Mercurial > repos > iuc > bbtools_bbmap
changeset 3:8157a81f511c draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 425671870866660485ef6a35c94d3736f5c1df97"
| author | iuc |
|---|---|
| date | Tue, 01 Feb 2022 23:01:08 +0000 |
| parents | e0ca2ec4f5d9 |
| children | 6d44c9f1a42b |
| files | bbmap.xml macros.xml |
| diffstat | 2 files changed, 7 insertions(+), 9 deletions(-) [+] |
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--- a/bbmap.xml Thu Nov 11 16:38:09 2021 +0000 +++ b/bbmap.xml Tue Feb 01 23:01:08 2022 +0000 @@ -16,18 +16,16 @@ #if str($input_type_cond.input_type) in ['single', 'pair']: #set read1 = $input_type_cond.read1 - #set read1_identifier = re.sub('[^\s\w\-]', '_', str($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}' '${read1_file}' && #if str($input_type_cond.input_type) == 'pair': #set read2 = $input_type_cond.read2 - #set read2_identifier = re.sub('[^\s\w\-]', '_', str($read2.element_identifier)) - #set read2_file = $read2_identifier + $ext + #set read2_file = 'reverse' + $ext ln -s '${read2}' '${read2_file}' && #end if #else:
--- a/macros.xml Thu Nov 11 16:38:09 2021 +0000 +++ b/macros.xml Tue Feb 01 23:01:08 2022 +0000 @@ -1,6 +1,6 @@ <macros> <token name="@WRAPPER_VERSION@">1.0.0</token> - <token name="@VERSION_SUFFIX@">1.0.0</token> + <token name="@VERSION_SUFFIX@">2</token> <token name="@PROFILE@">20.09</token> <xml name="requirements"> <requirements> @@ -39,11 +39,11 @@ <option value="paired">List of dataset pairs</option> </param> <when value="single"> - <param name="read1" type="data" format="fastqsanger.gz,fastqsanger" label="Read1 fastq file"/> + <param name="read1" type="data" format="fastqsanger.gz,fastqsanger" label="Fastq file"/> </when> <when value="pair"> - <param name="read1" type="data" format="fastqsanger.gz,fastqsanger" label="Read1 fastq file"/> - <param name="read2" type="data" format="fastqsanger.gz,fastqsanger" label="Read2 fastq file"/> + <param name="read1" type="data" format="fastqsanger.gz,fastqsanger" label="Forward reads fastq file"/> + <param name="read2" type="data" format="fastqsanger.gz,fastqsanger" label="Reverse reads fastq file"/> </when> <when value="paired"> <param name="reads_collection" type="data_collection" format="fastqsanger,fastqsanger.gz" collection_type="paired" label="Collection of fastqsanger paired read files"/>