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

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/seal-galaxy-cc1b1911/seal/demux.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_demux" name="Demux" version="13986416aa79561bd0102cb7ccc1e0668ac9f0a4" force_history_refresh="True">
+  <description>Demultiplex Illumina runs 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 interpreter="python">
+    demux_galaxy.py
+    $input_data
+    $mismatches
+    $__new_file_path__
+    #if $num_reducers
+      $num_reducers
+    #else
+      null
+    #end if
+    $output1
+    $output1.id
+    $sample_sheet
+    $input_format
+    $output_format
+    $output_compression
+    #if $index.specify_index == 'present'
+      true
+    #else if $index.specify_index == 'not_present'
+      false
+    #else if $index.specify_index == 'dynamic'
+      $index_present
+    #else
+      #raise ValueError('Invalid index value!')
+    #end if
+    $separate_reads
+  </command>
+
+  <inputs>
+    <param name="input_data" type="data" format="pathset" label="Source data set"/>
+    <param name="sample_sheet" type="data" format="csv" label="Sample sheet" />
+
+    <conditional name="index">
+      <param name="specify_index" type="select" label="Index read" default="present">
+        <option value="present">Present</option>
+        <option value="not_present">Not present</option>
+        <option value="dynamic">Determine at runtime</option>
+      </param>
+      <when value="dynamic">
+        <param name="index_present" type="data" />
+      </when>
+    </conditional>
+
+    <param name="mismatches"
+      label="Barcode base mismatch limit"
+      type="integer"
+      value="0"
+      min="0"
+      max="3" />
+    <param name="num_reducers"
+      label="Number of reduce tasks"
+      type="integer"
+      value="90"
+      min="1"
+      optional="true"
+      />
+    <param name="input_format" type="select" label="Input data format" default="qseq">
+      <option value="qseq">Qseq</option>
+      <option value="fastq">Fastq</option>
+    </param>
+    <param name="output_format" type="select" label="Output data format" default="qseq">
+      <option value="qseq">Qseq</option>
+      <option value="fastq">Fastq</option>
+    </param>
+    <param name="output_compression" type="select" label="Output compression" default="none">
+      <option value="none">None</option>
+      <option value="gzip">Gzip</option>
+      <option value="bzip2">Bzip2</option>
+    </param>
+
+    <param name="separate_reads" type="boolean"
+      label="Separate reads by read number"
+      default="false"
+      truevalue="separate-reads"
+      />
+  </inputs>
+
+  <outputs>
+    <data name="output1" format="pathset" label="Demuxed" />
+  </outputs>
+
+  <stdio>
+    <exit_code range="1:" level="fatal" />
+  </stdio>
+
+  <help>
+    Demux is a Hadoop utility to demultiplex data from multiplexed Illumina runs.
+  </help>
+</tool>