Mercurial > repos > iuc > polypolish
comparison polypolish.xml @ 2:f355085dd2aa draft default tip
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 |
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| 1:bd2a15dbcea1 | 2:f355085dd2aa |
|---|---|
| 13 #*====================================== | 13 #*====================================== |
| 14 For single SAM | 14 For single SAM |
| 15 ======================================*# | 15 ======================================*# |
| 16 #if $input.sam_data_type.sam_selector == 'single' | 16 #if $input.sam_data_type.sam_selector == 'single' |
| 17 #if $input.sam_data_type.single_sam.is_of_type("unsorted.bam") | 17 #if $input.sam_data_type.single_sam.is_of_type("unsorted.bam") |
| 18 samtools view -h $input.sam_data_type.single_sam > input_sam && | 18 samtools view -@ \$addthreads -h $input.sam_data_type.single_sam > input_sam && |
| 19 #elif $input.sam_data_type.single_sam.ext == 'sam' | 19 #elif $input.sam_data_type.single_sam.ext == 'sam' |
| 20 ln -s $input.sam_data_type.single_sam input_sam && | 20 ln -s $input.sam_data_type.single_sam input_sam && |
| 21 #else | 21 #else |
| 22 echo "${input.sam_data_type.single_sam} not a sam/bam file" | 22 echo "${input.sam_data_type.single_sam} not a sam/bam file" |
| 23 #end if | 23 #end if |
| 25 #*====================================== | 25 #*====================================== |
| 26 For paired SAM | 26 For paired SAM |
| 27 ======================================*# | 27 ======================================*# |
| 28 #elif $input.sam_data_type.sam_selector == 'paired' | 28 #elif $input.sam_data_type.sam_selector == 'paired' |
| 29 #if $input.sam_data_type.R1_sam.is_of_type("unsorted.bam") | 29 #if $input.sam_data_type.R1_sam.is_of_type("unsorted.bam") |
| 30 samtools view -h $input.sam_data_type.R1_sam > sample_R1.sam && | 30 samtools view -@ \$addthreads -h $input.sam_data_type.R1_sam > sample_R1.sam && |
| 31 #elif $input.sam_data_type.R1_sam.ext == 'sam' | 31 #elif $input.sam_data_type.R1_sam.ext == 'sam' |
| 32 ln -s '$input.sam_data_type.R1_sam' sample_R1.sam && | 32 ln -s '$input.sam_data_type.R1_sam' sample_R1.sam && |
| 33 #else | 33 #else |
| 34 echo "${input.sam_data_type.single_sam} not a sam/bam file" | 34 echo "${input.sam_data_type.single_sam} not a sam/bam file" |
| 35 #end if | 35 #end if |
| 36 #if $input.sam_data_type.R2_sam.is_of_type("unsorted.bam") | 36 #if $input.sam_data_type.R2_sam.is_of_type("unsorted.bam") |
| 37 samtools view -h $input.sam_data_type.R2_sam > sample_R2.sam && | 37 samtools view -@ \$addthreads -h $input.sam_data_type.R2_sam > sample_R2.sam && |
| 38 #elif $input.sam_data_type.R2_sam.ext == 'sam' | 38 #elif $input.sam_data_type.R2_sam.ext == 'sam' |
| 39 ln -s '$input.sam_data_type.R2_sam' sample_R2.sam && | 39 ln -s '$input.sam_data_type.R2_sam' sample_R2.sam && |
| 40 #else | 40 #else |
| 41 echo "${input.sam_data_type.single_sam} not a sam/bam file" | 41 echo "${input.sam_data_type.single_sam} not a sam/bam file" |
| 42 #end if | 42 #end if |
| 56 ======================================*# | 56 ======================================*# |
| 57 #elif $input.sam_data_type.sam_selector == 'multiple_single' | 57 #elif $input.sam_data_type.sam_selector == 'multiple_single' |
| 58 mkdir single_collection && | 58 mkdir single_collection && |
| 59 #for $value, $single_sam in enumerate($input.sam_data_type.single_collection): | 59 #for $value, $single_sam in enumerate($input.sam_data_type.single_collection): |
| 60 #if $single_sam.is_of_type("unsorted.bam") | 60 #if $single_sam.is_of_type("unsorted.bam") |
| 61 samtools view -h $single_sam > 'single_collection/$(single_sam.element_identifier).sam' && | 61 samtools view -@ \$addthreads -h $single_sam > 'single_collection/$(single_sam.element_identifier).sam' && |
| 62 #elif $single_sam.ext == 'sam' | 62 #elif $single_sam.ext == 'sam' |
| 63 ln -s $single_sam 'single_collection/$(single_sam.element_identifier).$(single_sam.ext)' && | 63 ln -s $single_sam 'single_collection/$(single_sam.element_identifier).$(single_sam.ext)' && |
| 64 #else | 64 #else |
| 65 echo "${single_sam} is not a sam/bam file" | 65 echo "${single_sam} is not a sam/bam file" |
| 66 #end if | 66 #end if |
| 71 ======================================*# | 71 ======================================*# |
| 72 #elif $input.sam_data_type.sam_selector == "multiple_paired" | 72 #elif $input.sam_data_type.sam_selector == "multiple_paired" |
| 73 mkdir paired_collection && | 73 mkdir paired_collection && |
| 74 #for $value, $paired_sam in enumerate($input.sam_data_type.paired_collection): | 74 #for $value, $paired_sam in enumerate($input.sam_data_type.paired_collection): |
| 75 #if $paired_sam.forward.is_of_type("unsorted.bam") | 75 #if $paired_sam.forward.is_of_type("unsorted.bam") |
| 76 samtools view -h $paired_sam.forward > 'paired_collection/forward_input$(value)$(paired_sam.forward.element_identifier).sam' && | 76 samtools view -@ \$addthreads -h $paired_sam.forward > 'paired_collection/forward_input$(value)$(paired_sam.forward.element_identifier).sam' && |
| 77 #else | 77 #else |
| 78 ln -s '$paired_sam.forward' 'paired_collection/forward_input$(value)$(paired_sam.forward.element_identifier).sam' && | 78 ln -s '$paired_sam.forward' 'paired_collection/forward_input$(value)$(paired_sam.forward.element_identifier).sam' && |
| 79 #end if | 79 #end if |
| 80 #if $paired_sam.reverse.is_of_type("unsorted.bam") | 80 #if $paired_sam.reverse.is_of_type("unsorted.bam") |
| 81 samtools view -h $paired_sam.reverse > 'paired_collection/reverse_input$(value)$(paired_sam.reverse.element_identifier).sam' && | 81 samtools view -@ \$addthreads -h $paired_sam.reverse > 'paired_collection/reverse_input$(value)$(paired_sam.reverse.element_identifier).sam' && |
| 82 #else | 82 #else |
| 83 ln -s '$paired_sam.reverse' 'paired_collection/reverse_input$(value)$(paired_sam.reverse.element_identifier).sam' && | 83 ln -s '$paired_sam.reverse' 'paired_collection/reverse_input$(value)$(paired_sam.reverse.element_identifier).sam' && |
| 84 #end if | 84 #end if |
| 85 #if $input.sam_data_type.insert_filter.filter_select == 'filter' | 85 #if $input.sam_data_type.insert_filter.filter_select == 'filter' |
| 86 polypolish_insert_filter.py --low '$input.sam_data_type.insert_filter.low' | 86 polypolish_insert_filter.py --low '$input.sam_data_type.insert_filter.low' |