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1 <tool id="pyGTF2bedGraph" name="pyGTF2bedGraph">
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2 <description>converter</description>
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3 <requirements>
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4 <requirement type="package">pyCRAC</requirement>
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5 </requirements>
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6 <command interpreter="perl">pyGTF2bedGraph.pl --gtf $input --po $po --mo $mo
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7 --chromfile $addchr.chr
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8 -t $type
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9 --count $count
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10 $iclip
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11 #if $addtrack.track == "--track":
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12 --track
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13 --name $addtrack.name
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14 --description $addtrack.description
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15 #if $addtrack.colorscheme.colorsel == "default":
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16 --color $addtrack.colorscheme.color
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17 #else:
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18 -s '$addtrack.colorscheme.plus,$addtrack.colorscheme.minus'
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19 #end if#
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20 #end if#
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21 --id $po.id
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22 </command>
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23 <version_command>/usr/local/bin/pyGTF2bedGraph.py --version</version_command>
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24 <inputs>
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25 <param name="input" type="data" format="gtf" label="GTF file --gtf"/>
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26 <conditional name="addchr">
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27 <param name="chrfile" type="select" label="Choose Chromosome length file from">
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28 <option value="default" selected="true">Defaults</option>
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29 <option value="other">History</option>
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30 </param>
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31 <when value="default">
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32 <param name="chr" type="select" label="Chromosome length file -c" help="This file should have two columns: first column is the names of the chromosomes, second column is length of the chromosomes. Use pyCrac utility pyCalculateChromosomeLengths to create.">
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33 <options from_data_table="pycrac_chr"/>
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34 </param>
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35 </when>
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36 <when value="other">
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37 <param format="tabular" name="chr" type="data" label="Chromosome length file -c" help="This file should have two columns: first column is the names of the chromosomes, second column is length of the chromosomes"/>
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38 </when>
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39 </conditional>
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40 <param name="type" type="select" label="Choose type of data -t">
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41 <option value="reads" selected="true">Reads</option>
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42 <option value="substitutions">Substitutions</option>
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43 <option value="deletions">Deletions</option>
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44 </param>
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45 <param format="integer" name="count" type="integer" label="Count per feature --count " value="1" size="5" help="Takes the numbers in the 'score' column of the GTF file as the total number of reads for each position" >
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46 <validator type="in_range" min="1" message="Please enter a value >= 1"/>
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47 </param>
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48 <param name="iclip" type="select" label="iCLIP mode --iCLIP">
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49 <option value="" selected="true">OFF</option>
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50 <option value="--iCLIP">ON</option>
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51 </param>
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52 <conditional name="addtrack">
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53 <param name="track" type="select" label="Add UCSC track line to output">
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54 <option value="" selected="true">NO</option>
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55 <option value="--track">YES</option>
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56 </param>
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57 <when value=""/>
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58 <when value="--track">
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59 <param name="name" format="txt" type="text" value="User_supplied_track" size="80" label="Track name"/>
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60 <param name="description" format="txt" type="text" value="User_supplied_track" size="80" label="Track description"/>
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61 <conditional name="colorscheme">
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62 <param name="colorsel" type="select" label="Colouring scheme">
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63 <option value="default" selected="true">One Colour</option>
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64 <option value="strand">By Strand</option>
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65 </param>
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66 <when value="default">
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67 <param name="color" type="select" label="Choose track colour">
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68 <option value="black" selected="true">Black</option>
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69 <option value="red">Red</option>
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70 <option value="blue">Blue</option>
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71 <option value="green">Green</option>
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72 <option value="purple">Purple</option>
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73 </param>
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74 </when>
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75 <when value="strand">
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76 <param name="plus" type="select" label="Choose forward strand track colour">
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77 <option value="black" selected="true">Black</option>
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78 <option value="red">Red</option>
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79 <option value="blue">Blue</option>
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80 <option value="green">Green</option>
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81 <option value="purple">Purple</option>
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82 </param>
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83 <param name="minus" type="select" label="Choose minus strand track colour">
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84 <option value="black" selected="true">Black</option>
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85 <option value="red">Red</option>
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86 <option value="blue">Blue</option>
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87 <option value="green">Green</option>
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88 <option value="purple">Purple</option>
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89 </param>
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90 </when>
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91 </conditional>
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92 </when>
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93 </conditional>
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94 <param name="label" type="text" format="txt" size="30" value="pyGTF2bedGraph" label="Enter output file label -o" />
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95 </inputs>
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96 <outputs>
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97 <data name="po" format="bedgraph" label="${label.value}_plus_strand.bg"/>
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98 <data name="mo" format="bedgraph" label="${label.value}_minus_strand.bg"/>
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99 </outputs>
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100 <help>
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101
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102 .. class:: infomark
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103
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104 **pyGTF2bedGraph**
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105
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106 pyGTF2bedGraph is part of the pyCRAC_ package. Generates bedgraph files for each chromosome. An homage to bedtools genomecoverage. Takes a pyReadCounters GTF file as input file. Can also output bedGraph files for substitutions and deletions.
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107
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108 .. _pyCRAC: http://sandergranneman.bio.ed.ac.uk/Granneman_Lab/pyCRAC_software.html
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109
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110 ------
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111
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112 **Parameter list**
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113
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114 File input options::
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115
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116 --gtf=readdata.gtf
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117 type the path to the gtf file data file. Be default it
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118 expects data from the standard input
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119 -o converted
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120 provide a name for an output file. A file extension or
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121 strand information is not necessary.
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122 -c yeast.txt, --chromfile=yeast.txt
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123 Location of the chromosome info file. This file should
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124 have two columns: first column is the names of the
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125 chromosomes, second column is length of the
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126 chromosomes. Default is yeast
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127 -t TYPE, --type=TYPE
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128 this tool can generate bedGraph files for reads,
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129 substitutions or deletions. Please use
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130 'reads','substitutions' or 'deletions' to indicate the
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131 type of data. Default='reads'
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132 --count
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133 Takes the numbers in the 'score' column of the GTF
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134 file as the total number of reads for each position.
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135 Default is 1 for each interval.
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136 --iCLIP
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137 This turns on the iCLIP mode and the sgr reads or cDNA
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138 files will report cross-linking site frequencies in
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139 iCLIP data
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140 -v, --verbose
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141 to print status messages to a log file
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142
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143 These options can be used to add a track line for the UCSC genome browser::
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144
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145 --track
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146 Use this flag to add a UCSC genome browser track line
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147 to the beginning of your file
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148 -n NAME, --name=NAME
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149 For the USCS track line: provide a track name. Default
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150 = 'User_supplied_track'
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151 -d DESCRIPTION, --description=DESCRIPTION
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152 For the USCS track line: provide a track description.
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153 Default = 'User_supplied_track'
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154 --color=COLOR
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155 select the track color. Default = black
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156 -s STRANDS, --colorstrands=STRANDS
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157 select the colors for each strand. Default =
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158 'red,blue'
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159
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160 </help>
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161 </tool>
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162
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