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