| Previous changeset 1:bd2a15dbcea1 (2023-10-20) |
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Commit message:
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit 2a8a85c8b08a62edbd11c34126753192baf6da66 |
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modified:
macro.xml polypolish.xml |
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| diff -r bd2a15dbcea1 -r f355085dd2aa macro.xml --- a/macro.xml Fri Oct 20 12:41:27 2023 +0000 +++ b/macro.xml Thu Jan 11 16:44:56 2024 +0000 |
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| @@ -1,9 +1,14 @@ <macros> <token name="@TOOL_VERSION@">0.5.0</token> - <token name="@VERSION_SUFFIX@">1</token> + <token name="@VERSION_SUFFIX@">2</token> <token name="@PROFILE@">21.05</token> - <token name="@THREADS@">\${GALAXY_SLOTS:-7}</token> + + <token name="@THREADS@"><![CDATA[ + ##compute the number of ADDITIONAL threads to be used by samtools (-@) + addthreads=\${GALAXY_SLOTS:-1} && (( addthreads-- )) && + ]]></token> + <xml name="version_command"> <version_command><![CDATA[polypolish -V]]></version_command> </xml> @@ -15,7 +20,7 @@ <xml name="requirements"> <requirements> <requirement type="package" version="@TOOL_VERSION@">polypolish</requirement> - <requirement type="package" version="1.13">samtools</requirement> + <requirement type="package" version="1.19">samtools</requirement> </requirements> </xml> <xml name="citations"> |
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| diff -r bd2a15dbcea1 -r f355085dd2aa polypolish.xml --- a/polypolish.xml Fri Oct 20 12:41:27 2023 +0000 +++ b/polypolish.xml Thu Jan 11 16:44:56 2024 +0000 |
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| @@ -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 |