Mercurial > repos > iuc > bbtools_bbduk
changeset 1:ff3b87a0d205 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 425671870866660485ef6a35c94d3736f5c1df97"
| author | iuc |
|---|---|
| date | Tue, 01 Feb 2022 22:58:36 +0000 |
| parents | 132af91f11b9 |
| children | 0247076a9567 |
| files | bbduk.xml macros.xml |
| diffstat | 2 files changed, 11 insertions(+), 13 deletions(-) [+] |
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--- a/bbduk.xml Thu Nov 11 16:36:50 2021 +0000 +++ b/bbduk.xml Tue Feb 01 22:58:36 2022 +0000 @@ -10,18 +10,16 @@ #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)) ## bbduk 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}' '${read2_file}' && #end if #else: @@ -231,17 +229,17 @@ </conditional> </inputs> <outputs> - <data name="outputu" format="fastqsanger" label="${tool.name} on ${on_string} (Unmatched)"> + <data name="outputu" format="fastqsanger" label="${tool.name} on ${on_string} (Forward Unmatched)"> <filter>str(outputs_select).find('outu') >= 0</filter> <filter>'outu' in outputs_select</filter> </data> - <data name="outputu2" format="fastqsanger" label="${tool.name} on ${on_string} (Unmatched)"> + <data name="outputu2" format="fastqsanger" label="${tool.name} on ${on_string} (Reverse Unmatched)"> <filter>'outu' in outputs_select and input_type_cond['input_type'] != 'single'</filter> </data> - <data name="outputm" format="fastqsanger" label="${tool.name} on ${on_string} (Matched)"> + <data name="outputm" format="fastqsanger" label="${tool.name} on ${on_string} (Forward Matched)"> <filter>'outm' in outputs_select</filter> </data> - <data name="outputm2" format="fastqsanger" label="${tool.name} on ${on_string} (Matched)"> + <data name="outputm2" format="fastqsanger" label="${tool.name} on ${on_string} (Reverse Matched)"> <filter>'outm' in outputs_select and input_type_cond['input_type'] != 'single'</filter> </data> <data name="outputs" format="fastqsanger" label="${tool.name} on ${on_string} (Single)">
--- a/macros.xml Thu Nov 11 16:36:50 2021 +0000 +++ b/macros.xml Tue Feb 01 22:58:36 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"/>