comparison defuse.xml @ 27:d57fcac025e2

Add more info fields to defuse_results_to_vcf.py

26:8f0775c43739

 </requirements>
  <command interpreter="command"> /bin/bash $shscript </command>
 <inputs>
  <param name="left_pairendreads" type="data" format="fastq" label="left part of read pairs" help="The left and right reads pairs must be in the same order, and not have any unpaired reads.  (FASTQ interlacer will pair reads and remove the unpaired.   FASTQ de-interlacer will separate the result into left and right reads.)"/>
  <param name="right_pairendreads" type="data" format="fastq" label="right part of read pairs" help="In the same order as the left reads"/>
  <conditional name="refGenomeSource">
    <param name="genomeSource" type="select" label="Will you select a built-in DeFuse Reference Dataset, or supply a configuration from your history" help="">
      <option value="indexed">Use a built-in DeFuse Reference Dataset</option>
      <option value="history">Use a configuration from your history that specifies the DeFuse Reference Dataset</option>
    </param>

ln -s $defuse_out.extra_files_path  output_dir
#else
mkdir -p output_dir
#end if
## run defuse.pl
perl \${DEFUSE_PATH}/scripts/defuse.pl -c $defuse_config -1 data_dir/reads_1.fastq -2 data_dir/reads_2.fastq -o output_dir  -p 8
## copy primary results to output datasets
if [ -e output_dir/log/defuse.log ]; then cp output_dir/log/defuse.log $defuse_log; fi
## if [ -e output_dir/results.tsv ]; then cp output_dir/results.tsv $results_tsv; fi
if [ -e output_dir/results.filtered.tsv ]; then cp output_dir/results.filtered.tsv $results_filtered_tsv; fi
if [ -e output_dir/results.classify.tsv ]; then cp output_dir/results.classify.tsv $results_classify_tsv; fi

27:d57fcac025e2

 </requirements>
  <command interpreter="command"> /bin/bash $shscript </command>
 <inputs>
  <param name="left_pairendreads" type="data" format="fastq" label="left part of read pairs" help="The left and right reads pairs must be in the same order, and not have any unpaired reads.  (FASTQ interlacer will pair reads and remove the unpaired.   FASTQ de-interlacer will separate the result into left and right reads.)"/>
  <param name="right_pairendreads" type="data" format="fastq" label="right part of read pairs" help="In the same order as the left reads"/>
  <param name="library_name" type="text" value="unknown" label="library name" help="Value to put in the results library_name column">
    <validator type="length" min="1"/>
  </param>
  <conditional name="refGenomeSource">
    <param name="genomeSource" type="select" label="Will you select a built-in DeFuse Reference Dataset, or supply a configuration from your history" help="">
      <option value="indexed">Use a built-in DeFuse Reference Dataset</option>
      <option value="history">Use a configuration from your history that specifies the DeFuse Reference Dataset</option>
    </param>

ln -s $defuse_out.extra_files_path  output_dir
#else
mkdir -p output_dir
#end if
## run defuse.pl
perl \${DEFUSE_PATH}/scripts/defuse.pl -name "$library_name" -c $defuse_config -1 data_dir/reads_1.fastq -2 data_dir/reads_2.fastq -o output_dir  -p 8
## copy primary results to output datasets
if [ -e output_dir/log/defuse.log ]; then cp output_dir/log/defuse.log $defuse_log; fi
## if [ -e output_dir/results.tsv ]; then cp output_dir/results.tsv $results_tsv; fi
if [ -e output_dir/results.filtered.tsv ]; then cp output_dir/results.filtered.tsv $results_filtered_tsv; fi
if [ -e output_dir/results.classify.tsv ]; then cp output_dir/results.classify.tsv $results_classify_tsv; fi