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comparison SMART/galaxy/mergeTranscriptLists.xml @ 38:2c0c0a89fad7

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author m-zytnicki
date Thu, 02 May 2013 09:56:47 -0400
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37:d22fadc825e3 38:2c0c0a89fad7
1 <tool id="mergeTranscriptLists" name="merge transcript lists">
2 <description>Merge the elements of two lists of genomic coordinates.</description>
3 <requirements>
4 <requirement type="set_environment">PYTHONPATH</requirement>
5 </requirements>
6 <command interpreter="python">
7 ../Java/Python/mergeTranscriptLists.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
22 -j $formatType2.inputFileName2
23 #if $formatType2.FormatInputFileName2 == 'bed':
24 -g bed
25 #elif $formatType2.FormatInputFileName2 == 'gff':
26 -g gff
27 #elif $formatType2.FormatInputFileName2 == 'gff2':
28 -g gff2
29 #elif $formatType2.FormatInputFileName2 == 'gff3':
30 -g gff3
31 #elif $formatType2.FormatInputFileName2 == 'sam':
32 -g sam
33 #elif $formatType2.FormatInputFileName2 == 'gtf':
34 -g gtf
35 #end if
36
37 $all
38 $normalize
39
40 #if $OptionDistance.dis == 'Yes':
41 -d $OptionDistance.disVal
42 #end if
43
44 #if $OptionColinearOrAntiSens.OptionCA == 'Colinear':
45 -c
46 #elif $OptionColinearOrAntiSens.OptionCA == 'AntiSens':
47 -a
48 #end if
49
50 -o $outputFileGff
51 </command>
52
53 <inputs>
54 <conditional name="formatType">
55 <param name="FormatInputFileName1" type="select" label="Input File Format 1">
56 <option value="bed">bed</option>
57 <option value="gff">gff</option>
58 <option value="gff2">gff2</option>
59 <option value="gff3">gff3</option>
60 <option value="sam">sam</option>
61 <option value="gtf">gtf</option>
62 </param>
63 <when value="bed">
64 <param name="inputFileName1" format="bed" type="data" label="Input File 1"/>
65 </when>
66 <when value="gff">
67 <param name="inputFileName1" format="gff" type="data" label="Input File 1"/>
68 </when>
69 <when value="gff2">
70 <param name="inputFileName1" format="gff2" type="data" label="Input File 1"/>
71 </when>
72 <when value="gff3">
73 <param name="inputFileName1" format="gff3" type="data" label="Input File 1"/>
74 </when>
75 <when value="sam">
76 <param name="inputFileName1" format="sam" type="data" label="Input File 1"/>
77 </when>
78 <when value="gtf">
79 <param name="inputFileName1" format="gtf" type="data" label="Input File 1"/>
80 </when>
81 </conditional>
82
83 <conditional name="formatType2">
84 <param name="FormatInputFileName2" type="select" label="Input File Format 2">
85 <option value="bed">bed</option>
86 <option value="gff">gff</option>
87 <option value="gff2">gff2</option>
88 <option value="gff3">gff3</option>
89 <option value="sam">sam</option>
90 <option value="gtf">gtf</option>
91 </param>
92 <when value="bed">
93 <param name="inputFileName2" format="bed" type="data" label="Input File 2"/>
94 </when>
95 <when value="gff">
96 <param name="inputFileName2" format="gff" type="data" label="Input File 2"/>
97 </when>
98 <when value="gff2">
99 <param name="inputFileName2" format="gff2" type="data" label="Input File 2"/>
100 </when>
101 <when value="gff3">
102 <param name="inputFileName2" format="gff3" type="data" label="Input File 2"/>
103 </when>
104 <when value="sam">
105 <param name="inputFileName2" format="sam" type="data" label="Input File 2"/>
106 </when>
107 <when value="gtf">
108 <param name="inputFileName2" format="gtf" type="data" label="Input File 2"/>
109 </when>
110 </conditional>
111
112
113 <param name="all" type="boolean" truevalue="-k" falsevalue="" checked="false" label="print all the transcripts, not only those overlapping"/>
114 <param name="normalize" type="boolean" truevalue="-n" falsevalue="" checked="false" label="normalize the number of reads per cluster by the number of mappings per read "/>
115
116 <conditional name="OptionDistance">
117 <param name="dis" type="select" label="provide the number of reads" >
118 <option value="Yes">Yes</option>
119 <option value="No" selected="true">No</option>
120 </param>
121 <when value="Yes">
122 <param name="disVal" type="integer" value="0" label="max. distance between two transcripts" />
123 </when>
124 <when value="No">
125 </when>
126 </conditional>
127
128 <conditional name="OptionColinearOrAntiSens">
129 <param name="OptionCA" type="select" label="Colinear or anti-sens">
130 <option value="Colinear">Colinear</option>
131 <option value="AntiSens">AntiSens</option>
132 <option value="NONE" selected="true">NONE</option>
133 </param>
134 <when value="Colinear">
135 </when>
136 <when value="AntiSens">
137 </when>
138 <when value="NONE">
139 </when>
140 </conditional>
141
142 </inputs>
143
144 <outputs>
145 <data name="outputFileGff" format="gff3" label="[merge transcript lists] output file"/>
146 </outputs>
147
148 <help>
149 The script is similar to *compare overlapping*, except that when data of two different sets overlap, they are merged. You can use the same parameters as *compare overlapping* and use them to look for transcription on both strands, for example.
150
151 Optionally, you can also add to the output all the elements from the first set which do not overlap with the second set.
152 </help>
153 </tool>