Mercurial > repos > jjohnson > igvtools
annotate igvtools_tile.xml @ 1:ae2bc4e5fefc draft default tip
Fix igvtools_tile.xml tdf output and add log file output
| author | Jim Johnson <jj@umn.edu> |
|---|---|
| date | Tue, 27 Nov 2012 16:32:10 -0600 |
| parents | 2eb1e2924c1a |
| children |
| rev | line source |
|---|---|
|
1
ae2bc4e5fefc
Fix igvtools_tile.xml tdf output and add log file output
Jim Johnson <jj@umn.edu>
parents:
0
diff
changeset
|
1 <tool id="igvtools_tile" name="IGVtools tile" version="1.1"> |
| 0 | 2 <description>convert a sorted data input file to a binary tiled data (.tdf) file</description> |
| 3 <command interpreter="bash">igvtools tile | |
| 4 #if $zoom.__str__ != '': | |
| 5 -z $zoom | |
| 6 #end if | |
| 7 #if $window_functions.__str__ != '': | |
| 8 -f '$window_functions' | |
| 9 #end if | |
| 10 #if $probe.__str__ != '': | |
| 11 -p '$probe' | |
| 12 #end if | |
| 13 ## IGVTools relies on the file extension to determine format | |
| 14 #if $input.datatype.file_ext == 'wig': | |
| 15 #set $input_name='input_file.wig' | |
| 16 #elif $input.datatype.file_ext == 'igv.snp': | |
| 17 #set $input_name='input_file.snp' | |
| 18 #elif $input.datatype.file_ext == 'igv.gct': | |
| 19 #set $input_name='input_file.gct' | |
| 20 #elif $input.datatype.file_ext == 'igv.cn': | |
| 21 #set $input_name='input_file.cn' | |
| 22 #elif $input.datatype.file_ext == 'igv': | |
| 23 #set $input_name='input_file.igv' | |
| 24 #end if | |
|
1
ae2bc4e5fefc
Fix igvtools_tile.xml tdf output and add log file output
Jim Johnson <jj@umn.edu>
parents:
0
diff
changeset
|
25 `ln -s $input $input_name; echo $input_name` output.tdf $refGenomeSource.ref 1> igv.stdout |
| 0 | 26 </command> |
| 27 <inputs> | |
| 28 <conditional name="refGenomeSource"> | |
| 29 <param name="refGenomeSource_type" type="select" label="Will you select a reference genome from your history or use a built-in reference?"> | |
| 30 <option value="built-in">Use a built-in reference</option> | |
| 31 <option value="history">Use one from the history</option> | |
| 32 </param> | |
| 33 <when value="built-in"> | |
| 34 <param name="ref" type="select" label="Select a reference genome"> | |
| 35 <options from_file="igv_indices.loc"> | |
| 36 <column name="dbkey" index="0" /> | |
| 37 <column name="name" index="1" /> | |
| 38 <column name="value" index="2" /> | |
| 39 <filter type="sort_by" column="1" /> | |
| 40 <validator type="no_options" message="No indexes are available" /> | |
| 41 </options> | |
| 42 </param> | |
| 43 </when> | |
| 44 <when value="history"> | |
| 45 <param name="ref" type="data" format="igv.genome" metadata_name="dbkey" label="Select a reference from history" /> | |
| 46 </when> | |
| 47 </conditional> | |
| 48 <param name="input" type="data" format="wig,igv,igv.cn,igv.snp,igv.gct" label="Input file" help="The input WIG,CN,IGV,GCT,SNP feature file"/> | |
| 49 <param name="zoom" type="integer" value="7" optional="true" label="-z maximum zoom level to precompute" | |
| 50 help="The default value is 7 and is sufficient for most files. To reduce file | |
| 51 size at the expense of IGV performance this value can be reduced." /> | |
| 52 <param name="window_functions" type="select" display="checkboxes" multiple="True" label="-f Functions to calculate over windows" | |
| 53 help="If none are selected, will default to mean"> | |
| 54 <option value="mean" selected="true">mean</option> | |
| 55 <option value="min">min</option> | |
| 56 <option value="max">max</option> | |
| 57 </param> | |
| 58 <param name="probe" type="data" format="bed" optional="true" label="Probe file for GCT input" | |
| 59 help="Specifies a bed file to be used to map probe identifiers to locations. | |
| 60 This option is useful when preprocessing .gct files. | |
| 61 The bed file should contain 4 columns: | |
| 62 chr start end name | |
| 63 where name is the probe name in the .gct file."/> | |
| 64 </inputs> | |
| 65 <outputs> | |
| 66 <data format="igv.tdf" name="output_tdf" metadata_source="input" label="${tool.name} on ${on_string}: igv.tdf" from_work_dir="output.tdf"/> | |
|
1
ae2bc4e5fefc
Fix igvtools_tile.xml tdf output and add log file output
Jim Johnson <jj@umn.edu>
parents:
0
diff
changeset
|
67 <data format="txt" name="logfile" metadata_source="input" label="${tool.name} on ${on_string}: igv.log" from_work_dir="igv.stdout"/> |
| 0 | 68 </outputs> |
| 69 <tests> | |
| 70 </tests> | |
| 71 <help> | |
| 72 **What it does** | |
| 73 | |
| 74 The IGVTools_ tile command converts a sorted data input file to a binary tiled data (.tdf) file. Use this command to pre-process large datasets for improved IGV performance. | |
| 75 | |
| 76 .. _IGVTools: http://www.broadinstitute.org/software/igv/igvtools_commandline | |
| 77 .. _IGV: http://www.broadinstitute.org/igv/ | |
| 78 | |
| 79 ------ | |
| 80 | |
| 81 To cite your use of IGV in your publication:: | |
| 82 | |
| 83 James T. Robinson, Helga Thorvaldsdottir, Wendy Winckler, Mitchell Guttman, Eric S. Lander, Gad Getz, Jill P. Mesirov. | |
| 84 Integrative Genomics Viewer. Nature Biotechnology 29, 24-26 (2011) | |
| 85 | |
| 86 ------ | |
| 87 | |
| 88 **Input formats** | |
| 89 | |
| 90 Supported input file formats are: .wig, .cn, .snp, .igv, and .gct. | |
| 91 | |
| 92 ------ | |
| 93 | |
| 94 **Outputs** | |
| 95 | |
| 96 The output format is IGV tiled data file (TDF) file (.tdf) | |
| 97 | |
| 98 ------- | |
| 99 | |
| 100 | |
| 101 **IGVTools count parameter list** | |
| 102 | |
| 103 This is an exhaustive list of igvtools count options: | |
| 104 | |
| 105 For **count**:: | |
| 106 | |
| 107 -z Integer Specifies the maximum zoom level to precompute. The default | |
| 108 value is 7 and is sufficient for most files. To reduce file | |
| 109 size at the expense of IGV performance this value can be | |
| 110 reduced. | |
| 111 | |
| 112 -p file Specifies a "bed" file to be used to map probe identifiers | |
| 113 to locations. This option is useful when preprocessing . gct | |
| 114 files. The bed file should contain 4 columns: | |
| 115 chr start end name | |
| 116 where name is the probe name in the .gct file. | |
| 117 | |
| 118 -f list A comma delimited list specifying window functions to use | |
| 119 when reducing the data to precomputed tiles. Possible | |
| 120 values are min, max, and mean. By default only the mean | |
| 121 is calculated. | |
| 122 | |
| 123 | |
| 124 | |
| 125 </help> | |
| 126 </tool> |