comparison SMART/galaxy/getNb.xml @ 6:769e306b7933

Change the repository level.
author yufei-luo
date Fri, 18 Jan 2013 04:54:14 -0500
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5:ea3082881bf8 6:769e306b7933
1 <tool id="getNumber" name="get number">
2 <description>Get the distribution of exons per transcripts, or mapping per read, or transcript per cluster.</description>
3 <command interpreter="python">
4 ../Java/Python/getNb.py -i $formatType.inputFileName
5 #if $formatType.FormatInputFileName == 'bed':
6 -f bed
7 #elif $formatType.FormatInputFileName == 'gff':
8 -f gff
9 #elif $formatType.FormatInputFileName == 'gff2':
10 -f gff2
11 #elif $formatType.FormatInputFileName == 'gff3':
12 -f gff3
13 #elif $formatType.FormatInputFileName == 'sam':
14 -f sam
15 #elif $formatType.FormatInputFileName == 'gtf':
16 -f gtf
17 #end if
18 -o $outputFilePNG
19 -q $query
20 $barPlot
21 #if $optionXMAX.XMAX == 'Yes':
22 -x $optionXMAX.xMaxValue
23 #end if
24
25 </command>
26
27 <inputs>
28 <conditional name="formatType">
29 <param name="FormatInputFileName" type="select" label="Input File Format">
30 <option value="bed">bed</option>
31 <option value="gff">gff</option>
32 <option value="gff2">gff2</option>
33 <option value="gff3">gff3</option>
34 <option value="sam">sam</option>
35 <option value="gtf">gtf</option>
36 </param>
37 <when value="bed">
38 <param name="inputFileName" format="bed" type="data" label="Input File"/>
39 </when>
40 <when value="gff">
41 <param name="inputFileName" format="gff" type="data" label="Input File"/>
42 </when>
43 <when value="gff2">
44 <param name="inputFileName" format="gff2" type="data" label="Input File"/>
45 </when>
46 <when value="gff3">
47 <param name="inputFileName" format="gff3" type="data" label="Input File"/>
48 </when>
49 <when value="sam">
50 <param name="inputFileName" format="sam" type="data" label="Input File"/>
51 </when>
52 <when value="gtf">
53 <param name="inputFileName" format="gtf" type="data" label="Input File"/>
54 </when>
55 </conditional>
56
57 <param name="query" type="text" value="None" label="compulsory option, choice (exon, transcript, cluster)" />
58 <param name="barPlot" type="boolean" truevalue="-b" falsevalue="" checked="false" label="use barplot representation"/>
59
60 <conditional name="optionXMAX">
61 <param name="XMAX" type="select" label="maximum value on the x-axis to plot ">
62 <option value="Yes">Yes</option>
63 <option value="No" selected="true">No</option>
64 </param>
65 <when value="Yes">
66 <param name="xMaxValue" type="integer" value="0" />
67 </when>
68 <when value="No">
69 </when>
70 </conditional>
71
72 </inputs>
73
74 <outputs>
75 <data name="outputFilePNG" format="png" label="[getNB]out file"/>
76 </outputs>
77
78 </tool>