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comparison smart_toolShed/SMART/galaxy/getSizes.xml @ 0:e0f8dcca02ed

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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
author yufei-luo
date Thu, 17 Jan 2013 10:52:14 -0500
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-1:000000000000 0:e0f8dcca02ed
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 $excel $excelOutput
25 </command>
26
27 <inputs>
28 <conditional name="formatType">
29 <param name="FormatInputFileName" type="select" label="Input File Format">
30 <option value="-f bed">bed</option>
31 <option value="-f gff">gff</option>
32 <option value="-f gff2">gff2</option>
33 <option value="-f gff3">gff3</option>
34 <option value="-f sam">sam</option>
35 <option value="-f gtf">gtf</option>
36 <option value="-f fasta">fasta</option>
37 <option value="-f fastq">fastq</option>
38 </param>
39 <when value="-f bed">
40 <param name="inputFileName" format="bed" type="data" label="Input File"/>
41 </when>
42 <when value="-f gff">
43 <param name="inputFileName" format="gff" type="data" label="Input gff File"/>
44 </when>
45 <when value="-f gff2">
46 <param name="inputFileName" format="gff" type="data" label="Input gff2 File"/>
47 </when>
48 <when value="-f gff3">
49 <param name="inputFileName" format="gff3" type="data" label="Input gff3 File"/>
50 </when>
51 <when value="-f sam">
52 <param name="inputFileName" format="sam" type="data" label="Input gff2 File"/>
53 </when>
54 <when value="-f gtf">
55 <param name="inputFileName" format="gtf" type="data" label="Input gff3 File"/>
56 </when>
57 <when value="-f fasta">
58 <param name="inputFileName" format="fasta" type="data" label="Input fasta File"/>
59 </when>
60 <when value="-f fastq">
61 <param name="inputFileName" format="fastq" type="data" label="Input fastq File"/>
62 </when>
63 </conditional>
64
65 <conditional name="OptionQuery">
66 <param name="OptionQ" type="select" label="mesure type">
67 <option value="-q size">size</option>
68 <option value="-q intron size">intron size</option>
69 <option value="-q exon size">exon size</option>
70 <option value="-q 1st exon size">1st exon size</option>
71 <option value="NONE" selected="true">NONE</option>
72 </param>
73 <when value="-q size">
74 </when>
75 <when value="-q intron size">
76 </when>
77 <when value="-q exon size">
78 </when>
79 <when value="-q 1st exon size">
80 </when>
81 <when value="NONE">
82
83 </when>
84 </conditional>
85
86 <conditional name="OptionXMax">
87 <param name="xMax" type="select" label="maximum value on the x-axis to plot [format: int]">
88 <option value="Yes">Yes</option>
89 <option value="No" selected="true">No</option>
90 </param>
91 <when value="Yes">
92 <param name="maxValue" type="integer" value="1000"/>
93 </when>
94 <when value="No">
95 </when>
96 </conditional>
97
98 <conditional name="OptionX">
99 <param name="xLab" type="select" label="X label title">
100 <option value="Yes">Yes</option>
101 <option value="No" selected="true">No</option>
102 </param>
103 <when value="Yes">
104 <param name="xLabValue" type="text" value="Size" label="Notice: The title should not have spaces. EX. Size_of_transcript"/>
105 </when>
106 <when value="No">
107 </when>
108 </conditional>
109
110 <conditional name="OptionY">
111 <param name="yLab" type="select" label="Y label title">
112 <option value="Yes">Yes</option>
113 <option value="No" selected="true">No</option>
114 </param>
115 <when value="Yes">
116 <param name="yLabValue" type="text" value="#_reads" label="Notice: The title should not have spaces. EX. Number_of_reads"/>
117 </when>
118 <when value="No">
119 </when>
120 </conditional>
121
122
123
124 <param name="barPlot" type="boolean" truevalue="-B" falsevalue="" checked="false" label="use barplot representation"/>
125
126 <param name="excel" type="boolean" truevalue="-c" falsevalue="" checked="false" label="excel option" help="This option creates a csv file."/>
127 </inputs>
128
129 <outputs>
130 <data name="outputFile" format="png" label="[Get size] Output file"/>
131 <data name="excelOutput" format="csv">
132 <filter>excel</filter>
133 </data>
134 </outputs>
135 </tool>