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comparison SMART/galaxy/CompareOverlappingAdapt.xml @ 60:90f4b29d884f

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Uploaded
author m-zytnicki
date Fri, 21 Feb 2014 08:32:36 -0500
parents 169d364ddd91
children 783e6ed4eb66
comparison
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59:2a4884ba3e5c 60:90f4b29d884f
2 <description>Provide the queries that overlap with a reference.</description> 2 <description>Provide the queries that overlap with a reference.</description>
3 <requirements> 3 <requirements>
4 <requirement type="set_environment">PYTHONPATH</requirement> 4 <requirement type="set_environment">PYTHONPATH</requirement>
5 </requirements> 5 </requirements>
6 <command interpreter="python"> 6 <command interpreter="python">
7 ../Java/Python/CompareOverlappingAdapt.py -i $formatType.inputFileName1 7 ../Java/Python/CompareOverlappingAdapt.py -i $formatType.inputFileName1 -f $formatType.FormatInputFileName1 -j $formatType2.inputFileName2 -g $formatType2.FormatInputFileName2 -o $outputFileGff $InvertMatch $NotOverlapping -m $NbOverlap
8 #if $formatType.FormatInputFileName1 == 'bed':
9 -f bed
10 #elif $formatType.FormatInputFileName1 == 'gff':
11 -f gff
12 #elif $formatType.FormatInputFileName1 == 'gff2':
13 -f gff2
14 #elif $formatType.FormatInputFileName1 == 'gff3':
15 -f gff3
16 #elif $formatType.FormatInputFileName1 == 'sam':
17 -f sam
18 #elif $formatType.FormatInputFileName1 == 'gtf':
19 -f gtf
20 #end if
21 -j $formatType2.inputFileName2
22 #if $formatType2.FormatInputFileName2 == 'bed':
23 -g bed
24 #elif $formatType2.FormatInputFileName2 == 'gff':
25 -g gff
26 #elif $formatType2.FormatInputFileName2 == 'gff2':
27 -g gff2
28 #elif $formatType2.FormatInputFileName2 == 'gff3':
29 -g gff3
30 #elif $formatType2.FormatInputFileName2 == 'sam':
31 -g sam
32 #elif $formatType2.FormatInputFileName2 == 'gtf':
33 -g gtf
34 #end if
35 -o $outputFileGff
36 #if $OptionDistance.Dist == 'Yes': 8 #if $OptionDistance.Dist == 'Yes':
37 -d $OptionDistance.distance 9 -d $OptionDistance.distance
38 #end if 10 #end if
39 #if $OptionCollinearOrAntiSens.OptionCA == 'Collinear': 11 #if $OptionCA == 'Collinear':
40 -c 12 -c
41 #elif $OptionCollinearOrAntiSens.OptionCA == 'AntiSens': 13 #elif $OptionCA == 'AntiSense':
42 -a 14 -a
43 #end if 15 #end if
44 $InvertMatch
45 $NotOverlapping
46 </command> 16 </command>
47 17
48 <inputs> 18 <inputs>
49 <conditional name="formatType"> 19 <conditional name="formatType">
50 <param name="FormatInputFileName1" type="select" label="Input Query File Format"> 20 <param name="FormatInputFileName1" type="select" label="Input Query File Format">
112 <param name="distance" type="integer" value="0"/> 82 <param name="distance" type="integer" value="0"/>
113 </when> 83 </when>
114 <when value="No"> 84 <when value="No">
115 </when> 85 </when>
116 </conditional> 86 </conditional>
117 <conditional name="OptionCollinearOrAntiSens"> 87 <param name="OptionCA" type="select" label="Collinear or anti-sense features only">
118 <param name="OptionCA" type="select" label="Collinear or anti-sens"> 88 <option value="Collinear">Collinear</option>
119 <option value="Collinear">Collinear</option> 89 <option value="AntiSense">AntiSense</option>
120 <option value="AntiSens">AntiSens</option> 90 <option value="All" selected="true">All</option>
121 <option value="NONE" selected="true">NONE</option> 91 </param>
122 </param>
123 <when value="Collinear">
124 </when>
125 <when value="AntiSens">
126 </when>
127 <when value="NONE">
128 </when>
129 </conditional>
130 <param name="InvertMatch" type="boolean" truevalue="-x" falsevalue="" checked="false" label="Invert match: the output file will contain all query elements which do NOT overlap"/> 92 <param name="InvertMatch" type="boolean" truevalue="-x" falsevalue="" checked="false" label="Invert match: the output file will contain all query elements which do NOT overlap"/>
131 <param name="NotOverlapping" type="boolean" truevalue="-O" falsevalue="" checked="false" label="Also report the query data which do not overlap, with the nbOverlaps tag set to 0."/> 93 <param name="NotOverlapping" type="boolean" truevalue="-O" falsevalue="" checked="false" label="Also report the query data which do not overlap, with the nbOverlaps tag set to 0."/>
94 <param name="NbOverlap" type="integer" value="1" label="Min. # of overlapping nt. to declare an overlap."/>
132 </inputs> 95 </inputs>
133 96
134 <outputs> 97 <outputs>
135 <data name="outputFileGff" format="gff3"/> 98 <data name="outputFileGff" format="gff3"/>
136 </outputs> 99 </outputs>