# HG changeset patch
# User drosofff
# Date 1481122323 18000
# Node ID 2f41fac75575cefcc3f2bef9c5c2e34751c9bdae
# Parent  0bd777f0d6d82f4a628460262dacbd494fd9c69f
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit 66d42b0d63ff5d72c6611106ed3366a58c73a55d

diff -r 0bd777f0d6d8 -r 2f41fac75575 lumpy.xml
--- a/lumpy.xml	Wed Dec 07 05:26:21 2016 -0500
+++ b/lumpy.xml	Wed Dec 07 09:52:03 2016 -0500
@@ -25,7 +25,7 @@
                 samtools sort input.discordants.unsorted.bam > input.discordants.bam &&
                 samtools sort input.splitters.unsorted.bam > input.splitters.bam &&
                 samtools view -r readgroup input.bam
-                    |tail -n +$seq_method.additional_params.samplingValue
+                    |tail -n +1
                     |python $__tool_directory__/pairend_distro.py -r 101 -X 4 -N $seq_method.additional_params.samplingValue -o input.lib.histo > meandev.txt &&
                 mean=\$(cat meandev.txt | sed s/mean:// | sed -r s/stdev:.+//) &&
                 stdev=\$(cat meandev.txt | sed -r s/mean:.+stdev://) &&
@@ -58,10 +58,10 @@
                 samtools sort input.A.splitters.unsorted.bam > input.A.splitters.bam &&
                 samtools sort input.B.splitters.unsorted.bam > input.B.splitters.bam &&
                 samtools view -r readgroup input.A.bam
-                    |tail -n +$seq_method.additional_params.samplingValue
+                    |tail -n +1
                     |python $__tool_directory__/pairend_distro.py -r 101 -X 4 -N $seq_method.additional_params.samplingValue -o input.A.lib.histo > meandevA.txt &&
                 samtools view -r readgroup input.B.bam
-                    |tail -n +$seq_method.additional_params.samplingValue
+                    |tail -n +1
                     |python $__tool_directory__/pairend_distro.py -r 101 -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:.+//) &&               
@@ -146,25 +146,25 @@
     </inputs>
 
     <outputs>
-        <data format="tabular" name="histogram" type="data" label="Lumpy on ${analysis_type.input_file.element_identifier}: Fragment size distribution">
+        <data format="tabular" name="histogram" label="Lumpy on ${analysis_type.input_file.element_identifier}: Fragment size distribution">
             <filter>seq_method['seq_method_list'] == "paired-end"</filter>
         </data>
-        <data format="tabular" name="histogramB" type="data" label="Lumpy on ${analysis_type.input_fileB.element_identifier}: Fragment size distribution">
+        <data format="tabular" name="histogramB" label="Lumpy on ${analysis_type.input_fileB.element_identifier}: Fragment size distribution">
             <filter>seq_method['seq_method_list'] == "paired-end"</filter>
             <filter>analysis_type['analysis_type_list'] == "two_sample"</filter>
         </data>
-        <data format="bam" name="splits" type="data" label="Lumpy on ${analysis_type.input_file.element_identifier}: Split Reads (Bam format)"/>
-        <data format="bam" name="splitsB" type="data" label="Lumpy on ${analysis_type.input_fileB.element_identifier}: Split Reads (Bam format)">
+        <data format="bam" name="splits" label="Lumpy on ${analysis_type.input_file.element_identifier}: Split Reads (Bam format)"/>
+        <data format="bam" name="splitsB" label="Lumpy on ${analysis_type.input_fileB.element_identifier}: Split Reads (Bam format)">
             <filter>analysis_type['analysis_type_list'] == "two_sample"</filter>
         </data>
-        <data format="bam" name="discordants" type="data" label="Lumpy on ${analysis_type.input_file.element_identifier}: Discordant Pairs (Bam format)">
+        <data format="bam" name="discordants" label="Lumpy on ${analysis_type.input_file.element_identifier}: Discordant Pairs (Bam format)">
             <filter>seq_method['seq_method_list'] == "paired-end"</filter>
         </data>
-        <data format="bam" name="discordantsB" type="data" label="Lumpy on ${analysis_type.input_fileB.element_identifier}: Discordant Pairs (Bam format)">
+        <data format="bam" name="discordantsB" label="Lumpy on ${analysis_type.input_fileB.element_identifier}: Discordant Pairs (Bam format)">
             <filter>seq_method['seq_method_list'] == "paired-end"</filter>
             <filter>analysis_type['analysis_type_list'] == "two_sample"</filter>
         </data>
-        <data format="vcf" name="vcf_call" type="data" label="Lumpy Variant Calling (vcf format)"/>
+        <data format="vcf" name="vcf_call" label="Lumpy Variant Calling (vcf format)"/>
     </outputs>
 
     <tests>