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comparison find_in_reference.xml @ 2:30975b3ff0dc

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Allow user to add annotation columns from reference to found input entries
author Jim Johnson <jj@umn.edu>
date Thu, 23 Jan 2014 10:52:30 -0600
parents 856033fb26e8
children fe044d480b3a
comparison
equal deleted inserted replaced
1:856033fb26e8 2:30975b3ff0dc
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"
16 #if $annotate.from_ref == 'yes' and str($annotate.annotation_columns) != 'None':
17 --annotation_columns $annotate.annotation_columns
18 #if $annotate.annotation_separator != '':
19 --annotation_separator '$annotate.annotation_separator'
20 #end if
21 #if $annotate.annotation_col_sep != '':
22 --annotation_col_sep '$annotate.annotation_col_sep'
23 #end if
24 #end if
16 #end if 25 #end if
17 </command> 26 </command>
18 <inputs> 27 <inputs>
19 <param name="input" type="data" format="tabular" label="Input file to be filtered" 28 <param name="input" type="data" format="tabular" label="Input file to be filtered"
20 help="e.g. a peptide fasta converted to tabular"/> 29 help="e.g. a peptide fasta converted to tabular"/>
36 <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"/>
37 <param name="outputs" type="select" multiple="true" display="checkboxes" label="Choose outputs"> 46 <param name="outputs" type="select" multiple="true" display="checkboxes" label="Choose outputs">
38 <option value="novel" selected="true">lines with no match in reference</option> 47 <option value="novel" selected="true">lines with no match in reference</option>
39 <option value="found">lines with match in reference</option> 48 <option value="found">lines with match in reference</option>
40 </param> 49 </param>
50 <conditional name="annotate">
51 <param name="from_ref" type="select" label="Annotate found input entries with columns from reference">
52 <option value="no" selected="true">No</option>
53 <option value="yes">Yes</option>
54 </param>
55 <when value="no"/>
56 <when value="yes">
57 <param name="annotation_columns" type="data_column" data_ref="reference" multiple="true" label="columns from reference to append to found input lines"
58 help=""/>
59 <param name="annotation_separator" type="text" value="" optional="true" label="separator to place between annotations from different reference lines"
60 help="defaults to ;"/>
61 <param name="annotation_col_sep" type="text" value="" optional="true" label="separator to place between annotation columns from the same reference line"
62 help="defaults to ,"/>
63 </when>
64 </conditional>
41 </inputs> 65 </inputs>
42 <stdio> 66 <stdio>
43 <exit_code range="1:" level="fatal" description="Error" /> 67 <exit_code range="1:" level="fatal" description="Error" />
44 </stdio> 68 </stdio>
45 <outputs> 69 <outputs>