Mercurial > repos > jjohnson > igvtools

comparison igvtools_count.xml @ 0:2eb1e2924c1a

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded
author jjohnson
date Tue, 17 Jan 2012 21:53:25 -0500
parents
children
comparison
equal deleted inserted replaced
-1:000000000000 0:2eb1e2924c1a
1 <tool id="igvtools_count" name="IGVtools count" version="1.0">
2 <description>average feature density across the genome</description>
3 <command interpreter="bash">igvtools count
4 #if $zoom.__str__ != '':
5 -z $zoom
6 #end if
7 #if $window.__str__ != '':
8 -w $window
9 #end if
10 #if $extend.__str__ != '':
11 -e $extend
12 #end if
13 #if $window_functions.__str__ != '':
14 -f '$window_functions'
15 #end if
16 ## IGVTools relies on the file extension to determine format
17 #if $input.datatype.file_ext == 'bam':
18 #set $input_name='input_file.bam'
19 #elif $input.datatype.file_ext == 'sam':
20 #set $input_name='input_file.sam'
21 #elif $input.datatype.file_ext == 'bed':
22 #set $input_name='input_file.bed'
23 #elif $input.datatype.file_ext == 'psl':
24 #set $input_name='input_file.psl'
25 #end if
26 `ln -s $input $input_name; echo $input_name` '$output_fmt' $refGenomeSource.ref
27 </command>
28 <inputs>
29 <conditional name="refGenomeSource">
30 <param name="refGenomeSource_type" type="select" label="Will you select a reference genome from your history or use a built-in reference?">
31 <option value="built-in">Use a built-in reference</option>
32 <option value="history">Use one from the history</option>
33 </param>
34 <when value="built-in">
35 <param name="ref" type="select" label="Select a reference genome">
36 <options from_file="igv_indices.loc">
37 <column name="dbkey" index="0" />
38 <column name="name" index="1" />
39 <column name="value" index="2" />
40 <filter type="sort_by" column="1" />
41 <validator type="no_options" message="No indexes are available" />
42 </options>
43 </param>
44 </when>
45 <when value="history">
46 <param name="ref" type="data" format="igv.genome" metadata_name="dbkey" label="Select a reference from history" />
47 </when>
48 </conditional>
49 <param name="input" type="data" format="sam,bam,bed,psl" label="Input file" help="The input BAM,SAM,BED,PSL feature file"/>
50 <param name="zoom" type="integer" value="7" optional="true" label="-z maximum zoom level to precompute"
51 help="The default value is 7 and is sufficient for most files. To reduce file
52 size at the expense of IGV performance this value can be reduced." />
53 <param name="window" type="integer" value="25" optional="true" label="-w Window size"
54 help="The window size over which coverage is averaged. Defaults to 25 bp." />
55 <param name="extend" type="integer" value="" optional="true" label="Extend feature length"
56 help="The read or feature is extended by the specified distance in bp prior to counting.
57 This option is useful for chip-seq and rna-seq applications. The value is generally set to the
58 average fragment length of the library." />
59 <param name="window_functions" type="select" display="checkboxes" multiple="True" label="-f Functions to calculate over windows"
60 help="If none are selected, will default to mean">
61 <option value="mean" selected="true">mean</option>
62 <option value="min">min</option>
63 <option value="max">max</option>
64 </param>
65 <param name="output_fmt" type="select" display="checkboxes" multiple="True" force_select="true" label="Select output format"
66 help="If none are selected, will default to mean">
67 <option value="output.tdf" selected="true">IGV tdf</option>
68 <option value="output.wig">wig</option>
69 </param>
70 </inputs>
71 <outputs>
72 <data format="igv.tdf" name="output_tdf" metadata_source="input" label="${tool.name} on ${on_string}: igv.tdf" from_work_dir="output.tdf">
73 <filter>('output.tdf' in output_fmt)</filter>
74 </data>
75 <data format="wig" name="output_wig" metadata_source="input" label="${tool.name} on ${on_string}: igv.wig" from_work_dir="output.wig">
76 <filter>('output.wig' in output_fmt)</filter>
77 </data>
78 </outputs>
79 <tests>
80 </tests>
81 <help>
82 **What it does**
83
84 The IGVTools_ count command computes average feature density over a specified window size across the genome. Common usages include computing coverage for alignment files and counting hits in Chip-seq experiments. By default, the resulting file will be displayed as a bar chart when loaded into IGV_.
85
86 .. _IGVTools: http://www.broadinstitute.org/software/igv/igvtools_commandline
87 .. _IGV: http://www.broadinstitute.org/igv/
88
89 ------
90
91 To cite your use of IGV in your publication::
92
93 James T. Robinson, Helga Thorvaldsdottir, Wendy Winckler, Mitchell Guttman, Eric S. Lander, Gad Getz, Jill P. Mesirov.
94 Integrative Genomics Viewer. Nature Biotechnology 29, 24-26 (2011)
95
96 ------
97
98 **Input formats**
99
100 Supported input file formats are: .sam, .bam, .aligned, .psl, .pslx, and .bed.
101
102 ------
103
104 **Outputs**
105
106 The output formats are IGV tiled data file (TDF) file (.tdf) and/or WIG file (.wig)
107
108 -------
109
110
111 **IGVTools count parameter list**
112
113 This is an exhaustive list of igvtools count options:
114
115 For **count**::
116
117 -z Integer Specifies the maximum zoom level to precompute. The default
118 value is 7 and is sufficient for most files. To reduce file
119 size at the expense of IGV performance this value can be
120 reduced.
121
122 -w Integer The window size over which coverage is averaged. Defaults to 25 bp.
123
124 -e Integer The read or feature is extended by the specified distance
125 in bp prior to counting. This option is useful for chip-seq
126 and rna-seq applications. The value is generally set to the
127 average fragment length of the library.
128
129 -f list A comma delimited list specifying window functions to use
130 when reducing the data to precomputed tiles. Possible
131 values are min, max, and mean. By default only the mean
132 is calculated.
133
134
135
136 </help>
137 </tool>