Mercurial > repos > yufei-luo > s_mart

comparison SMART/galaxy/CompareOverlappingSmallQuery.xml @ 6:769e306b7933

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Change the repository level.
author yufei-luo
date Fri, 18 Jan 2013 04:54:14 -0500
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children 2da30502c2f1
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5:ea3082881bf8 6:769e306b7933
1 <tool id="CompareOverlappingSmallQuery" name="Compare Overlapping Small Query">
2 <description>Provide the queries that overlap with a reference, when the query is small.</description>
3 <command interpreter="python">
4 ../Java/Python/CompareOverlappingSmallQuery.py -i $formatType.inputFileName1
5 #if $formatType.FormatInputFileName1 == 'bed':
6 -f bed
7 #elif $formatType.FormatInputFileName1 == 'gff':
8 -f gff
9 #elif $formatType.FormatInputFileName1 == 'gff2':
10 -f gff2
11 #elif $formatType.FormatInputFileName1 == 'gff3':
12 -f gff3
13 #elif $formatType.FormatInputFileName1 == 'sam':
14 -f sam
15 #elif $formatType.FormatInputFileName1 == 'gtf':
16 -f gtf
17 #end if
18 -j $formatType2.inputFileName2
19 #if $formatType2.FormatInputFileName2 == 'bed':
20 -g bed
21 #elif $formatType2.FormatInputFileName2 == 'gff':
22 -g gff
23 #elif $formatType2.FormatInputFileName2 == 'gff2':
24 -g gff2
25 #elif $formatType2.FormatInputFileName2 == 'gff3':
26 -g gff3
27 #elif $formatType2.FormatInputFileName2 == 'sam':
28 -g sam
29 #elif $formatType2.FormatInputFileName2 == 'gtf':
30 -g gtf
31 #end if
32 -o $outputFileGff
33 #if $OptionDistance.Dist == 'Yes':
34 -d $OptionDistance.distance
35 #end if
36 #if $OptionColinearOrAntiSens.OptionCA == 'Colinear':
37 -c
38 #elif $OptionColinearOrAntiSens.OptionCA == 'AntiSens':
39 -a
40 #end if
41 $InvertMatch
42 $NotOverlapping
43 </command>
44
45 <inputs>
46 <conditional name="formatType">
47 <param name="FormatInputFileName1" type="select" label="Input Query File Format">
48 <option value="bed">bed</option>
49 <option value="gff">gff</option>
50 <option value="gff2">gff2</option>
51 <option value="gff3">gff3</option>
52 <option value="sam">sam</option>
53 <option value="gtf">gtf</option>
54 </param>
55 <when value="bed">
56 <param name="inputFileName1" format="bed" type="data" label="Input File 1"/>
57 </when>
58 <when value="gff">
59 <param name="inputFileName1" format="gff" type="data" label="Input File 1"/>
60 </when>
61 <when value="gff2">
62 <param name="inputFileName1" format="gff2" type="data" label="Input File 1"/>
63 </when>
64 <when value="gff3">
65 <param name="inputFileName1" format="gff3" type="data" label="Input File 1"/>
66 </when>
67 <when value="sam">
68 <param name="inputFileName1" format="sam" type="data" label="Input File 1"/>
69 </when>
70 <when value="gtf">
71 <param name="inputFileName1" format="gtf" type="data" label="Input File 1"/>
72 </when>
73 </conditional>
74
75 <conditional name="formatType2">
76 <param name="FormatInputFileName2" type="select" label="Input Reference File Format">
77 <option value="bed">bed</option>
78 <option value="gff">gff</option>
79 <option value="gff2">gff2</option>
80 <option value="gff3">gff3</option>
81 <option value="sam">sam</option>
82 <option value="gtf">gtf</option>
83 </param>
84 <when value="bed">
85 <param name="inputFileName2" format="bed" type="data" label="Input File 2"/>
86 </when>
87 <when value="gff">
88 <param name="inputFileName2" format="gff" type="data" label="Input File 2"/>
89 </when>
90 <when value="gff2">
91 <param name="inputFileName2" format="gff2" type="data" label="Input File 2"/>
92 </when>
93 <when value="gff3">
94 <param name="inputFileName2" format="gff3" type="data" label="Input File 2"/>
95 </when>
96 <when value="sam">
97 <param name="inputFileName2" format="sam" type="data" label="Input File 2"/>
98 </when>
99 <when value="gtf">
100 <param name="inputFileName2" format="gtf" type="data" label="Input File 2"/>
101 </when>
102 </conditional>
103 <conditional name="OptionDistance">
104 <param name="Dist" type="select" label="Maximum Distance between two reads">
105 <option value="Yes">Yes</option>
106 <option value="No" selected="true">No</option>
107 </param>
108 <when value="Yes">
109 <param name="distance" type="integer" value="0"/>
110 </when>
111 <when value="No">
112 </when>
113 </conditional>
114 <conditional name="OptionColinearOrAntiSens">
115 <param name="OptionCA" type="select" label="Colinear or anti-sens">
116 <option value="Colinear">Colinear</option>
117 <option value="AntiSens">AntiSens</option>
118 <option value="NONE" selected="true">NONE</option>
119 </param>
120 <when value="Colinear">
121 </when>
122 <when value="AntiSens">
123 </when>
124 <when value="NONE">
125 </when>
126 </conditional>
127 <param name="InvertMatch" type="boolean" truevalue="-x" falsevalue="" checked="false" label="Invert match"/>
128 <param name="NotOverlapping" type="boolean" truevalue="-O" falsevalue="" checked="false" label="When there is no overlapping, the number of Overlapping will be set to 0 by defalt."/>
129 </inputs>
130
131 <outputs>
132 <data name="outputFileGff" format="gff3"/>
133 </outputs>
134 </tool>