# HG changeset patch
# User artbio
# Date 1571051521 14400
# Node ID 6059f4cb4cf25bcf78b7125c167fa8a07742e96a
# Parent  1ed8619a5611bd69b7744a0577788ee75c00330d
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy-sv commit 6a109f553d1691e243372258ad564244586875c3"

diff -r 1ed8619a5611 -r 6059f4cb4cf2 lumpy.xml
--- a/lumpy.xml	Wed Jul 26 18:17:01 2017 -0400
+++ b/lumpy.xml	Mon Oct 14 07:12:01 2019 -0400
@@ -1,4 +1,4 @@
-<tool id="lumpy" name="lumpy-sv" version="1.0.1">
+<tool id="lumpy" name="lumpy-sv" version="1.1.0">
     <description>find structural variants</description>
     <requirements>
         <requirement type="package" version="0.2.13">lumpy-sv</requirement>
@@ -27,9 +27,9 @@
         #if $analysis_type.analysis_type_list == "one_sample":
 
             #if $seq_method.seq_method_list == "paired-end":
-                samtools view -u -F 1294 '$one_sample_bam' | samtools sort -O bam -o input.discordants.bam &&
-                samtools view -h '$one_sample_bam' | python $__tool_directory__/extractSplitReads_BwaMem.py -i stdin | samtools sort -O bam -o input.splitters.bam &&
-                samtools view '$one_sample_bam'
+                samtools view -@ \${GALAXY_SLOTS:-4} -u -F 1294 '$one_sample_bam' | samtools sort -@ \${GALAXY_SLOTS:-4} -O bam -o input.discordants.bam &&
+                samtools view -@ \${GALAXY_SLOTS:-4} -h '$one_sample_bam' | python $__tool_directory__/extractSplitReads_BwaMem.py -i stdin | samtools sort -@ \${GALAXY_SLOTS:-4} -O bam -o input.splitters.bam &&
+                samtools view -@ \${GALAXY_SLOTS:-4} '$one_sample_bam'
                     |python $__tool_directory__/pairend_distro.py -r $analysis_type.readLength -X 4 -N $seq_method.additional_params.samplingValue -o input.lib.histo > meandev.txt &&
                 mean=\$(cat meandev.txt | sed s/mean:// | sed -r s/stdev:.+//) &&
                 stdev=\$(cat meandev.txt | sed -r s/mean:.+stdev://) &&
@@ -40,7 +40,7 @@
                     -pe id:'$one_sample_bam',bam_file:input.discordants.bam,histo_file:input.lib.histo,mean:"\$mean",stdev:"\$stdev",read_length:$analysis_type.readLength,min_non_overlap:$seq_method.additional_params.min_non_overlap,discordant_z:$seq_method.additional_params.discordant_z,back_distance:$seq_method.additional_params.back_distance,weight:$seq_method.additional_params.weight,min_mapping_threshold:$seq_method.additional_params.min_mapping_threshold
                     -sr id:'$one_sample_bam',bam_file:input.splitters.bam,back_distance:$seq_method.additional_params.back_distance,weight:$seq_method.additional_params.weight,min_mapping_threshold:$seq_method.additional_params.min_mapping_threshold > '$vcf_call'
             #elif $seq_method.seq_method_list == "single-read":
-                samtools view -h '$one_sample_bam' | python $__tool_directory__/extractSplitReads_BwaMem.py -i stdin | samtools sort -O bam -o input.splitters.bam &&
+                samtools view -@ \${GALAXY_SLOTS:-4} -h '$one_sample_bam' | python $__tool_directory__/extractSplitReads_BwaMem.py -i stdin | samtools sort -@ \${GALAXY_SLOTS:-4} -O bam -o input.splitters.bam &&
                 lumpy $seq_method.additional_params.evidence $seq_method.additional_params.probability_curve -mw $seq_method.additional_params.mw -tt $seq_method.additional_params.tt
                     #if $output_format == "BEDPE":
                         -b
@@ -49,13 +49,13 @@
             #end if
         #else:
             #if $seq_method.seq_method_list == "paired-end":
-                samtools view -u -F 1294 '$sample_a_bam' | samtools sort -O bam -o input.discordants.bam &&
-                samtools view -u -F 1294 '$sample_b_bam' | samtools sort -O bam -o input.B.discordants.bam &&
-                samtools view -h '$sample_a_bam' | python $__tool_directory__/extractSplitReads_BwaMem.py -i stdin | samtools sort -O bam -o input.splitters.bam &&
-                samtools view -h '$sample_b_bam' | python $__tool_directory__/extractSplitReads_BwaMem.py -i stdin | samtools sort -O bam -o input.B.splitters.bam &&
-                samtools view  '$sample_a_bam'
+                samtools view -@ \${GALAXY_SLOTS:-4} -u -F 1294 '$sample_a_bam' | samtools sort -@ \${GALAXY_SLOTS:-4} -O bam -o input.discordants.bam &&
+                samtools view -@ \${GALAXY_SLOTS:-4} -u -F 1294 '$sample_b_bam' | samtools sort -@ \${GALAXY_SLOTS:-4} -O bam -o input.B.discordants.bam &&
+                samtools view -@ \${GALAXY_SLOTS:-4} -h '$sample_a_bam' | python $__tool_directory__/extractSplitReads_BwaMem.py -i stdin | samtools sort -@ \${GALAXY_SLOTS:-4} -O bam -o input.splitters.bam &&
+                samtools view -@ \${GALAXY_SLOTS:-4} -h '$sample_b_bam' | python $__tool_directory__/extractSplitReads_BwaMem.py -i stdin | samtools sort -@ \${GALAXY_SLOTS:-4} -O bam -o input.B.splitters.bam &&
+                samtools view -@ \${GALAXY_SLOTS:-4} '$sample_a_bam'
                     |python $__tool_directory__/pairend_distro.py -r $analysis_type.readLength -X 4 -N $seq_method.additional_params.samplingValue -o input.lib.histo > meandevA.txt &&
-                samtools view  '$sample_b_bam'
+                samtools view -@ \${GALAXY_SLOTS:-4} '$sample_b_bam'
                     |python $__tool_directory__/pairend_distro.py -r $analysis_type.readLengthB -X 4 -N $seq_method.additional_params.samplingValue -o input.B.lib.histo > meandevB.txt &&
                 meanA=\$(cat meandevA.txt | sed s/mean:// | sed -r s/stdev:.+//) &&
                 meanB=\$(cat meandevB.txt | sed s/mean:// | sed -r s/stdev:.+//) &&
@@ -70,8 +70,8 @@
                     -sr id:inputA.bam,bam_file:input.splitters.bam,back_distance:$seq_method.additional_params.back_distance,weight:$seq_method.additional_params.weight,min_mapping_threshold:$seq_method.additional_params.min_mapping_threshold
                     -sr id:inputB.bam,bam_file:input.B.splitters.bam,back_distance:$seq_method.additional_params.back_distance,weight:$seq_method.additional_params.weight,min_mapping_threshold:$seq_method.additional_params.min_mapping_threshold > '$vcf_call'
             #elif $seq_method.seq_method_list == "single-read":
-                samtools view -h '$sample_a_bam' | python $__tool_directory__/extractSplitReads_BwaMem.py -i stdin | samtools sort -O bam -o input.splitters.bam &&
-                samtools view -h '$sample_b_bam' | python $__tool_directory__/extractSplitReads_BwaMem.py -i stdin | samtools sort -O bam -o input.B.splitters.bam &&
+                samtools view -@ \${GALAXY_SLOTS:-4} -h '$sample_a_bam' | python $__tool_directory__/extractSplitReads_BwaMem.py -i stdin | samtools sort -@ \${GALAXY_SLOTS:-4} -O bam -o input.splitters.bam &&
+                samtools view -@ \${GALAXY_SLOTS:-4} -h '$sample_b_bam' | python $__tool_directory__/extractSplitReads_BwaMem.py -i stdin | samtools sort -@ \${GALAXY_SLOTS:-4} -O bam -o input.B.splitters.bam &&
                 lumpy $seq_method.additional_params.evidence $seq_method.additional_params.probability_curve -mw $seq_method.additional_params.mw -tt $seq_method.additional_params.tt
                     #if $output_format == "BEDPE":
                         -b