diff picard_ReorderSam.xml @ 0:b76a4f17bbbb draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/picard_ReorderSam.xml	Thu Oct 23 11:31:30 2014 -0400
@@ -0,0 +1,131 @@
+<tool name="ReorderSam" id="picard_ReorderSam" version="1.122.0">
+  <description>reorder reads to match ordering in reference sequences</description>
+  <requirements><requirement type="package" version="1.122.0">picard</requirement></requirements>
+  
+  <macros>
+    <import>picard_macros.xml</import>
+  </macros>
+  
+  <command>
+    @java_options@
+    #set $picard_dict = "localref.dict"
+    #set $ref_fasta = "localref.fa"     ## This is done because picards "likes" .fa extension
+    
+    ln -s "${reference_source.ref_file}" "${ref_fasta}" &amp;&amp;
+       
+    #if str( $reference_source.reference_source_selector ) == "history":
+        
+      java -jar \$JAVA_JAR_PATH/CreateSequenceDictionary.jar REFERENCE="${ref_fasta}" OUTPUT="${picard_dict}"
+      QUIET=true
+      VERBOSITY=ERROR
+      
+      &amp;&amp;
+      
+    #else:
+    
+      #set $ref_fasta = str( $reference_source.ref_file.fields.path )
+    
+    #end if
+    
+    java -jar \$JAVA_JAR_PATH/ReorderSam.jar
+      INPUT="${inputFile}"
+      OUTPUT="${outFile}"
+      REFERENCE="${ref_fasta}"
+      ALLOW_INCOMPLETE_DICT_CONCORDANCE="${allow_incomplete_dict_concordance}"
+      ALLOW_CONTIG_LENGTH_DISCORDANCE="${allow_contig_length_discordance}"
+      
+      VALIDATION_STRINGENCY="${validation_stringency}"
+      QUIET=true
+      VERBOSITY=ERROR
+      
+  </command>
+  
+  <inputs>
+    
+     <conditional name="reference_source">
+      <param name="reference_source_selector" type="select" label="Load reference genome from">
+        <option value="cached">Local cache</option>
+        <option value="history">History</option>
+      </param>
+      <when value="cached">
+        <param name="ref_file" type="select" label="Use dictionary from the list" help="Select genome from the list">
+          <options from_data_table="picard_indexes">
+            <filter type="sort_by" column="2" />
+            <validator type="no_options" message="No indexes are available" />
+          </options>
+          <validator type="no_options" message="A built-in dictionary is not available for the build associated with the selected input file"/>
+        </param>
+      </when>
+      <when value="history"> 
+        <param name="ref_file" type="data" format="fasta" label="Use the following dataset to create dictionary" help="You can upload a FASTA sequence to the history from which Picard will automatically generate dictionary using CreateSequenceDictionary command" />
+      </when>
+    </conditional>
+
+    <param format="sam,bam" name="inputFile" type="data" label="Select SAM/BAM dataset or dataset collection" help="If empty, upload or import a SAM/BAM dataset"/>
+    <param name="allow_incomplete_dict_concordance" type="boolean" label="If true, then allows only a partial overlap of the BAM contigs with the new reference sequence contigs" help="ALLOW_INCOMPLETE_DICT_CONCORDANCE; By default, this tool requires a corresponding contig in the new reference for each read contig; default=False"/>
+    <param name="allow_contig_length_discordance" type="boolean" label="If true, then permits mapping from a read contig to a new reference contig with the same name but a different length" help="ALLOW_CONTIG_LENGTH_DISCORDANCE; HIGHLY DANGEROUS! Only use if you know what you are doing; default=False"/>
+    <expand macro="VS" />
+    
+  </inputs>
+  <outputs>
+    <data name="outFile" format="bam" label="${tool.name} on ${on_string}: Reordered BAM"/>
+  </outputs>
+  <tests>
+    <test>
+      <param name="reference_source_selector" value="history" />
+      <param name="ref_file" value="picard_ReorderSam_ref.fa" ftype="fasta" />
+      <param name="inputFile" value="picard_ReorderSam.bam" ftype="bam"/>
+      <param name="allow_incomplete_dict_concordance" value="false"/>
+      <param name="allow_contig_length_discordance" value="false"/>
+      <output name="outFile" file="picard_ReorderSam_test1.bam" ftype="bam" lines_diff="2"/>
+    </test>
+  </tests>
+  
+  <stdio>
+    <exit_code range="1:"  level="fatal"/>
+  </stdio>
+  
+  <help>
+
+.. class:: infomark
+
+**Purpose**
+
+ReorderSam reorders reads in a SAM/BAM file to match the contig ordering in a provided reference file, as determined by exact name matching of contigs.  Reads mapped to contigs absent in the new reference are dropped.
+
+@dataset_collections@
+
+----
+
+.. class:: warningmark
+
+Not to be confused with **SortSam**.
+
+@description@
+
+  ALLOW_INCOMPLETE_DICT_CONCORDANCE=Boolean
+  S=Boolean                     If true, then allows only a partial overlap of the BAM contigs with the new reference 
+                                sequence contigs.  By default, this tool requires a corresponding contig in the new 
+                                reference for each read contig  Default value: false. Possible values: {true, false} 
+  
+  ALLOW_CONTIG_LENGTH_DISCORDANCE=Boolean
+  U=Boolean                     If true, then permits mapping from a read contig to a new reference contig with the same 
+                                name but a different length.  Highly dangerous, only use if you know what you are doing.  
+                                Default value: false.  Possible values: {true, false} 
+
+@more_info@
+  </help>
+</tool>
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