# HG changeset patch
# User artbio
# Date 1602168904 0
# Node ID b550841f568b6b32f3b94f75351a6aa2d2651865
# Parent  65d6d2b554b33a980a7df3df3075806bfaac007e
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_bam_cleaning commit 2d441fd84bf17c0899d0b57ea35c84cb83b77119"

diff -r 65d6d2b554b3 -r b550841f568b artbio_bam_cleaning.xml
--- a/artbio_bam_cleaning.xml	Fri Oct 02 00:17:33 2020 +0000
+++ b/artbio_bam_cleaning.xml	Thu Oct 08 14:55:04 2020 +0000
@@ -1,4 +1,4 @@
-<tool id="artbio_bam_cleaning" name="ARTbio bam cleaning" version="1.6+galaxy0">
+<tool id="artbio_bam_cleaning" name="ARTbio bam cleaning" version="1.6+galaxy1">
     <description>
         on flags and PCR Duplicates and MD recalibration
     </description>
@@ -19,27 +19,44 @@
     #set input_base = 'input'   
     ln -f -s $input_bam.metadata.bam_index input.bam.bai &&
     ln -s $input_bam input.bam &&
-    sambamba view -h -t 8 --filter='mapping_quality >= 1 and not(unmapped) and not(mate_is_unmapped)' -f 'bam' $input_base".bam"
+    sambamba view -h -t \${GALAXY_SLOTS:-2} --filter='mapping_quality >= 1 and not(unmapped) and not(mate_is_unmapped)' -f 'bam' $input_base".bam"
     | samtools rmdup - -
     |tee $input_base".filt1.dedup.bam"| bamleftalign --fasta-reference reference.fa -c --max-iterations "5" -
-    | samtools calmd  -C 50 -b -@ \${GALAXY_SLOTS:-2} - reference.fa > $input_base".filt1.dedup.bamleft.calmd.bam" &&
-    sambamba view -h -t 8 --filter='mapping_quality <= 254' -f 'bam' -o $input_base".filt1.dedup.bamleft.calmd.filt2.bam" $input_base".filt1.dedup.bamleft.calmd.bam"
+    | samtools calmd  -C 50 -b -@ \${GALAXY_SLOTS:-2} - reference.fa > $calmd
+    #if $pipeline == 'fullfilter':
+    && sambamba view -h -t \${GALAXY_SLOTS:-2} --filter='mapping_quality <= 254' -f 'bam' -o $fullfilter $calmd
+    #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="pipeline" type="select" label="where to stop the pipeline">
+            <option value="CalMD">At CalMD processing, to keep split read alignments</option>
+            <option value="fullfilter" selected="true">Full bam processing, will eliminate split read alignments in the final bam file</option>
+        </param>
     </inputs>
     <outputs>
-        <data name="calmd" format="bam" label="CalMD filter (for lumpy-smoove)" from_work_dir="./input.filt1.dedup.bamleft.calmd.bam"/>
-        <data name="fullfilter" format="bam" label="Full filtering (for somatic-varscan)" from_work_dir="./input.filt1.dedup.bamleft.calmd.filt2.bam"/>
+        <data name="calmd" format="bam" label="CalMD filter (for lumpy-smoove)">
+            <filter>pipeline == 'CalMD'</filter>
+        </data>
+        <data name="fullfilter" format="bam" label="Full filtering (for somatic-varscan)">
+             <filter>pipeline == 'fullfilter'</filter>
+        </data>
+       
     </outputs>
     <tests>
         <test>
             <param name="input_bam" value="match_chr21_DBA_974.bam" ftype="bam" />
             <param name="reference_source_selector" value="history" />
             <param name="ref_file" value="chr21.fa" />
+            <output name="fullfilter" file="match_chr21_DBA_974.filt1.dedup.bamleft.calmd.filt2.bam" ftype="bam" />
+        </test>
+        <test>
+            <param name="input_bam" value="match_chr21_DBA_974.bam" ftype="bam" />
+            <param name="reference_source_selector" value="history" />
+            <param name="ref_file" value="chr21.fa" />
+            <param name="pipeline" value="CalMD"/>
             <output name="calmd" file="match_chr21_DBA_974.filt1.dedup.bamleft.calmd.bam" ftype="bam" />
-            <output name="fullfilter" file="match_chr21_DBA_974.filt1.dedup.bamleft.calmd.filt2.bam" ftype="bam" />
         </test>
     </tests>
     <help>