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comparison find_in_reference.xml @ 1:e83e0ce8fb68

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Add option to reverse the search, find reference field in input field
author Jim Johnson <jj@umn.edu>
date Wed, 13 Aug 2014 15:01:33 -0500
parents e7e56b51d156
children c4fd2ea4f988
comparison
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0:e7e56b51d156 1:e83e0ce8fb68
1 <?xml version="1.0"?> 1 <?xml version="1.0"?>
2 <tool id="find_in_reference" name="find in reference" version="0.0.1"> 2 <tool id="find_in_reference" name="find in reference" version="0.0.2">
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 10 $case_insensitive $reverse_find
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"
41 <param name="reference_column" type="data_column" data_ref="reference" label="column in reference (defaults to last column)" 41 <param name="reference_column" type="data_column" data_ref="reference" label="column in reference (defaults to last column)"
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="outputs" type="select" multiple="true" display="checkboxes" label="Choose outputs"> 47 <param name="outputs" type="select" multiple="true" display="checkboxes" label="Choose outputs">
47 <option value="novel" selected="true">lines with no match in reference</option> 48 <option value="novel" selected="true">lines with no match in reference</option>
48 <option value="found">lines with match in reference</option> 49 <option value="found">lines with match in reference</option>
49 </param> 50 </param>
50 <conditional name="annotate"> 51 <conditional name="annotate">
98 <test> 99 <test>
99 <param name="input" value="human_peptides.tabular" ftype="tabular" dbkey="hg19"/> 100 <param name="input" value="human_peptides.tabular" ftype="tabular" dbkey="hg19"/>
100 <param name="reference" value="human_proteins.tabular" ftype="tabular" dbkey="hg19"/> 101 <param name="reference" value="human_proteins.tabular" ftype="tabular" dbkey="hg19"/>
101 <output name="novel" file="novel_peptides.tabular"/> 102 <output name="novel" file="novel_peptides.tabular"/>
102 </test> 103 </test>
104 <test>
105 <param name="input" value="human_proteins.tabular" ftype="tabular" dbkey="hg19"/>
106 <param name="reference" value="human_peptides.tabular" ftype="tabular" dbkey="hg19"/>
107 <param name="reverse_find" value="True"/>
108 <param name="outputs" value="found"/>
109 <output name="found" file="found_proteins.tabular"/>
110 </test>
103 </tests> 111 </tests>
104 <help> 112 <help>
105 **Find in Reference** 113 **Find in Reference**
106 114
107 Filters lines of a tabular input file by checking if the selected input column value 115 Filters lines of a tabular input file by checking if the selected input column value