Mercurial > repos > yufei-luo > s_mart

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

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
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
parents
children
comparison
equal deleted inserted replaced
-1:000000000000 0:e0f8dcca02ed
1 <tool id="clusterizeBySlidingWindows" name="clusterize By SlidingWindows">
2 <description>Produces a GFF3 file that clusters a list of transcripts using a sliding window. Cluster the data into regions (defined by size and overlap with next region) and keep only highest peaks.</description>
3 <command interpreter="python">
4 ../Java/Python/clusterizeBySlidingWindows.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 -s $size
19 -e $overlap
20 -o $outputFileGff
21 $normalize
22 $strands
23
24 #if $OptionTag.tag == "Yes":
25 -g $OptionTag.value
26 #end if
27
28 #if $OptionsOperation.operation == "Yes":
29 -r $OptionsOperation.value
30 #end if
31
32 #if $OptionWriteTag.writeTag == "Yes":
33 -w $OptionWriteTag.value
34 #end if
35
36 $strand
37 $plot $plotPng
38 $excel $excelOutput
39
40
41 </command>
42
43 <inputs>
44 <conditional name="formatType">
45 <param name="FormatInputFileName" type="select" label="Input File Format">
46 <option value="bed">bed</option>
47 <option value="gff">gff</option>
48 <option value="gff2">gff2</option>
49 <option value="gff3">gff3</option>
50 <option value="sam">sam</option>
51 <option value="gtf">gtf</option>
52 </param>
53 <when value="bed">
54 <param name="inputFileName" format="bed" type="data" label="Input File"/>
55 </when>
56 <when value="gff">
57 <param name="inputFileName" format="gff" type="data" label="Input File"/>
58 </when>
59 <when value="gff2">
60 <param name="inputFileName" format="gff2" type="data" label="Input File"/>
61 </when>
62 <when value="gff3">
63 <param name="inputFileName" format="gff3" type="data" label="Input File"/>
64 </when>
65 <when value="sam">
66 <param name="inputFileName" format="sam" type="data" label="Input File"/>
67 </when>
68 <when value="gtf">
69 <param name="inputFileName" format="gtf" type="data" label="Input File"/>
70 </when>
71 </conditional>
72
73
74 <param name="size" type="text" value="50000" label="Size option" help="Size of the regions."/>
75 <param name="overlap" type="text" value="50" label="Overlap option" help="Overlap between two consecutive regions."/>
76 <param name="normalize" type="boolean" truevalue="-m" falsevalue="" checked="false" label="Normalize option for only GFF3 file format" help="This option normalizes (Warning!! Only for GFF3 file!)"/>
77 <param name="strands" type="boolean" truevalue="-2" falsevalue="" checked="false" label="strands option" help="Consider the two strands separately."/>
78
79 <conditional name="OptionTag">
80 <param name="tag" type="select" label="use a given tag as input (instead of summing number of features)">
81 <option value="Yes">Yes</option>
82 <option value="No" selected="true">No</option>
83 </param>
84 <when value="Yes">
85 <param name="value" type="text" value="None" label="tag option" help="write a tag name you want to observe."/>
86 </when>
87 <when value="No">
88 </when>
89 </conditional>
90
91
92 <conditional name="OptionsOperation">
93 <param name="operation" type="select" label="combine tag value with given operation [choice (sum, avg, med, min, max)]">
94 <option value="Yes">Yes</option>
95 <option value="No" selected="true">No</option>
96 </param>
97 <when value="Yes">
98 <param name="value" type="text" value="None" label="operation option" help="You can ONLY choose one of fowlling operation : sum, avg, med, min, max."/>
99 </when>
100 <when value="No">
101 </when>
102 </conditional>
103
104
105 <conditional name="OptionWriteTag">
106 <param name="writeTag" type="select" label="write a new tag in output file">
107 <option value="Yes">Yes</option>
108 <option value="No" selected="true">No</option>
109 </param>
110 <when value="Yes">
111 <param name="value" type="text" value="nbElements" label="write tag option" help="print the result in the given tag (default usually is 'nbElements')"/>
112 </when>
113 <when value="No">
114 </when>
115 </conditional>
116
117 <param name="strand" type="boolean" truevalue="-2" falsevalue="" checked="false" label="strand option" help="This option considers the two strands separately."/>
118 <param name="plot" type="boolean" truevalue="-p" falsevalue="" checked="false" label="plot option" help="This option creates a png file."/>
119 <param name="excel" type="boolean" truevalue="-x" falsevalue="" checked="false" label="excel option" help="This option creates a csv file."/>
120
121 </inputs>
122
123 <outputs>
124 <data name="outputFileGff" format="gff3"/>
125 <data name="excelOutput" format="csv">
126 <filter>excel</filter>
127 </data>
128 <data name="plotPng" format="png">
129 <filter>plot</filter>
130 </data>
131 </outputs>
132 </tool>