# HG changeset patch
# User artbio
# Date 1617759111 0
# Node ID 999c2b871f36a0b6387239efb19889b6f8b63048
# Parent  ebdaf5b3d6a70bad04d28bdd946a3b7901d5629b
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_bam_cleaning commit 587b99e907726b20f0cdd978be8f9ed257a68243"

diff -r ebdaf5b3d6a7 -r 999c2b871f36 artbio_bam_cleaning.xml
--- a/artbio_bam_cleaning.xml	Mon Mar 29 15:09:23 2021 +0000
+++ b/artbio_bam_cleaning.xml	Wed Apr 07 01:31:51 2021 +0000
@@ -1,4 +1,4 @@
-<tool id="artbio_bam_cleaning" name="ARTbio bam cleaning" version="1.6+galaxy5">
+<tool id="artbio_bam_cleaning" name="ARTbio bam cleaning" version="1.6+galaxy6">
     <description>
         on flags and PCR Duplicates and MD recalibration
     </description>
@@ -25,21 +25,32 @@
     #end if
     | bamleftalign --fasta-reference reference.fa -c --max-iterations "5" -
     | samtools calmd  -C 50 -b -@ \${GALAXY_SLOTS:-2} - reference.fa
-    | tee $calmd
-    | sambamba view -h -t \${GALAXY_SLOTS:-2} --filter='mapping_quality <= 254' -f 'bam' /dev/stdin > $fullfilter
+    #if $skip_laststep == 'yes':
+        > $calmd
+    #else if $skip_laststep == 'no':
+        | tee $calmd
+        | sambamba view -h -t \${GALAXY_SLOTS:-2} --filter='mapping_quality <= 254' -f 'bam' /dev/stdin > $fullfilter
+    #end if
     ]]></command>
     <inputs>
         <expand macro="reference_source_conditional" />
         <param name="input_bam" type="data" format="bam" label="BAM or SAM file to process"/>
-            <param name="skip_rmdup" type="select" label="skip remove pcr duplicate step ?" display="radio"
-                   help="useful if duplicates are already marked by other tools">
-                <option value="no" selected="true">No</option>
-                <option value="yes">Yes</option>
-            </param>
+        <param name="skip_rmdup" type="select" label="skip remove pcr duplicate step ?" display="radio"
+               help="useful if duplicates are already marked by other tools">
+            <option value="no" selected="true">No</option>
+            <option value="yes">Yes</option>
+        </param>
+        <param name="skip_laststep" type="select" label="skip last samtool view filter ?" display="radio"
+               help="Only generate the calMD output">
+            <option value="no" selected="true">No</option>
+            <option value="yes">Yes</option>
+        </param>
     </inputs>
     <outputs>
         <data name="calmd" format="bam" label="CalMD filter (for lumpy-smoove)" />
-        <data name="fullfilter" format="bam" label="Full filtering (for somatic-varscan)" />
+        <data name="fullfilter" format="bam" label="Full filtering (for somatic-varscan)">
+            <filter>skip_laststep == "no"</filter>
+        </data>
     </outputs>
     <tests>
         <test>