| Previous changeset 0:e86d1c122ee7 (2019-05-14) |
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Commit message:
planemo upload |
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modified:
nanostat.xml |
| b |
| diff -r e86d1c122ee7 -r 845458a694e0 nanostat.xml --- a/nanostat.xml Tue May 14 05:36:34 2019 -0400 +++ b/nanostat.xml Fri May 17 09:23:59 2019 -0400 |
| b |
| @@ -10,9 +10,21 @@ ## Galaxy creates xyz.dat but nanostat relies on suffix to detect compressed fasta/fastq; otoh Galaxy provides 'element_identifier' #if str($input_type.type) == "fastq" or str($input_type.type) == "fasta" #set $named_input_files = '' - #for $i_file in $input_type.file - ## Add single quotes around each input file identifier - #set $_input_file = "'{}'".format($i_file.element_identifier) + #for $counter, $i_file in enumerate($input_type.file): + #if $i_file.is_of_type('fastqsanger', 'fastq'): + #set $ext = 'fastq' + #elif $i_file.is_of_type('fastqsanger.gz', 'fastq.gz'): + #set $ext = 'fastq.gz' + #elif $i_file.is_of_type('fastqsanger.bz2', 'fastq.bz2'): + #set $ext = 'fastq.bz2' + #elif $i_file.is_of_type('fasta'): + #set $ext = 'fasta' + #elif $i_file.is_of_type('fasta.gz'): + #set $ext = 'fasta.gz' + #elif $i_file.is_of_type('fasta.bz2'): + #set $ext = 'fasta.bz2' + #end if + #set $_input_file = "./input_" + str($counter) + "." + $ext #set $named_input_files = $named_input_files + ' ' + $_input_file ln -s '${i_file}' ${_input_file} && #end for @@ -45,16 +57,16 @@ <option value="summary">Use albacore or guppy summary file for quality scores</option> </param> <when value="fastq"> - <param type="data" name="file" format="fastqsanger,fastqsanger.gz,fastqsanger.bz2, fastqsanger.bgz" multiple="true" label="One or more (compressed) fastq file(s)." optional="true"/> + <param type="data" multiple="true" name="file" format="fastqsanger,fastqsanger.gz,fastqsanger.bz2, fastqsanger.bgz" label="One or more (compressed) fastq file(s)." optional="true"/> </when> <when value="fasta"> - <param type="data" name="file" format="fasta, fasta.gz, fasta.bz2, fasta.bgz" multiple="true" label="One or more (compressed) fasta file(s)." optional="true"/> + <param type="data" multiple="true" name="file" format="fasta, fasta.gz, fasta.bz2, fasta.bgz" label="One or more (compressed) fasta file(s)." optional="true"/> </when> <when value="bam"> - <param type="data" name="file" format="bam" label="One or more sorted bam file(s)." multiple="true" optional="true"/> + <param type="data" multiple="true" name="file" format="bam" label="One or more sorted bam file(s)." optional="true"/> </when> <when value="summary"> - <param type="data" name="file" format="tabular" label="Summary file generated by albacore or guppy." multiple="true" optional="true"/> + <param type="data" multiple="true" name="file" format="tabular" label="Summary file generated by albacore or guppy." optional="true"/> <param name="barcoded" argument="--barcoded" type="boolean" truevalue="--barcode" falsevalue="" checked="false" label="Do you want to split the summary file by barcode?" help="Default:No"/> <param name="readtype" argument="--readtype" type="select" label="Which read type to extract information about from summary?"> <option value="1D" selected="true">1D</option> |