Mercurial > repos > iuc > polypolish

diff polypolish.xml @ 2:f355085dd2aa draft default tip

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planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit 2a8a85c8b08a62edbd11c34126753192baf6da66
author iuc
date Thu, 11 Jan 2024 16:44:56 +0000
parents bd2a15dbcea1
children
line wrap: on
line diff
--- a/polypolish.xml	Fri Oct 20 12:41:27 2023 +0000
+++ b/polypolish.xml	Thu Jan 11 16:44:56 2024 +0000
@@ -15,7 +15,7 @@
         ======================================*#
         #if $input.sam_data_type.sam_selector == 'single'
             #if $input.sam_data_type.single_sam.is_of_type("unsorted.bam")
-                samtools view -h $input.sam_data_type.single_sam > input_sam &&
+                samtools view -@ \$addthreads -h $input.sam_data_type.single_sam > input_sam &&
             #elif $input.sam_data_type.single_sam.ext == 'sam'
                 ln -s $input.sam_data_type.single_sam input_sam &&
             #else
@@ -27,14 +27,14 @@
         ======================================*#
         #elif $input.sam_data_type.sam_selector == 'paired'
             #if $input.sam_data_type.R1_sam.is_of_type("unsorted.bam")
-                samtools view -h $input.sam_data_type.R1_sam > sample_R1.sam &&
+                samtools view -@ \$addthreads -h $input.sam_data_type.R1_sam > sample_R1.sam &&
             #elif $input.sam_data_type.R1_sam.ext == 'sam'
                 ln -s '$input.sam_data_type.R1_sam' sample_R1.sam &&
             #else
                 echo "${input.sam_data_type.single_sam} not a sam/bam file"
             #end if
             #if $input.sam_data_type.R2_sam.is_of_type("unsorted.bam")
-                samtools view -h $input.sam_data_type.R2_sam > sample_R2.sam &&
+                samtools view -@ \$addthreads -h $input.sam_data_type.R2_sam > sample_R2.sam &&
             #elif $input.sam_data_type.R2_sam.ext == 'sam'
                 ln -s '$input.sam_data_type.R2_sam' sample_R2.sam &&
             #else
@@ -58,7 +58,7 @@
             mkdir single_collection &&
             #for $value, $single_sam in enumerate($input.sam_data_type.single_collection):
                 #if $single_sam.is_of_type("unsorted.bam")
-                    samtools view -h $single_sam > 'single_collection/$(single_sam.element_identifier).sam' &&
+                    samtools view -@ \$addthreads -h $single_sam > 'single_collection/$(single_sam.element_identifier).sam' &&
                 #elif $single_sam.ext == 'sam'
                     ln -s $single_sam 'single_collection/$(single_sam.element_identifier).$(single_sam.ext)' &&
                 #else
@@ -73,12 +73,12 @@
             mkdir paired_collection &&
             #for $value, $paired_sam in enumerate($input.sam_data_type.paired_collection):
                 #if $paired_sam.forward.is_of_type("unsorted.bam")
-                    samtools view -h $paired_sam.forward > 'paired_collection/forward_input$(value)$(paired_sam.forward.element_identifier).sam' &&
+                    samtools view -@ \$addthreads -h $paired_sam.forward > 'paired_collection/forward_input$(value)$(paired_sam.forward.element_identifier).sam' &&
                 #else
                     ln -s '$paired_sam.forward' 'paired_collection/forward_input$(value)$(paired_sam.forward.element_identifier).sam' &&
                 #end if
                 #if $paired_sam.reverse.is_of_type("unsorted.bam")
-                    samtools view -h $paired_sam.reverse > 'paired_collection/reverse_input$(value)$(paired_sam.reverse.element_identifier).sam' &&
+                    samtools view -@ \$addthreads -h $paired_sam.reverse > 'paired_collection/reverse_input$(value)$(paired_sam.reverse.element_identifier).sam' &&
                 #else
                     ln -s '$paired_sam.reverse' 'paired_collection/reverse_input$(value)$(paired_sam.reverse.element_identifier).sam' &&
                 #end if