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comparison find_in_reference.xml @ 2:c4fd2ea4f988

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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)
author Jim Johnson <jj@umn.edu>
date Thu, 13 Nov 2014 14:09:50 -0600
parents e83e0ce8fb68
children 2429b413d90a
comparison
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1:e83e0ce8fb68 2:c4fd2ea4f988
1 <?xml version="1.0"?> 1 <?xml version="1.0"?>
2 <tool id="find_in_reference" name="find in reference" version="0.0.2"> 2 <tool id="find_in_reference" name="find in reference" version="0.0.3">
3 <description>filter peptides that are present in proteins</description> 3 <description>filter peptides that are present in proteins</description>
4 <command interpreter="python">find_in_reference.py --input "$input" 4 <command interpreter="python">find_in_reference.py --input "$input"
5 --reference "$reference" 5 --reference "$reference"
6 #if $column.set == 'yes': 6 #if $column.set == 'yes':
7 --input_column $column.input_column 7 --input_column $column.input_column
8 --reference_column $column.reference_column 8 --reference_column $column.reference_column
9 #end if 9 #end if
10 $case_insensitive $reverse_find 10 $case_insensitive $reverse_find $test_reverse $test_dna_reverse_complement
11 #if 'novel' in $outputs.__str__ or not 'found' in $outputs.__str__: 11 #if 'novel' in $outputs.__str__ or not 'found' in $outputs.__str__:
12 --output "$novel" 12 --output "$novel"
13 #end if 13 #end if
14 #if 'found' in $outputs.__str__: 14 #if 'found' in $outputs.__str__:
15 --filtered "$found" 15 --filtered "$found"
42 help=""/> 42 help=""/>
43 </when> 43 </when>
44 </conditional> 44 </conditional>
45 <param name="case_insensitive" type="boolean" truevalue="--case_insensitive" falsevalue="" checked="false" label="Ignore case when comparing"/> 45 <param name="case_insensitive" type="boolean" truevalue="--case_insensitive" falsevalue="" checked="false" label="Ignore case when comparing"/>
46 <param name="reverse_find" type="boolean" truevalue="--reverse_find" falsevalue="" checked="false" label="reverse search: find the reference in the input" /> 46 <param name="reverse_find" type="boolean" truevalue="--reverse_find" falsevalue="" checked="false" label="reverse search: find the reference in the input" />
47 <param name="test_reverse" type="boolean" truevalue="--test_reverse" falsevalue="" checked="false" label="Also search for reversed input string in the reference" />
48 <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" />
47 <param name="outputs" type="select" multiple="true" display="checkboxes" label="Choose outputs"> 49 <param name="outputs" type="select" multiple="true" display="checkboxes" label="Choose outputs">
48 <option value="novel" selected="true">lines with no match in reference</option> 50 <option value="novel" selected="true">lines with no match in reference</option>
49 <option value="found">lines with match in reference</option> 51 <option value="found">lines with match in reference</option>
50 </param> 52 </param>
51 <conditional name="annotate"> 53 <conditional name="annotate">