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comparison SMART/galaxy/getSizes.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="GetSizes" name="get sizes">
2 <description>Get the sizes of a set of genomic coordinates.</description>
3 <requirements>
4 <requirement type="set_environment">PYTHONPATH</requirement>
5 </requirements>
6 <command interpreter="python">
7 ../Java/Python/getSizes.py -i $formatType.inputFileName $formatType.FormatInputFileName
8
9 #if $OptionQuery.OptionQ == 'NONE':
10 -q size
11 #else:
12 $OptionQuery.OptionQ
13 #end if
14
15 -o $outputFile
16
17 #if $OptionXMax.xMax == "Yes":
18 -x $OptionXMax.maxValue
19 #end if
20 #if $OptionX.xLab == "Yes":
21 -a $OptionX.xLabValue
22 #end if
23 #if $OptionY.yLab == "Yes":
24 -b $OptionY.yLabValue
25 #end if
26 $barPlot
27 </command>
28
29 <inputs>
30 <conditional name="formatType">
31 <param name="FormatInputFileName" type="select" label="Input File Format">
32 <option value="-f bed">bed</option>
33 <option value="-f gff">gff</option>
34 <option value="-f gff2">gff2</option>
35 <option value="-f gff3">gff3</option>
36 <option value="-f sam">sam</option>
37 <option value="-f gtf">gtf</option>
38 <option value="-f fasta">fasta</option>
39 <option value="-f fastq">fastq</option>
40 </param>
41 <when value="-f bed">
42 <param name="inputFileName" format="bed" type="data" label="Input File"/>
43 </when>
44 <when value="-f gff">
45 <param name="inputFileName" format="gff" type="data" label="Input gff File"/>
46 </when>
47 <when value="-f gff2">
48 <param name="inputFileName" format="gff" type="data" label="Input gff2 File"/>
49 </when>
50 <when value="-f gff3">
51 <param name="inputFileName" format="gff3" type="data" label="Input gff3 File"/>
52 </when>
53 <when value="-f sam">
54 <param name="inputFileName" format="sam" type="data" label="Input gff2 File"/>
55 </when>
56 <when value="-f gtf">
57 <param name="inputFileName" format="gtf" type="data" label="Input gff3 File"/>
58 </when>
59 <when value="-f fasta">
60 <param name="inputFileName" format="fasta" type="data" label="Input fasta File"/>
61 </when>
62 <when value="-f fastq">
63 <param name="inputFileName" format="fastq" type="data" label="Input fastq File"/>
64 </when>
65 </conditional>
66
67 <conditional name="OptionQuery">
68 <param name="OptionQ" type="select" label="mesure type">
69 <option value="-q size">size</option>
70 <option value="-q intron size">intron size</option>
71 <option value="-q exon size">exon size</option>
72 <option value="-q 1st exon size">1st exon size</option>
73 <option value="NONE" selected="true">NONE</option>
74 </param>
75 <when value="-q size">
76 </when>
77 <when value="-q intron size">
78 </when>
79 <when value="-q exon size">
80 </when>
81 <when value="-q 1st exon size">
82 </when>
83 <when value="NONE">
84
85 </when>
86 </conditional>
87
88 <conditional name="OptionXMax">
89 <param name="xMax" type="select" label="maximum x-value to plot">
90 <option value="Yes">Yes</option>
91 <option value="No" selected="true">No</option>
92 </param>
93 <when value="Yes">
94 <param name="maxValue" type="integer" value="1000"/>
95 </when>
96 <when value="No">
97 </when>
98 </conditional>
99
100 <conditional name="OptionX">
101 <param name="xLab" type="select" label="X label title">
102 <option value="Yes">Yes</option>
103 <option value="No" selected="true">No</option>
104 </param>
105 <when value="Yes">
106 <param name="xLabValue" type="text" value="Size" label="Notice: The title should not have spaces. EX. Size_of_transcript"/>
107 </when>
108 <when value="No">
109 </when>
110 </conditional>
111
112 <conditional name="OptionY">
113 <param name="yLab" type="select" label="Y label title">
114 <option value="Yes">Yes</option>
115 <option value="No" selected="true">No</option>
116 </param>
117 <when value="Yes">
118 <param name="yLabValue" type="text" value="#_reads" label="Notice: The title should not have spaces. EX. Number_of_reads"/>
119 </when>
120 <when value="No">
121 </when>
122 </conditional>
123
124 <param name="barPlot" type="boolean" truevalue="-B" falsevalue="" checked="false" label="use barplot representation"/>
125 </inputs>
126
127 <outputs>
128 <data name="outputFile" format="png" label="[get sizes] output file"/>
129 </outputs>
130
131 <help>
132 Get the sequence/annotation size distribution. A point (*x*, *y*) means that *y* elements have a size of *x* nucleotides.
133
134 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.
135 </help>
136 </tool>