
+        <option value="fastq" />
+      </param>
+      <when value="qseq">
+        <param name="bq_encoding" type="select" label="BQ encoding" default="illumina">
+          <option value="illumina">Illumina</option>
+          <option value="sanger">Sanger</option>
+        </param>
+      </when>
+      <when value="fastq">
+        <param name="bq_encoding" type="select" label="BQ encoding" default="sanger">
+          <option value="sanger">Sanger</option>
+          <option value="illumina">Illumina</option>
+        </param>
+      </when>
+    </conditional>
+
+    <param name="num_reducers"
+      label="Number of reduce tasks"
+      type="integer"
+      value="90"
+      min="1"
+      />
+
+    <!-- prq-specific parameters -->
+    <param name="bpr"
+      label="Min bases per read"
+      type="integer"
+      help="If neither read in a pair has at least this many known bases the pair is dropped (prop: seal.prq.min-bases-per-read)."
+      value="30"
+      min="0"
+      />
+    <param name="drop_failed"
+      label="Filter by machine quality check"
+      type="boolean"
+      help="Drop pairs if both reads failed machine quality checks (prop: seal.prq.drop-failed-filter)."
+      checked="true"
+      />
+    <param name="warn_unpaired"
+      label="Warn only on unpaired reads"
+      type="boolean"
+      help="PRQ normally gives an error if it finds an unpaired read. If this setting is checked it will instead emit a warning, drop the unpaired read and keep going (prop: seal.prq.warning-only-if-unpaired)."
+      checked="false"
+      />
+  </inputs>
+
+  <outputs>
+    <data name="output1" format="pathset" />
+  </outputs>
+
+  <stdio>
+    <exit_code range="1:" level="fatal" />
+  </stdio>
+
+  <help>
+PairReadsQSeq (PRQ) is a Hadoop utility to convert  Illumina qseq files into
+prq file format.  For the full help see the `manual &lt;http://biodoop-seal.sourceforge.net/prq_index.html&gt;`_.
+  </help>
+
+</tool>