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

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/seal-galaxy-cc1b1911/seal/recab_table.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_recab_table" name="Recab Table" version="13986416aa79561bd0102cb7ccc1e0668ac9f0a4">
+  <description>Calculate a base quality recalibration table 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">
+    recab_table_galaxy.py
+    $input_data
+    $output1
+   
+    #if $dbsnp.db_source == "history":
+        $dbsnp.ownFile
+    #else:
+        ${dbsnp.built-inFile.fields.path} 
+    #end if
+
+    $num_reducers
+
+    #if $default_rg:
+    -D seal.recab.rg-covariate.default-rg=$default_rg
+    #end if
+
+    #if $smoothing:
+    -D seal.recab.smoothing=$smoothing
+    #end if 
+
+    #if $max_qscore:
+    -D seal.recab.max-qscore=$max_qscore
+    #end if
+  </command>
+
+  <inputs>
+    <param name="input_data" type="data" format="pathset" label="Input data" />
+    <param name="input_format" type="select" label="Input format" default="sam">
+      <option value="sam" />
+      <option value="bam" />
+    </param>
+
+    <conditional name="dbsnp"> 
+      <param name="db_source" type="select" label="Select database of known variation sites">        
+        <option value="built-in">Select a different built-in database</option>
+        <option value="history">Use a database (vcf format) from my history</option>
+      </param>       
+
+        <when value="built-in">
+        <param name="built-inFile" type="select" label="Select a built-in database">
+          <options from_data_table="variant_tables"/>
+        </param>
+      </when>
+
+      <when value="history">
+        <param name="ownFile" type="data" format="vcf" label="Select a database from history"/>
+      </when>
+    </conditional>
+
+
+    <param name="num_reducers"
+      label="Number of reduce tasks"
+      type="integer"
+      value="90"
+      min="1"
+      />
+
+    <!-- recab-specific parameters -->
+    <param name="default_rg"
+      label="Default read group"
+      type="text"
+      help="Read group to assign to mappings without an RG tag. This value is mandatory if your data includes mappings that do not have a read group tag (RG) Seal RecabTable property: seal.recab.rg-covariate.default-rg."
+      />
+    <param name="smoothing"
+      label="Smoothing"
+      type="integer"
+      value="0"
+      help="Smoothing parameter for empirical quality calculation. Seal RecabTable property: seal.recab.smoothing."
+      min="0"
+      />
+    <param name="max_qscore"
+      label="Max quality score"
+      type="integer"
+      value="40"
+      min="1"
+      help="Upper limit for the empirical quality scores. Seal RecabTable property: seal.recab.max-qscore."
+      />
+  </inputs>
+
+  <outputs>
+    <data name="output1" format="csv" />
+  </outputs>
+
+  <stdio>
+    <exit_code range="1:" level="fatal" />
+  </stdio>
+
+  <help>
+RecabTable is a Hadoop program to calculate a table of base qualities for all values of a given set of factors. It computes a result equivalent to the GATK CountCovariatesWalker.
+For the full help see the `manual &lt;http://biodoop-seal.sourceforge.net/recab_table_index.html&gt;`_.
+  </help>
+</tool>