annotate SMART/galaxy/getDifference.xml @ 71:d96f6c9a39e0 draft default tip

Removed pyc files.
author m-zytnicki
date Thu, 07 Apr 2016 09:25:18 -0400
parents 2c0c0a89fad7
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
38
2c0c0a89fad7 Uploaded
m-zytnicki
parents:
diff changeset
1 <tool id="getDifference" name="get difference">
2c0c0a89fad7 Uploaded
m-zytnicki
parents:
diff changeset
2 <description>Gets all the regions of the genome, except the one given in an annotation file. Alternatively, it may also give all the elements from the first set which does not ovelap with the second set (at the nucleotide level).</description>
2c0c0a89fad7 Uploaded
m-zytnicki
parents:
diff changeset
3 <requirements>
2c0c0a89fad7 Uploaded
m-zytnicki
parents:
diff changeset
4 <requirement type="set_environment">PYTHONPATH</requirement>
2c0c0a89fad7 Uploaded
m-zytnicki
parents:
diff changeset
5 </requirements>
2c0c0a89fad7 Uploaded
m-zytnicki
parents:
diff changeset
6 <command interpreter="python">
2c0c0a89fad7 Uploaded
m-zytnicki
parents:
diff changeset
7 ../Java/Python/getDifference.py -i $formatType.inputFileName1
2c0c0a89fad7 Uploaded
m-zytnicki
parents:
diff changeset
8 #if $formatType.FormatInputFileName1 == 'bed':
2c0c0a89fad7 Uploaded
m-zytnicki
parents:
diff changeset
9 -f bed
2c0c0a89fad7 Uploaded
m-zytnicki
parents:
diff changeset
10 #elif $formatType.FormatInputFileName1 == 'gff':
2c0c0a89fad7 Uploaded
m-zytnicki
parents:
diff changeset
11 -f gff
2c0c0a89fad7 Uploaded
m-zytnicki
parents:
diff changeset
12 #elif $formatType.FormatInputFileName1 == 'gff2':
2c0c0a89fad7 Uploaded
m-zytnicki
parents:
diff changeset
13 -f gff2
2c0c0a89fad7 Uploaded
m-zytnicki
parents:
diff changeset
14 #elif $formatType.FormatInputFileName1 == 'gff3':
2c0c0a89fad7 Uploaded
m-zytnicki
parents:
diff changeset
15 -f gff3
2c0c0a89fad7 Uploaded
m-zytnicki
parents:
diff changeset
16 #elif $formatType.FormatInputFileName1 == 'sam':
2c0c0a89fad7 Uploaded
m-zytnicki
parents:
diff changeset
17 -f sam
2c0c0a89fad7 Uploaded
m-zytnicki
parents:
diff changeset
18 #elif $formatType.FormatInputFileName1 == 'gtf':
2c0c0a89fad7 Uploaded
m-zytnicki
parents:
diff changeset
19 -f gtf
2c0c0a89fad7 Uploaded
m-zytnicki
parents:
diff changeset
20 #end if
2c0c0a89fad7 Uploaded
m-zytnicki
parents:
diff changeset
21
2c0c0a89fad7 Uploaded
m-zytnicki
parents:
diff changeset
22 -j $formatType2.inputFileName2
2c0c0a89fad7 Uploaded
m-zytnicki
parents:
diff changeset
23 #if $formatType2.FormatInputFileName2 == 'bed':
2c0c0a89fad7 Uploaded
m-zytnicki
parents:
diff changeset
24 -g bed
2c0c0a89fad7 Uploaded
m-zytnicki
parents:
diff changeset
25 #elif $formatType2.FormatInputFileName2 == 'gff':
2c0c0a89fad7 Uploaded
m-zytnicki
parents:
diff changeset
26 -g gff
2c0c0a89fad7 Uploaded
m-zytnicki
parents:
diff changeset
27 #elif $formatType2.FormatInputFileName2 == 'gff2':
2c0c0a89fad7 Uploaded
m-zytnicki
parents:
diff changeset
28 -g gff2
2c0c0a89fad7 Uploaded
m-zytnicki
parents:
diff changeset
29 #elif $formatType2.FormatInputFileName2 == 'gff3':
2c0c0a89fad7 Uploaded
m-zytnicki
parents:
diff changeset
30 -g gff3
2c0c0a89fad7 Uploaded
m-zytnicki
parents:
diff changeset
31 #elif $formatType2.FormatInputFileName2 == 'sam':
2c0c0a89fad7 Uploaded
m-zytnicki
parents:
diff changeset
32 -g sam
2c0c0a89fad7 Uploaded
m-zytnicki
parents:
diff changeset
33 #elif $formatType2.FormatInputFileName2 == 'gtf':
2c0c0a89fad7 Uploaded
m-zytnicki
parents:
diff changeset
34 -g gtf
2c0c0a89fad7 Uploaded
m-zytnicki
parents:
diff changeset
35 #end if
2c0c0a89fad7 Uploaded
m-zytnicki
parents:
diff changeset
36
2c0c0a89fad7 Uploaded
m-zytnicki
parents:
diff changeset
37 $split
2c0c0a89fad7 Uploaded
m-zytnicki
parents:
diff changeset
38
2c0c0a89fad7 Uploaded
m-zytnicki
parents:
diff changeset
39 #if $OptionSequence.option == "Yes":
2c0c0a89fad7 Uploaded
m-zytnicki
parents:
diff changeset
40 -s $OptionSequence.sequence
2c0c0a89fad7 Uploaded
m-zytnicki
parents:
diff changeset
41 #end if
2c0c0a89fad7 Uploaded
m-zytnicki
parents:
diff changeset
42
2c0c0a89fad7 Uploaded
m-zytnicki
parents:
diff changeset
43 -o $outputFileGff
2c0c0a89fad7 Uploaded
m-zytnicki
parents:
diff changeset
44
2c0c0a89fad7 Uploaded
m-zytnicki
parents:
diff changeset
45
2c0c0a89fad7 Uploaded
m-zytnicki
parents:
diff changeset
46 </command>
2c0c0a89fad7 Uploaded
m-zytnicki
parents:
diff changeset
47
2c0c0a89fad7 Uploaded
m-zytnicki
parents:
diff changeset
48 <inputs>
2c0c0a89fad7 Uploaded
m-zytnicki
parents:
diff changeset
49 <conditional name="formatType">
2c0c0a89fad7 Uploaded
m-zytnicki
parents:
diff changeset
50 <param name="FormatInputFileName1" type="select" label="Input File Format 1">
2c0c0a89fad7 Uploaded
m-zytnicki
parents:
diff changeset
51 <option value="bed">bed</option>
2c0c0a89fad7 Uploaded
m-zytnicki
parents:
diff changeset
52 <option value="gff">gff</option>
2c0c0a89fad7 Uploaded
m-zytnicki
parents:
diff changeset
53 <option value="gff2">gff2</option>
2c0c0a89fad7 Uploaded
m-zytnicki
parents:
diff changeset
54 <option value="gff3">gff3</option>
2c0c0a89fad7 Uploaded
m-zytnicki
parents:
diff changeset
55 <option value="sam">sam</option>
2c0c0a89fad7 Uploaded
m-zytnicki
parents:
diff changeset
56 <option value="gtf">gtf</option>
2c0c0a89fad7 Uploaded
m-zytnicki
parents:
diff changeset
57 </param>
2c0c0a89fad7 Uploaded
m-zytnicki
parents:
diff changeset
58 <when value="bed">
2c0c0a89fad7 Uploaded
m-zytnicki
parents:
diff changeset
59 <param name="inputFileName1" format="bed" type="data" label="Input File "/>
2c0c0a89fad7 Uploaded
m-zytnicki
parents:
diff changeset
60 </when>
2c0c0a89fad7 Uploaded
m-zytnicki
parents:
diff changeset
61 <when value="gff">
2c0c0a89fad7 Uploaded
m-zytnicki
parents:
diff changeset
62 <param name="inputFileName1" format="gff" type="data" label="Input File "/>
2c0c0a89fad7 Uploaded
m-zytnicki
parents:
diff changeset
63 </when>
2c0c0a89fad7 Uploaded
m-zytnicki
parents:
diff changeset
64 <when value="gff2">
2c0c0a89fad7 Uploaded
m-zytnicki
parents:
diff changeset
65 <param name="inputFileName1" format="gff2" type="data" label="Input File "/>
2c0c0a89fad7 Uploaded
m-zytnicki
parents:
diff changeset
66 </when>
2c0c0a89fad7 Uploaded
m-zytnicki
parents:
diff changeset
67 <when value="gff3">
2c0c0a89fad7 Uploaded
m-zytnicki
parents:
diff changeset
68 <param name="inputFileName1" format="gff3" type="data" label="Input File "/>
2c0c0a89fad7 Uploaded
m-zytnicki
parents:
diff changeset
69 </when>
2c0c0a89fad7 Uploaded
m-zytnicki
parents:
diff changeset
70 <when value="sam">
2c0c0a89fad7 Uploaded
m-zytnicki
parents:
diff changeset
71 <param name="inputFileName1" format="sam" type="data" label="Input File "/>
2c0c0a89fad7 Uploaded
m-zytnicki
parents:
diff changeset
72 </when>
2c0c0a89fad7 Uploaded
m-zytnicki
parents:
diff changeset
73 <when value="gtf">
2c0c0a89fad7 Uploaded
m-zytnicki
parents:
diff changeset
74 <param name="inputFileName1" format="gtf" type="data" label="Input File "/>
2c0c0a89fad7 Uploaded
m-zytnicki
parents:
diff changeset
75 </when>
2c0c0a89fad7 Uploaded
m-zytnicki
parents:
diff changeset
76 </conditional>
2c0c0a89fad7 Uploaded
m-zytnicki
parents:
diff changeset
77
2c0c0a89fad7 Uploaded
m-zytnicki
parents:
diff changeset
78 <conditional name="formatType2">
2c0c0a89fad7 Uploaded
m-zytnicki
parents:
diff changeset
79 <param name="FormatInputFileName2" type="select" label="Input File Format 2">
2c0c0a89fad7 Uploaded
m-zytnicki
parents:
diff changeset
80 <option value="bed">bed</option>
2c0c0a89fad7 Uploaded
m-zytnicki
parents:
diff changeset
81 <option value="gff">gff</option>
2c0c0a89fad7 Uploaded
m-zytnicki
parents:
diff changeset
82 <option value="gff2">gff2</option>
2c0c0a89fad7 Uploaded
m-zytnicki
parents:
diff changeset
83 <option value="gff3">gff3</option>
2c0c0a89fad7 Uploaded
m-zytnicki
parents:
diff changeset
84 <option value="sam">sam</option>
2c0c0a89fad7 Uploaded
m-zytnicki
parents:
diff changeset
85 <option value="gtf">gtf</option>
2c0c0a89fad7 Uploaded
m-zytnicki
parents:
diff changeset
86 </param>
2c0c0a89fad7 Uploaded
m-zytnicki
parents:
diff changeset
87 <when value="bed">
2c0c0a89fad7 Uploaded
m-zytnicki
parents:
diff changeset
88 <param name="inputFileName2" format="bed" type="data" label="reference file"/>
2c0c0a89fad7 Uploaded
m-zytnicki
parents:
diff changeset
89 </when>
2c0c0a89fad7 Uploaded
m-zytnicki
parents:
diff changeset
90 <when value="gff">
2c0c0a89fad7 Uploaded
m-zytnicki
parents:
diff changeset
91 <param name="inputFileName2" format="gff" type="data" label="reference file"/>
2c0c0a89fad7 Uploaded
m-zytnicki
parents:
diff changeset
92 </when>
2c0c0a89fad7 Uploaded
m-zytnicki
parents:
diff changeset
93 <when value="gff2">
2c0c0a89fad7 Uploaded
m-zytnicki
parents:
diff changeset
94 <param name="inputFileName2" format="gff2" type="data" label="reference file"/>
2c0c0a89fad7 Uploaded
m-zytnicki
parents:
diff changeset
95 </when>
2c0c0a89fad7 Uploaded
m-zytnicki
parents:
diff changeset
96 <when value="gff3">
2c0c0a89fad7 Uploaded
m-zytnicki
parents:
diff changeset
97 <param name="inputFileName2" format="gff3" type="data" label="reference file"/>
2c0c0a89fad7 Uploaded
m-zytnicki
parents:
diff changeset
98 </when>
2c0c0a89fad7 Uploaded
m-zytnicki
parents:
diff changeset
99 <when value="sam">
2c0c0a89fad7 Uploaded
m-zytnicki
parents:
diff changeset
100 <param name="inputFileName2" format="sam" type="data" label="reference file"/>
2c0c0a89fad7 Uploaded
m-zytnicki
parents:
diff changeset
101 </when>
2c0c0a89fad7 Uploaded
m-zytnicki
parents:
diff changeset
102 <when value="gtf">
2c0c0a89fad7 Uploaded
m-zytnicki
parents:
diff changeset
103 <param name="inputFileName2" format="gtf" type="data" label="reference file"/>
2c0c0a89fad7 Uploaded
m-zytnicki
parents:
diff changeset
104 </when>
2c0c0a89fad7 Uploaded
m-zytnicki
parents:
diff changeset
105 </conditional>
2c0c0a89fad7 Uploaded
m-zytnicki
parents:
diff changeset
106
2c0c0a89fad7 Uploaded
m-zytnicki
parents:
diff changeset
107 <param name="split" type="boolean" truevalue="-p" falsevalue="" checked="false" label="When comparing to a set of genomic coordinates, do not join into exons."/>
2c0c0a89fad7 Uploaded
m-zytnicki
parents:
diff changeset
108
2c0c0a89fad7 Uploaded
m-zytnicki
parents:
diff changeset
109 <conditional name="OptionSequence">
2c0c0a89fad7 Uploaded
m-zytnicki
parents:
diff changeset
110 <param name="option" type="select" label="Compare with a reference fasta file.">
2c0c0a89fad7 Uploaded
m-zytnicki
parents:
diff changeset
111 <option value="Yes">Yes</option>
2c0c0a89fad7 Uploaded
m-zytnicki
parents:
diff changeset
112 <option value="No" selected="true">No</option>
2c0c0a89fad7 Uploaded
m-zytnicki
parents:
diff changeset
113 </param>
2c0c0a89fad7 Uploaded
m-zytnicki
parents:
diff changeset
114 <when value="Yes">
2c0c0a89fad7 Uploaded
m-zytnicki
parents:
diff changeset
115 <param name="sequence" type="data" label="Fasta File" format="fasta"/>
2c0c0a89fad7 Uploaded
m-zytnicki
parents:
diff changeset
116 </when>
2c0c0a89fad7 Uploaded
m-zytnicki
parents:
diff changeset
117 <when value="No">
2c0c0a89fad7 Uploaded
m-zytnicki
parents:
diff changeset
118 </when>
2c0c0a89fad7 Uploaded
m-zytnicki
parents:
diff changeset
119 </conditional>
2c0c0a89fad7 Uploaded
m-zytnicki
parents:
diff changeset
120
2c0c0a89fad7 Uploaded
m-zytnicki
parents:
diff changeset
121 </inputs>
2c0c0a89fad7 Uploaded
m-zytnicki
parents:
diff changeset
122
2c0c0a89fad7 Uploaded
m-zytnicki
parents:
diff changeset
123
2c0c0a89fad7 Uploaded
m-zytnicki
parents:
diff changeset
124 <outputs>
2c0c0a89fad7 Uploaded
m-zytnicki
parents:
diff changeset
125 <data name="outputFileGff" format="gff3" label="[get difference] output file."/>
2c0c0a89fad7 Uploaded
m-zytnicki
parents:
diff changeset
126 </outputs>
2c0c0a89fad7 Uploaded
m-zytnicki
parents:
diff changeset
127
2c0c0a89fad7 Uploaded
m-zytnicki
parents:
diff changeset
128 <help>
2c0c0a89fad7 Uploaded
m-zytnicki
parents:
diff changeset
129 This tools has two different (but similar) uses. When given two sets of transcripts, it trims the elements of the set so that they do not overlap with the second set.
2c0c0a89fad7 Uploaded
m-zytnicki
parents:
diff changeset
130
2c0c0a89fad7 Uploaded
m-zytnicki
parents:
diff changeset
131 When only one set of transcripts is given, together with a reference genome, it produces a list of transcripts which complements the first set.
2c0c0a89fad7 Uploaded
m-zytnicki
parents:
diff changeset
132 </help>
2c0c0a89fad7 Uploaded
m-zytnicki
parents:
diff changeset
133 </tool>