changeset 83:39c4ba55e172 draft

Deleted selected files

--- a/picard_MergeSam.xml	Thu Feb 20 18:25:46 2014 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,72 +0,0 @@
-<tool id="picard_mergesam" name="Merge SAM or BAM files" version="1.106.0">
-    <!-- Documentation: http://picard.sourceforge.net/command-line-overview.shtml#MergeSamFiles
-Merges multiple SAM/BAM files into one file.
--->
-  <description>merges SAM or BAM files together</description>
-  <requirements><requirement type="package" version="1.106.0">picard</requirement></requirements>
-  <command interpreter="bash">
-    mergesam_wrapper.sh $output1 $outformat I=$input1 I=$input2 
-      #for $i in $inputs
-        I=${i.input}
-      #end for 
-      MSD=$mergeSD VALIDATION_STRINGENCY=LENIENT TMP_DIR=$__new_file_path__
-          2&gt; $outlog
-    ##|| echo "Error running Picard MergeSamFiles" >&amp;2
-  </command>
-  <inputs>
-    <param name="title" label="Name for the output merged bam file" type="text" default="Merged.bam"
-       help="This name will appear in your history so use it to remember what the new file in your history contains" />
-    <param name="outformat" type="select" label="Output format" >
-      <option value="bam" selected="True">BAM</option>
-      <option value="sam">SAM</option>
-    </param>
-    <param name="mergeSD" value="true" type="boolean"  label="Merge all component bam file headers into the merged bam file"
-      truevalue="true" falsevalue="false" checked="yes" 
-      help="Control the MERGE_SEQUENCE_DICTIONARIES flag for Picard MergeSamFiles. Default (true) correctly propagates read groups and other important metadata" />
-    <param name="input1" label="First file" type="data" format="bam,sam" />
-    <param name="input2" label="with file" type="data" format="bam,sam" help="Need to add more files? Use controls below." />
-    <repeat name="inputs" title="Input Files">
-      <param name="input" label="Add file" type="data" format="bam,sam" />
-    </repeat>
-  </inputs>
-  <outputs>
-    <data format="bam" name="output1" label="${title}.${outformat}" >
-       <change_format>
-           <when input="outformat" value="sam" format="sam" />
-       </change_format>
-    </data>
-    <data format="txt" name="outlog" label="${title}_${tool.name}.log" />
-  </outputs>
-  <tests>
-    <!-- TODO: add ability to test framework to test without at least 
-         one repeat element value
-    -->
-    <test>
-      <param name="title" value="test1" />
-      <param name="mergeSD" value="true" />
-      <param name="input1" value="sam_merge_in1.bam" ftype="bam" /> 
-      <param name="input2" value="sam_merge_in2.bam" ftype="bam" />
-      <output name="output1" file="sam_merge_out1.bam" ftype="bam" />
-      <output name="outlog" file="sam_merge_out1.log" ftype="txt" lines_diff="11"/>
-    </test>
-    <test>
-      <param name="title" value="test2" />
-      <param name="mergeSD" value="true" />
-      <param name="input1" value="sam_merge_in1.bam" ftype="bam" /> 
-      <param name="input2" value="sam_merge_in2.bam" ftype="bam" />
-      <param name="input" value="sam_merge_in3.bam" ftype="bam" />
-      <output name="output1" file="sam_merge_out2.bam" ftype="bam" />
-      <output name="outlog" file="sam_merge_out2.log" ftype="txt" lines_diff="11"/>
-    </test>
-  </tests>
-  <help>
-
-**What it does**
-
-This tool uses the Picard_ merge command to merge any number of BAM files together into one BAM file while preserving the BAM
-metadata such as read groups
-
-.. _Picard: http://picard.sourceforge.net/command-line-overview.shtml#MergeSamFiles
-
-  </help>
-</tool>