comparison find_in_reference.xml @ 2:30975b3ff0dc

Allow user to add annotation columns from reference to found input entries

1:856033fb26e8

  #if 'novel' in $outputs.__str__ or not 'found' in $outputs.__str__:
    --output "$novel"
  #end if
  #if 'found' in $outputs.__str__:
    --filtered "$found"
  #end if
  </command>
  <inputs>
    <param name="input" type="data" format="tabular" label="Input file to be filtered" 
           help="e.g. a peptide fasta converted to tabular"/> 

    <param name="case_insensitive" type="boolean" truevalue="--case_insensitive" falsevalue="" checked="false" label="Ignore case when comparing"/>
    <param name="outputs" type="select" multiple="true" display="checkboxes" label="Choose outputs">
      <option value="novel" selected="true">lines with no match in reference</option>
      <option value="found">lines with match in reference</option>
    </param>
  </inputs>
  <stdio>
    <exit_code range="1:" level="fatal" description="Error" />
  </stdio>
  <outputs>

2:30975b3ff0dc

  #if 'novel' in $outputs.__str__ or not 'found' in $outputs.__str__:
    --output "$novel"
  #end if
  #if 'found' in $outputs.__str__:
    --filtered "$found"
    #if $annotate.from_ref == 'yes' and str($annotate.annotation_columns) != 'None':
      --annotation_columns $annotate.annotation_columns
      #if $annotate.annotation_separator != '':
        --annotation_separator '$annotate.annotation_separator'
      #end if
      #if $annotate.annotation_col_sep != '':
        --annotation_col_sep '$annotate.annotation_col_sep'
      #end if
    #end if
  #end if
  </command>
  <inputs>
    <param name="input" type="data" format="tabular" label="Input file to be filtered" 
           help="e.g. a peptide fasta converted to tabular"/> 

    <param name="case_insensitive" type="boolean" truevalue="--case_insensitive" falsevalue="" checked="false" label="Ignore case when comparing"/>
    <param name="outputs" type="select" multiple="true" display="checkboxes" label="Choose outputs">
      <option value="novel" selected="true">lines with no match in reference</option>
      <option value="found">lines with match in reference</option>
    </param>
    <conditional name="annotate">
      <param name="from_ref" type="select" label="Annotate found input entries with columns from reference">
        <option value="no" selected="true">No</option>
        <option value="yes">Yes</option>
      </param>
      <when value="no"/>
      <when value="yes">
        <param name="annotation_columns" type="data_column" data_ref="reference" multiple="true" label="columns from reference to append to found input lines" 
           help=""/>
        <param name="annotation_separator" type="text" value="" optional="true" label="separator to place between annotations from different reference lines"
           help="defaults to ;"/>
        <param name="annotation_col_sep" type="text" value="" optional="true" label="separator to place between annotation columns from the same reference line"
           help="defaults to ,"/>
      </when>
    </conditional>
  </inputs>
  <stdio>
    <exit_code range="1:" level="fatal" description="Error" />
  </stdio>
  <outputs>