diff picard_MergeSamFiles.xml @ 0:40d9376df6d6 draft

planemo upload for repository https://github.com/scottx611x/picard_MergeSamFiles commit 46a5f872db68a7664cfae127b777e85fde8e6d98-dirty

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/picard_MergeSamFiles.xml	Mon Dec 04 09:23:06 2017 -0500
@@ -0,0 +1,117 @@
+<tool name="MergeSamFiles" id="picard_MergeSamFiles" version="@TOOL_VERSION@.0">
+  <description>merges multiple SAM/BAM datasets into one</description>
+  <macros>
+    <import>picard_macros.xml</import>
+  </macros>
+  <expand macro="requirements" />
+  <command detect_errors="exit_code"><![CDATA[
+    @java_options@
+    #for $index, $listCollection in enumerate($inputList):
+      && 
+      picard
+      MergeSamFiles
+
+      #for $element in $listCollection:
+        INPUT="${element}"
+      #end for
+
+      OUTPUT="${'merged{}.bam'.format($index)}"
+      MERGE_SEQUENCE_DICTIONARIES="${merge_sequence_dictionaries}"
+      ASSUME_SORTED="${assume_sorted}"
+      #for $element in $comments:
+        COMMENT="${element.comment}"
+      #end for
+      USE_THREADING=true
+      SORT_ORDER=coordinate
+      VALIDATION_STRINGENCY="${validation_stringency}"
+      QUIET=true
+      VERBOSITY=ERROR 
+    #end for
+  ]]></command>
+  <inputs>
+    <param format="sam,bam" name="inputList" type="data_collection" collection_type="list:list" label="Select SAM/BAM dataset collection" help="If empty, upload or import a SAM/BAM dataset"/>
+    <param name="merge_sequence_dictionaries" type="boolean" label="Merge the sequence dictionaries of the datasets being merged" help="MERGE_SEQUENCE_DICTIONARIES; default=False"/>
+    <param name="assume_sorted" type="boolean" label="Assume the input file is already sorted" help="ASSUME_SORTED; default=False"/>
+
+    <repeat name="comments" title="Comment" min="0" help="You can provide multiple comments">
+      <param name="comment" type="text" label="Add this comment to BAM dataset" help="COMMENT"/>
+    </repeat>
+
+    <expand macro="VS" />
+
+  </inputs>
+
+  <outputs>
+    <data format="bam" name="merged">
+        <discover_datasets pattern="__designation_and_ext__" visible="true" />
+    </data>
+  </outputs>
+
+  <tests>
+    <test>
+      <param name="inputList">
+        <collection type="list:list">
+          <element name="list 1">
+            <collection type="list">
+              <element name="l1_input1" value="picard_MergeSamFiles_input1.bam" />
+              <element name="l1_input2" value="picard_MergeSamFiles_input2.bam" />
+              <element name="l1_input3" value="picard_MergeSamFiles_input3.bam" />
+            </collection>
+          </element>
+          <element name="list 2">
+          <collection type="list">
+              <element name="l2_input1" value="picard_MergeSamFiles_input1.bam" />
+              <element name="l2_input2" value="picard_MergeSamFiles_input2.bam" />
+              <element name="l2_input3" value="picard_MergeSamFiles_input3.bam" />
+            </collection>
+          </element>
+        </collection>
+      </param>
+      <param name="assume_sorted" value="False"/>
+      <param name="merge_sequence_dictionaries" value="False"/>
+      <param name="validation_stringency" value="LENIENT"/>
+      <output name="merged0" ftype="bam">
+        <assert_contents>
+          <has_text text=""/>
+        </assert_contents>
+      </output>
+      <output name="merged1" ftype="bam">
+        <assert_contents>
+          <has_text text=""/>
+        </assert_contents>
+      </output>
+    </test>
+  </tests>
+  
+  <stdio>
+    <exit_code range="1:"  level="fatal"/>
+  </stdio>
+  
+  <help>
+
+**Purpose**
+
+Merges multiple SAM/BAM datasets into one.
+
+@dataset_collections@
+
+@description@
+
+  ASSUME_SORTED=Boolean
+  AS=Boolean                    If true, assume that the input files are in the same sort order as the requested output
+                                sort order, even if their headers say otherwise.  Default value: false. This option can
+                                be set to 'null' to clear the default value. Possible values: {true, false}
+
+  MERGE_SEQUENCE_DICTIONARIES=Boolean
+  MSD=Boolean                   Merge the sequence dictionaries  Default value: false. This option can be set to 'null'
+                                to clear the default value. Possible values: {true, false}
+
+  COMMENT=String
+  CO=String                     Comment(s) to include in the merged output file's header.  This option may be specified 0
+                                or more times.
+
+
+@more_info@
+
+  </help>
+</tool>