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comparison SMART/galaxy/getDifference.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 440ceca58672
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5:ea3082881bf8 6:769e306b7933
1 <tool id="getDifference" name="get Difference">
2 <description>Gets all the regions of the genome, except the one given or get all the elements from the first set which does not ovelap with the second set (at the nucleotide level).</description>
3 <command interpreter="python">
4 ../Java/Python/getDifference.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
19 -j $formatType2.inputFileName2
20 #if $formatType2.FormatInputFileName2 == 'bed':
21 -g bed
22 #elif $formatType2.FormatInputFileName2 == 'gff':
23 -g gff
24 #elif $formatType2.FormatInputFileName2 == 'gff2':
25 -g gff2
26 #elif $formatType2.FormatInputFileName2 == 'gff3':
27 -g gff3
28 #elif $formatType2.FormatInputFileName2 == 'sam':
29 -g sam
30 #elif $formatType2.FormatInputFileName2 == 'gtf':
31 -g gtf
32 #end if
33
34
35 $split
36
37 #if $OptionSequence.option == "Yes":
38 -s $OptionSequence.sequence
39 #end if
40
41 -o $outputFileGff
42
43
44 </command>
45
46 <inputs>
47 <conditional name="formatType">
48 <param name="FormatInputFileName1" type="select" label="Input File Format 1">
49 <option value="bed">bed</option>
50 <option value="gff">gff</option>
51 <option value="gff2">gff2</option>
52 <option value="gff3">gff3</option>
53 <option value="sam">sam</option>
54 <option value="gtf">gtf</option>
55 </param>
56 <when value="bed">
57 <param name="inputFileName1" format="bed" type="data" label="Input File "/>
58 </when>
59 <when value="gff">
60 <param name="inputFileName1" format="gff" type="data" label="Input File "/>
61 </when>
62 <when value="gff2">
63 <param name="inputFileName1" format="gff2" type="data" label="Input File "/>
64 </when>
65 <when value="gff3">
66 <param name="inputFileName1" format="gff3" type="data" label="Input File "/>
67 </when>
68 <when value="sam">
69 <param name="inputFileName1" format="sam" type="data" label="Input File "/>
70 </when>
71 <when value="gtf">
72 <param name="inputFileName1" format="gtf" type="data" label="Input File "/>
73 </when>
74 </conditional>
75
76 <conditional name="formatType2">
77 <param name="FormatInputFileName2" type="select" label="Input File Format 2">
78 <option value="bed">bed</option>
79 <option value="gff">gff</option>
80 <option value="gff2">gff2</option>
81 <option value="gff3">gff3</option>
82 <option value="sam">sam</option>
83 <option value="gtf">gtf</option>
84 </param>
85 <when value="bed">
86 <param name="inputFileName2" format="bed" type="data" label="reference file"/>
87 </when>
88 <when value="gff">
89 <param name="inputFileName2" format="gff" type="data" label="reference file"/>
90 </when>
91 <when value="gff2">
92 <param name="inputFileName2" format="gff2" type="data" label="reference file"/>
93 </when>
94 <when value="gff3">
95 <param name="inputFileName2" format="gff3" type="data" label="reference file"/>
96 </when>
97 <when value="sam">
98 <param name="inputFileName2" format="sam" type="data" label="reference file"/>
99 </when>
100 <when value="gtf">
101 <param name="inputFileName2" format="gtf" type="data" label="reference file"/>
102 </when>
103 </conditional>
104
105 <param name="split" type="boolean" truevalue="-p" falsevalue="" checked="false" label="split option" help="When comparing to a set of genomic coordinates, do not join."/>
106
107
108 <conditional name="OptionSequence">
109 <param name="option" type="select" label="Compare with a reference fasta file.">
110 <option value="Yes">Yes</option>
111 <option value="No" selected="true">No</option>
112 </param>
113 <when value="Yes">
114 <param name="sequence" type="data" label="Fasta File" format="fasta"/>
115 </when>
116 <when value="No">
117 </when>
118 </conditional>
119
120 </inputs>
121
122
123 <outputs>
124 <data name="outputFileGff" format="gff3" label="[getDifference]output File."/>
125 </outputs>
126
127 </tool>