comparison nanostat.xml @ 1:845458a694e0 draft default tip

planemo upload

0:e86d1c122ee7

  <command detect_errors="exit_code"><![CDATA[
    #import re
    ## 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)
        #set $named_input_files = $named_input_files + ' ' + $_input_file
        ln -s '${i_file}' ${_input_file} &&
      #end for
    #end if
    #### alternative would be something like: x=`file o.xyz.gz; if [[ $x == *gzip* ]]; then echo "found gzip"; fi

        <option value="fasta">fasta (compressed or not)</option>
        <option value="bam">sorted bam</option>
        <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"/>
      </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"/>
      </when>
      <when value="bam">
        <param type="data" name="file" format="bam" label="One or more sorted bam file(s)." multiple="true" 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 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>
          <option value="2D">2D</option>
          <option value="1D2">1D2</option>

1:845458a694e0

  <command detect_errors="exit_code"><![CDATA[
    #import re
    ## 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 $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
    #end if
    #### alternative would be something like: x=`file o.xyz.gz; if [[ $x == *gzip* ]]; then echo "found gzip"; fi

        <option value="fasta">fasta (compressed or not)</option>
        <option value="bam">sorted bam</option>
        <option value="summary">Use albacore or guppy summary file for quality scores</option>
      </param>
      <when value="fastq">
        <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" 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" multiple="true" name="file" format="bam" label="One or more sorted bam file(s)." optional="true"/>
      </when>
      <when value="summary">
        <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>
          <option value="2D">2D</option>
          <option value="1D2">1D2</option>