changeset 66:828b3e80f250 draft

Deleted selected files

--- a/picard_SortSam.xml	Wed Feb 19 16:54:10 2014 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,48 +0,0 @@
-<tool name="Sort Sam" id="picard_SortSam" version="1.106.0">
-<!-- adapted from https://github.com/najoshi/ucd-biocore-galaxy/blob/master/tools/picard/picard_SortSam.xml -->
-  <requirements><requirement type="package" version="1.106.0">picard</requirement></requirements>
-  <command interpreter="python">
-    picard_wrapper.py
-      --input "$inputFile"
-      -s "$sort_order"
-      -o "$outFile"
-      --output-format $outputFormat
-      -j "\$JAVA_JAR_PATH/SortSam.jar"
-  </command>
-  <inputs>
-    <param format="bam,sam" name="inputFile" type="data" label="SAM/BAM dataset to be sorted"
-      help="If empty, upload or import a SAM/BAM dataset." />
-    <param name="sort_order" type="select" label="Sort order">
-      <option value="coordinate" selected="True">coordinate</option>
-      <option value="queryname">queryname</option>
-      <option value="unsorted">unsorted</option>
-    </param>
-    <param name="outputFormat" type="boolean" checked="True" truevalue="bam" falsevalue="sam" label="Output BAM instead of SAM" help="Uncheck for SAM output" />
-  </inputs>
-  <outputs>
-    <data name="outFile" format="bam" label="${tool.name} on ${on_string}: ${outputFormat}" />
-      <change_format>
-        <when input="outputFormat" value="sam" format="sam" />
-      </change_format>
-  </outputs>
- <help>
-
-SortSam
-
-USAGE: SortSam [options]
-
-Documentation: http://picard.sourceforge.net/command-line-overview.shtml#SortSam
-
-Sorts the input SAM or BAM.
-
-Input and output formats are determined by file extension.
-Option	Description
-INPUT=File	The BAM or SAM file to sort. Required.
-OUTPUT=File	The sorted BAM or SAM output file. Required.
-SORT_ORDER=SortOrder	Sort order of output file Required. Possible values: {unsorted, queryname, coordinate} 
-  </help>
-</tool>
-
-
-
-