comparison find_in_reference.xml @ 2:c4fd2ea4f988

Add the option to test the reversed sequence and the DNA reverse complement of the sequence (ignored if the sequence cannot be interpreted as DNA)

1:e83e0ce8fb68

<?xml version="1.0"?>
<tool id="find_in_reference" name="find in reference" version="0.0.2">
  <description>filter peptides that are present in proteins</description>
  <command interpreter="python">find_in_reference.py  --input "$input" 
  --reference "$reference" 
  #if $column.set == 'yes':
    --input_column $column.input_column
    --reference_column $column.reference_column
  #end if
  $case_insensitive $reverse_find
  #if 'novel' in $outputs.__str__ or not 'found' in $outputs.__str__:
    --output "$novel"
  #end if
  #if 'found' in $outputs.__str__:
    --filtered "$found"

           help=""/>
      </when>
    </conditional>
    <param name="case_insensitive" type="boolean" truevalue="--case_insensitive" falsevalue="" checked="false" label="Ignore case when comparing"/>
    <param name="reverse_find" type="boolean" truevalue="--reverse_find" falsevalue="" checked="false" label="reverse search: find the reference in the input" />
    <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">

2:c4fd2ea4f988

<?xml version="1.0"?>
<tool id="find_in_reference" name="find in reference" version="0.0.3">
  <description>filter peptides that are present in proteins</description>
  <command interpreter="python">find_in_reference.py  --input "$input" 
  --reference "$reference" 
  #if $column.set == 'yes':
    --input_column $column.input_column
    --reference_column $column.reference_column
  #end if
  $case_insensitive $reverse_find $test_reverse $test_dna_reverse_complement
  #if 'novel' in $outputs.__str__ or not 'found' in $outputs.__str__:
    --output "$novel"
  #end if
  #if 'found' in $outputs.__str__:
    --filtered "$found"

           help=""/>
      </when>
    </conditional>
    <param name="case_insensitive" type="boolean" truevalue="--case_insensitive" falsevalue="" checked="false" label="Ignore case when comparing"/>
    <param name="reverse_find" type="boolean" truevalue="--reverse_find" falsevalue="" checked="false" label="reverse search: find the reference in the input" />
    <param name="test_reverse" type="boolean" truevalue="--test_reverse" falsevalue="" checked="false" label="Also search for reversed input string in the reference" />
    <param name="test_dna_reverse_complement" type="boolean" truevalue="--test_dna_reverse_complement" falsevalue="" checked="false" label="Also search for the DNA reverse complementof of the input in the reference" />
    <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">