|
36
|
1 <tool id="GetSizes" name="get sizes">
|
|
|
2 <description>Get the sizes of a set of genomic coordinates.</description>
|
|
|
3 <command interpreter="python">
|
|
|
4 ../Java/Python/getSizes.py -i $formatType.inputFileName $formatType.FormatInputFileName
|
|
|
5
|
|
|
6 #if $OptionQuery.OptionQ == 'NONE':
|
|
|
7 -q size
|
|
|
8 #else:
|
|
|
9 $OptionQuery.OptionQ
|
|
|
10 #end if
|
|
|
11
|
|
|
12 -o $outputFile
|
|
|
13
|
|
|
14 #if $OptionXMax.xMax == "Yes":
|
|
|
15 -x $OptionXMax.maxValue
|
|
|
16 #end if
|
|
|
17 #if $OptionX.xLab == "Yes":
|
|
|
18 -a $OptionX.xLabValue
|
|
|
19 #end if
|
|
|
20 #if $OptionY.yLab == "Yes":
|
|
|
21 -b $OptionY.yLabValue
|
|
|
22 #end if
|
|
|
23 $barPlot
|
|
|
24 </command>
|
|
|
25
|
|
|
26 <inputs>
|
|
|
27 <conditional name="formatType">
|
|
|
28 <param name="FormatInputFileName" type="select" label="Input File Format">
|
|
|
29 <option value="-f bed">bed</option>
|
|
|
30 <option value="-f gff">gff</option>
|
|
|
31 <option value="-f gff2">gff2</option>
|
|
|
32 <option value="-f gff3">gff3</option>
|
|
|
33 <option value="-f sam">sam</option>
|
|
|
34 <option value="-f gtf">gtf</option>
|
|
|
35 <option value="-f fasta">fasta</option>
|
|
|
36 <option value="-f fastq">fastq</option>
|
|
|
37 </param>
|
|
|
38 <when value="-f bed">
|
|
|
39 <param name="inputFileName" format="bed" type="data" label="Input File"/>
|
|
|
40 </when>
|
|
|
41 <when value="-f gff">
|
|
|
42 <param name="inputFileName" format="gff" type="data" label="Input gff File"/>
|
|
|
43 </when>
|
|
|
44 <when value="-f gff2">
|
|
|
45 <param name="inputFileName" format="gff" type="data" label="Input gff2 File"/>
|
|
|
46 </when>
|
|
|
47 <when value="-f gff3">
|
|
|
48 <param name="inputFileName" format="gff3" type="data" label="Input gff3 File"/>
|
|
|
49 </when>
|
|
|
50 <when value="-f sam">
|
|
|
51 <param name="inputFileName" format="sam" type="data" label="Input gff2 File"/>
|
|
|
52 </when>
|
|
|
53 <when value="-f gtf">
|
|
|
54 <param name="inputFileName" format="gtf" type="data" label="Input gff3 File"/>
|
|
|
55 </when>
|
|
|
56 <when value="-f fasta">
|
|
|
57 <param name="inputFileName" format="fasta" type="data" label="Input fasta File"/>
|
|
|
58 </when>
|
|
|
59 <when value="-f fastq">
|
|
|
60 <param name="inputFileName" format="fastq" type="data" label="Input fastq File"/>
|
|
|
61 </when>
|
|
|
62 </conditional>
|
|
|
63
|
|
|
64 <conditional name="OptionQuery">
|
|
|
65 <param name="OptionQ" type="select" label="mesure type">
|
|
|
66 <option value="-q size">size</option>
|
|
|
67 <option value="-q intron size">intron size</option>
|
|
|
68 <option value="-q exon size">exon size</option>
|
|
|
69 <option value="-q 1st exon size">1st exon size</option>
|
|
|
70 <option value="NONE" selected="true">NONE</option>
|
|
|
71 </param>
|
|
|
72 <when value="-q size">
|
|
|
73 </when>
|
|
|
74 <when value="-q intron size">
|
|
|
75 </when>
|
|
|
76 <when value="-q exon size">
|
|
|
77 </when>
|
|
|
78 <when value="-q 1st exon size">
|
|
|
79 </when>
|
|
|
80 <when value="NONE">
|
|
|
81
|
|
|
82 </when>
|
|
|
83 </conditional>
|
|
|
84
|
|
|
85 <conditional name="OptionXMax">
|
|
|
86 <param name="xMax" type="select" label="maximum x-value to plot">
|
|
|
87 <option value="Yes">Yes</option>
|
|
|
88 <option value="No" selected="true">No</option>
|
|
|
89 </param>
|
|
|
90 <when value="Yes">
|
|
|
91 <param name="maxValue" type="integer" value="1000"/>
|
|
|
92 </when>
|
|
|
93 <when value="No">
|
|
|
94 </when>
|
|
|
95 </conditional>
|
|
|
96
|
|
|
97 <conditional name="OptionX">
|
|
|
98 <param name="xLab" type="select" label="X label title">
|
|
|
99 <option value="Yes">Yes</option>
|
|
|
100 <option value="No" selected="true">No</option>
|
|
|
101 </param>
|
|
|
102 <when value="Yes">
|
|
|
103 <param name="xLabValue" type="text" value="Size" label="Notice: The title should not have spaces. EX. Size_of_transcript"/>
|
|
|
104 </when>
|
|
|
105 <when value="No">
|
|
|
106 </when>
|
|
|
107 </conditional>
|
|
|
108
|
|
|
109 <conditional name="OptionY">
|
|
|
110 <param name="yLab" type="select" label="Y label title">
|
|
|
111 <option value="Yes">Yes</option>
|
|
|
112 <option value="No" selected="true">No</option>
|
|
|
113 </param>
|
|
|
114 <when value="Yes">
|
|
|
115 <param name="yLabValue" type="text" value="#_reads" label="Notice: The title should not have spaces. EX. Number_of_reads"/>
|
|
|
116 </when>
|
|
|
117 <when value="No">
|
|
|
118 </when>
|
|
|
119 </conditional>
|
|
|
120
|
|
|
121 <param name="barPlot" type="boolean" truevalue="-B" falsevalue="" checked="false" label="use barplot representation"/>
|
|
|
122 </inputs>
|
|
|
123
|
|
|
124 <outputs>
|
|
|
125 <data name="outputFile" format="png" label="[Get sizes] output file"/>
|
|
|
126 </outputs>
|
|
|
127
|
|
|
128 <help>
|
|
|
129 Get the sequence/annotation size distribution. A point (*x*, *y*) means that *y* elements have a size of *x* nucleotides.
|
|
|
130
|
|
|
131 When your mapping include exon/intron structures, you can decide to count the size of the introns, the sizes of the exons or the size of the first exons.
|
|
|
132 </help>
|
|
|
133 </tool>
|
