changeset 7:d97988f07983 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_calmd commit a972815cbd43dea553b3c0e4ad548f35d0023228-dirty

--- a/samtools_calmd.xml	Fri Nov 30 17:45:49 2018 -0500
+++ b/samtools_calmd.xml	Sun Jul 28 14:46:45 2019 -0400
@@ -7,23 +7,25 @@
     <expand macro="stdio"/>
     <expand macro="version_command"/>
     <command><![CDATA[
-        #if str( $reference_source.reference_source_selector ) == "history":
-            #set ref_fa = 'ref.fa'
-            ln -s '${reference_source.ref_fasta}' ref.fa &&
-            samtools faidx ref.fa &&
-        #else:
-            #set ref_fa = str( $reference_source.ref_fasta.fields.path )
-        #end if
+@ADDTHREADS@
+#if str( $reference_source.reference_source_selector ) == "history":
+    #set ref_fa = 'ref.fa'
+    ln -s '${reference_source.ref_fasta}' ref.fa &&
+    samtools faidx ref.fa &&
+#else:
+    #set ref_fa = str( $reference_source.ref_fasta.fields.path )
+#end if
 
-        samtools calmd
-            $baq_settings.use_baq $baq_settings.modify_quality $baq_settings.extended_baq
-            #if str($option_set.option_sets) == 'advanced':
-                $option_set.change_identical -C $option_set.adjust_mq
-            #end if
-            -b
-            '$input_bam'
-            '$ref_fa'
-            > '$calmd_output'
+samtools calmd
+    $baq_settings.use_baq $baq_settings.modify_quality $baq_settings.extended_baq
+    #if str($option_set.option_sets) == 'advanced':
+        $option_set.change_identical -C $option_set.adjust_mq
+    #end if
+    -b
+    -@ \$addthreads
+    '$input_bam'
+    '$ref_fa'
+    > '$calmd_output'
     ]]></command>
     <inputs>
         <param name="input_bam" type="data" format="bam" label="BAM file to recalculate" />