--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/seal-galaxy-cc1b1911/seal/bcl2qseq.xml	Wed Oct 15 09:41:10 2014 -0400
@@ -0,0 +1,112 @@
+
+<!--
+  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="dist_bcl2qseq" name="Dist Bcl2Qseq" version="13986416aa79561bd0102cb7ccc1e0668ac9f0a4">
+  <description>Convert Illumina bcl files to qseq 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
+    --executable seal
+    --input $input_data
+    --output $output1
+    bcl2qseq
+    #if $advanced.control == 'show'
+      #if $advanced.bcl2qseq_bin:
+      --bclToQseq-path $advanced.bcl2qseq_bin
+      #end if
+
+      #if $advanced.additional_ld_path
+      --append-ld-library-path $advanced.additional_ld_path
+      #end if
+
+      #if $advanced.ignore_missing_bcl
+      --ignore-missing-bcl
+      #end if
+
+      #if $advanced.ignore_missing_control
+      --ignore-missing-control
+      #end if
+
+      #if $advanced.exclude_controls
+      --exclude-controls
+      #end if
+
+      #if $advanced.no_eamss
+      --no-eamss
+      #end if
+    #end if
+  </command>
+
+  <inputs>
+    <param name="input_data" type="data" format="pathset" label="Source data set"/>
+    <conditional name="advanced">
+      <param name="control" type="select" label="Advanced controls" default="hide">
+        <option value="hide">Hide</option>
+        <option value="show">Show</option>
+      </param>
+      <when value="show">
+        <param name="ignore_missing_bcl"
+          type="boolean" default="false"
+          label="Interpret missing *.bcl files as a base calling of '.'"
+          />
+        <param name="ignore_missing_control"
+          type="boolean" default="false"
+          label="Don't throw an error when *.control files are missing"
+          />
+        <param name="exclude_controls"
+          type="boolean" default="false"
+          label="Do not include clusters that are used as controls"
+          />
+        <param name="no_eamss"
+          type="boolean" default="false"
+          label="Do not apply the EAMSS masking on the quality values"
+          />
+        <param name="bcl2qseq_bin"
+          type="text"
+          default=""
+          size="80"
+          label="Full path to bclToQseq binary (needed only if the executable isn't in the PATH)"
+          />
+        <param name="additional_ld_path"
+          type="text" default="" size="80"
+          label="paths to append to the value of LD_LIBRARY_PATH"
+          />
+      </when>
+    </conditional>
+  </inputs>
+
+  <outputs>
+    <data name="output1" format="pathset" label="Qseq" />
+  </outputs>
+
+  <stdio>
+    <exit_code range="1:" level="fatal" />
+  </stdio>
+
+  <help>
+    This is a Pydoop-based distributed version of Illumina's bclToQseq tool.
+  </help>
+</tool>