comparison optitype.xml @ 2:61fc10014a9e draft

Uploaded

1:bd817c1fdd63

&& cp \$OPTITYPE_DIR/config.ini .
&& ln -s \$OPTITYPE_DIR/data data
#set $input_fq = ' '.join($fastqs)
&& python  \$OPTITYPE_DIR/OptiTypePipeline.py 
$read_type --input  ${' '.join($fastqs)}
#if $beta != None: 
 --beta $beta
#end if
#if $enumerate != None: 
 --enumerate $enumerations
#end if
--outdir $outdir
&& cp $outdir/*/*_coverage_plot.pdf $coverage_plot
&& cp $outdir/*/*_result.tsv $result

    <param name="read_type" type="select" label="Nucleotide Type" help="">
      <option value="--rna">RNA</option>
      <option value="--dna">DNA</option>
    </param>
    <param name="beta" type="float" value="" min="0.0" max="0.1" optional="true" label="homozygosity beta" help="The beta value for for homozygosity detection"/>
    <param name="enumerations" type="integer" value="" min="1" max="5" optional="true" label="Enunerations" help="The number of enumerations"/>
    <param name="outdir" type="hidden" value="output_dir"/>
  </inputs>
  <outputs>
    <data format="pdf" name="coverage_plot" label="${tool.name} on ${on_string} coverage_plot.pdf"/>
    <data format="tabular" name="result" label="${tool.name} on ${on_string} result.tsv"/>

2:61fc10014a9e

&& cp \$OPTITYPE_DIR/config.ini .
&& ln -s \$OPTITYPE_DIR/data data
#set $input_fq = ' '.join($fastqs)
&& python  \$OPTITYPE_DIR/OptiTypePipeline.py 
$read_type --input  ${' '.join($fastqs)}
#if str($beta) != '': 
 --beta $beta
#end if
#if str($enumerations) != '': 
 --enumerate $enumerations
#end if
--outdir $outdir
&& cp $outdir/*/*_coverage_plot.pdf $coverage_plot
&& cp $outdir/*/*_result.tsv $result

    <param name="read_type" type="select" label="Nucleotide Type" help="">
      <option value="--rna">RNA</option>
      <option value="--dna">DNA</option>
    </param>
    <param name="beta" type="float" value="" min="0.0" max="0.1" optional="true" label="homozygosity beta" help="The beta value for for homozygosity detection"/>
    <param name="enumerations" type="integer" value="" min="1" max="5" optional="true" label="Enumerations" help="The number of enumerations"/>
    <param name="outdir" type="hidden" value="output_dir"/>
  </inputs>
  <outputs>
    <data format="pdf" name="coverage_plot" label="${tool.name} on ${on_string} coverage_plot.pdf"/>
    <data format="tabular" name="result" label="${tool.name} on ${on_string} result.tsv"/>