Mercurial > repos > yufei-luo > s_mart

comparison SMART/galaxy/getSizes.xml @ 36:44d5973c188c

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded
author m-zytnicki
date Tue, 30 Apr 2013 15:02:29 -0400
parents
children
comparison
equal deleted inserted replaced
35:d94018ca4ada 36:44d5973c188c
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>