Mercurial > repos > iuc > bbtools_bbmap
changeset 11:7f19559b8b55 draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 8f659e3524ff3fbf70ce9f4090e3fe8a49048b29
| author | iuc |
|---|---|
| date | Wed, 24 Apr 2024 20:25:42 +0000 |
| parents | b394de3cf6e8 |
| children | |
| files | bbmap.xml macros.xml |
| diffstat | 2 files changed, 4 insertions(+), 9 deletions(-) [+] |
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--- a/bbmap.xml Fri Apr 12 20:20:17 2024 +0000 +++ b/bbmap.xml Wed Apr 24 20:25:42 2024 +0000 @@ -6,9 +6,6 @@ <expand macro="edam_ontology"/> <expand macro="requirements"/> <command detect_errors="exit_code"><![CDATA[ -#import os -#import re - #if str($ref_source_cond.ref_source) == 'cached' #set ref = str($ref_source_cond.reference.fields.path) #else: @@ -31,17 +28,15 @@ #end if #else: #set read1 = $input_type_cond.reads_collection['forward'] - #set read1_identifier = re.sub('[^\s\w\-]', '_', str($read1.element_identifier)) ## bbmap uses the file extension to determine the input format. - #set ext = $read1_identifier + '.fastq' + #set ext = '.fastq' #if $read1.ext.endswith('.gz'): #set ext = $ext + '.gz' #end if - #set read1_file = $read1_identifier + $ext + #set read1_file = 'forward' + $ext ln -s '${read1}' '${read1_file}' && #set read2 = $input_type_cond.reads_collection['reverse'] - #set read2_identifier = re.sub('[^\s\w\-]', '_', str($read2.element_identifier)) - #set read2_file = $read2_identifier + $ext + #set read2_file = 'reverse' + $ext ln -s '${read2}' '${read2_file}' && #end if
--- a/macros.xml Fri Apr 12 20:20:17 2024 +0000 +++ b/macros.xml Wed Apr 24 20:25:42 2024 +0000 @@ -1,6 +1,6 @@ <macros> <token name="@TOOL_VERSION@">39.06</token> - <token name="@VERSION_SUFFIX@">1</token> + <token name="@VERSION_SUFFIX@">2</token> <token name="@PROFILE@">22.01</token> <xml name="edam_ontology"> <edam_topics>