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1 <tool id="igvtools_tile" name="IGVtools tile" version="1.0">
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2 <description>convert a sorted data input file to a binary tiled data (.tdf) file</description>
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3 <command interpreter="bash">igvtools tile
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4 #if $zoom.__str__ != '':
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5 -z $zoom
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6 #end if
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7 #if $window_functions.__str__ != '':
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8 -f '$window_functions'
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9 #end if
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10 #if $probe.__str__ != '':
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11 -p '$probe'
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12 #end if
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13 ## IGVTools relies on the file extension to determine format
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14 #if $input.datatype.file_ext == 'wig':
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15 #set $input_name='input_file.wig'
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16 #elif $input.datatype.file_ext == 'igv.snp':
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17 #set $input_name='input_file.snp'
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18 #elif $input.datatype.file_ext == 'igv.gct':
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19 #set $input_name='input_file.gct'
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20 #elif $input.datatype.file_ext == 'igv.cn':
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21 #set $input_name='input_file.cn'
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22 #elif $input.datatype.file_ext == 'igv':
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23 #set $input_name='input_file.igv'
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24 #end if
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25 `ln -s $input $input_name; echo $input_name` $output_tdf $refGenomeSource.ref
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26 </command>
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27 <inputs>
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28 <conditional name="refGenomeSource">
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29 <param name="refGenomeSource_type" type="select" label="Will you select a reference genome from your history or use a built-in reference?">
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30 <option value="built-in">Use a built-in reference</option>
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31 <option value="history">Use one from the history</option>
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32 </param>
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33 <when value="built-in">
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34 <param name="ref" type="select" label="Select a reference genome">
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35 <options from_file="igv_indices.loc">
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36 <column name="dbkey" index="0" />
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37 <column name="name" index="1" />
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38 <column name="value" index="2" />
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39 <filter type="sort_by" column="1" />
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40 <validator type="no_options" message="No indexes are available" />
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41 </options>
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42 </param>
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43 </when>
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44 <when value="history">
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45 <param name="ref" type="data" format="igv.genome" metadata_name="dbkey" label="Select a reference from history" />
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46 </when>
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47 </conditional>
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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"/>
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49 <param name="zoom" type="integer" value="7" optional="true" label="-z maximum zoom level to precompute"
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50 help="The default value is 7 and is sufficient for most files. To reduce file
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51 size at the expense of IGV performance this value can be reduced." />
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52 <param name="window_functions" type="select" display="checkboxes" multiple="True" label="-f Functions to calculate over windows"
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53 help="If none are selected, will default to mean">
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54 <option value="mean" selected="true">mean</option>
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55 <option value="min">min</option>
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56 <option value="max">max</option>
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57 </param>
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58 <param name="probe" type="data" format="bed" optional="true" label="Probe file for GCT input"
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59 help="Specifies a bed file to be used to map probe identifiers to locations.
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60 This option is useful when preprocessing .gct files.
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61 The bed file should contain 4 columns:
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62 chr start end name
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63 where name is the probe name in the .gct file."/>
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64 </inputs>
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65 <outputs>
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66 <data format="igv.tdf" name="output_tdf" metadata_source="input" label="${tool.name} on ${on_string}: igv.tdf" from_work_dir="output.tdf"/>
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67 </outputs>
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68 <tests>
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69 </tests>
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70 <help>
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71 **What it does**
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72
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73 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.
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74
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75 .. _IGVTools: http://www.broadinstitute.org/software/igv/igvtools_commandline
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76 .. _IGV: http://www.broadinstitute.org/igv/
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77
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78 ------
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79
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80 To cite your use of IGV in your publication::
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81
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82 James T. Robinson, Helga Thorvaldsdottir, Wendy Winckler, Mitchell Guttman, Eric S. Lander, Gad Getz, Jill P. Mesirov.
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83 Integrative Genomics Viewer. Nature Biotechnology 29, 24-26 (2011)
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84
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85 ------
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86
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87 **Input formats**
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88
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89 Supported input file formats are: .wig, .cn, .snp, .igv, and .gct.
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90
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91 ------
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92
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93 **Outputs**
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94
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95 The output format is IGV tiled data file (TDF) file (.tdf)
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96
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97 -------
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98
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99
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100 **IGVTools count parameter list**
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101
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102 This is an exhaustive list of igvtools count options:
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103
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104 For **count**::
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105
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106 -z Integer Specifies the maximum zoom level to precompute. The default
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107 value is 7 and is sufficient for most files. To reduce file
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108 size at the expense of IGV performance this value can be
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109 reduced.
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110
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111 -p file Specifies a "bed" file to be used to map probe identifiers
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112 to locations. This option is useful when preprocessing . gct
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113 files. The bed file should contain 4 columns:
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114 chr start end name
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115 where name is the probe name in the .gct file.
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116
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117 -f list A comma delimited list specifying window functions to use
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118 when reducing the data to precomputed tiles. Possible
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119 values are min, max, and mean. By default only the mean
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120 is calculated.
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121
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122
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123
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124 </help>
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125 </tool>
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