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comparison SMART/galaxy/CompareOverlappingAdapt.xml @ 46:169d364ddd91

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author m-zytnicki
date Mon, 30 Sep 2013 03:19:26 -0400
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children 90f4b29d884f
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45:e454402ba9d9 46:169d364ddd91
1 <tool id="CompareOverlappingAdapt" name="compare overlapping">
2 <description>Provide the queries that overlap with a reference.</description>
3 <requirements>
4 <requirement type="set_environment">PYTHONPATH</requirement>
5 </requirements>
6 <command interpreter="python">
7 ../Java/Python/CompareOverlappingAdapt.py -i $formatType.inputFileName1
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':
37 -d $OptionDistance.distance
38 #end if
39 #if $OptionCollinearOrAntiSens.OptionCA == 'Collinear':
40 -c
41 #elif $OptionCollinearOrAntiSens.OptionCA == 'AntiSens':
42 -a
43 #end if
44 $InvertMatch
45 $NotOverlapping
46 </command>
47
48 <inputs>
49 <conditional name="formatType">
50 <param name="FormatInputFileName1" type="select" label="Input Query File Format">
51 <option value="bed">bed</option>
52 <option value="gff">gff</option>
53 <option value="gff2">gff2</option>
54 <option value="gff3">gff3</option>
55 <option value="sam">sam</option>
56 <option value="gtf">gtf</option>
57 </param>
58 <when value="bed">
59 <param name="inputFileName1" format="bed" type="data" label="Input File 1"/>
60 </when>
61 <when value="gff">
62 <param name="inputFileName1" format="gff" type="data" label="Input File 1"/>
63 </when>
64 <when value="gff2">
65 <param name="inputFileName1" format="gff2" type="data" label="Input File 1"/>
66 </when>
67 <when value="gff3">
68 <param name="inputFileName1" format="gff3" type="data" label="Input File 1"/>
69 </when>
70 <when value="sam">
71 <param name="inputFileName1" format="sam" type="data" label="Input File 1"/>
72 </when>
73 <when value="gtf">
74 <param name="inputFileName1" format="gtf" type="data" label="Input File 1"/>
75 </when>
76 </conditional>
77
78 <conditional name="formatType2">
79 <param name="FormatInputFileName2" type="select" label="Input Reference File Format">
80 <option value="bed">bed</option>
81 <option value="gff">gff</option>
82 <option value="gff2">gff2</option>
83 <option value="gff3">gff3</option>
84 <option value="sam">sam</option>
85 <option value="gtf">gtf</option>
86 </param>
87 <when value="bed">
88 <param name="inputFileName2" format="bed" type="data" label="Input File 2"/>
89 </when>
90 <when value="gff">
91 <param name="inputFileName2" format="gff" type="data" label="Input File 2"/>
92 </when>
93 <when value="gff2">
94 <param name="inputFileName2" format="gff2" type="data" label="Input File 2"/>
95 </when>
96 <when value="gff3">
97 <param name="inputFileName2" format="gff3" type="data" label="Input File 2"/>
98 </when>
99 <when value="sam">
100 <param name="inputFileName2" format="sam" type="data" label="Input File 2"/>
101 </when>
102 <when value="gtf">
103 <param name="inputFileName2" format="gtf" type="data" label="Input File 2"/>
104 </when>
105 </conditional>
106 <conditional name="OptionDistance">
107 <param name="Dist" type="select" label="Maximum Distance between two reads">
108 <option value="Yes">Yes</option>
109 <option value="No" selected="true">No</option>
110 </param>
111 <when value="Yes">
112 <param name="distance" type="integer" value="0"/>
113 </when>
114 <when value="No">
115 </when>
116 </conditional>
117 <conditional name="OptionCollinearOrAntiSens">
118 <param name="OptionCA" type="select" label="Collinear or anti-sens">
119 <option value="Collinear">Collinear</option>
120 <option value="AntiSens">AntiSens</option>
121 <option value="NONE" selected="true">NONE</option>
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"/>
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."/>
132 </inputs>
133
134 <outputs>
135 <data name="outputFileGff" format="gff3"/>
136 </outputs>
137
138 <help>
139 This script may be the most important one. It basically compares two sets of transcripts and keeps those from the first set which overlap with the second one. The first set is considered as the query set (basically, your data) and the second one is the reference set (RefSeq data, for example).
140
141 It is vital to understand that it will output the elements of the first file which overlap with the elements of the second one.
142
143 Various modifiers are also available:
144
145 -Invert selection (report those which do not overlap).
146
147 -Restrict to collinear / anti-sense overlapping data.
148
149 -Keep the query data even if they do not strictly overlap with the reference data, but are located not further away than *n* nucleotide from some reference data.
150
151 Some option reverses the selection. Put in other words, it performs the comparison as usual, and outputs all those query data which do not overlap.
152 </help>
153 </tool>