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1 <?xml version="1.0" encoding="utf-8"?>
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2 <tool id ="pyPileup" name="pyPileup">
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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="python">
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7 /usr/local/bin/pyPileup.py
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8 -f $ftype.input
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9 --file_type $ftype.file_type
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10 #if $geneOpt.alignGene == "gene":
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11 -g $geneOpt.genes
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12 #end if#
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13 #if $geneOpt.alignGene == "chr":
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14 --chr $geneOpt.chr
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15 #end if#
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16 #if ($ftype.file_type == "novo" or $ftype.file_type == "sam") and $ftype.disc.discard == "discard":
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17 --discarded $discarded
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18 #end if#
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19 --gtf=$addGTF.gtf
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20 --tab=$addTab.tab
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21 #if ($ftype.file_type == "novo" or $ftype.file_type == "sam") and $ftype.addAlignOpt.alignoptions == "edit":
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22 --align_quality=$ftype.addAlignOpt.align_quality
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23 --align_score=$ftype.addAlignOpt.align_score
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24 --distance=$ftype.addAlignOpt.d
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25 --length=$ftype.addAlignOpt.length
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26 #if int($ftype.addAlignOpt.max) > 0:
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27 --max=$ftype.addAlignOpt.max
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28 #end if#
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29 $ftype.addAlignOpt.unique
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30 $ftype.addAlignOpt.blocks
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31 $ftype.addAlignOpt.mutations
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32 #if $ftype.disc.discard == "--discarded":
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33 --discarded $discarded
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34 #end if#
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35 #end if#
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36 #if $addOpt.options == "edit":
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37 --range=$addOpt.range
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38 --overlap=$addOpt.overlap
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39 $addOpt.iclip
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40 $addOpt.ignore
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41 -s $addOpt.sequence
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42 #if int($addOpt.limit) > 0:
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43 --limit=$addOpt.limit
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44 #end if#
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45 #end if#
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46 -o $output
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47 </command>
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48 <version_command>/usr/local/bin/pyPileup.py --version</version_command>
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49 <inputs>
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50
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51
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52 <conditional name="geneOpt">
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53 <param name="alignGene" type="select" label="Do you want to align reads to genes or chromosome co-ordinates?">
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54 <option value="gene" selected="true">Genes</option>
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55 <option value="chr">Chromosome Co-ordinates</option>
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56 </param>
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57 <when value="chr">
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58 <param format="interval" name="chr" type="data" label="Choose a Chromosome Coordinate File" help="Tab delimited text file containing an identifier, chromosome name, start position, end position and strand ('-' or '+')"/>
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59 </when>
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60 <when value="gene">
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61 <param format="txt" name="genes" type="data" label="Choose a Gene List -g" help="Single column gene ID file"/>
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62 </when>
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63 </conditional>
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64 <conditional name="addGTF">
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65 <param name="gtfFile" type="select" label="Choose GTF File from">
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66 <option value="default" selected="true">Defaults</option>
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67 <option value="other">History</option>
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68 </param>
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69 <when value="default">
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70 <param name="gtf" type="select" label="GTF File --gtf" help="GTF file containing gene ID co-ordinates">
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71 <options from_data_table="pycrac_gtf"/>
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72 </param>
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73 </when>
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74 <when value="other">
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75 <param format="GTF" name="gtf" type="data" label="GTF File --gtf" help="GTF file containing gene ID co-ordinates"/>
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76 </when>
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77 </conditional>
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78 <conditional name="addTab">
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79 <param name="tabFile" type="select" label="Choose Genomic Reference Sequence from">
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80 <option value="default" selected="true">Defaults</option>
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81 <option value="other">History</option>
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82 </param>
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83 <when value="default">
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84 <param name="tab" type="select" label="Genomic Reference Sequence --tab" help="Tab file containing genomic reference sequence">
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85 <options from_data_table="pycrac_tab"/>
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86 </param>
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87 </when>
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88 <when value="other">
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89 <param format="tabular" name="tab" type="data" label="Genomic Reference Sequence --tab" help="Tab file containing genomic reference sequence"/>
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90 </when>
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91 </conditional>
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92
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93
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94 <conditional name="ftype">
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95 <param name="file_type" type="select" label="Input File Type --file_type">
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96 <option value="novo" selected="true">Novo</option>
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97 <option value="sam">Sam/BAM</option>
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98 <option value="gtf">GTF</option>
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99 </param>
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100 <when value="sam">
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101 <param format="sam,bam" name="input" type="data" label="Input File -f" help="Alignment file of type .sam or .bam" />
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102 <conditional name="disc">
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103 <param name="discard" type="select" label="Print discarded reads to a separate file">
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104 <option value="" selected="true">OFF</option>
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105 <option value="discard">ON</option>
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106 </param>
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107 <when value="discard">
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108 </when>
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109 <when value="">
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110 </when>
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111 </conditional>
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112 <conditional name="addAlignOpt">
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113 <param name="alignoptions" type="select" label="Alignment Options">
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114 <option value="default" selected="true">Default</option>
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115 <option value="edit">Edit</option>
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116 </param>
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117 <when value="edit">
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118 <param name="mutations" type="select" label="Filter reads by mutations --mutations" help="cross-linking sites are often highlighted by deletions and/or substitutions in the reads. You can use this option to filter reads based on whether they have mutations or not.">
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119 <option value="" selected="true">Off</option>
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120 <option value="--mutations=delsonly">deletions</option>
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121 <option value="--mutations=subsonly">substitutions</option>
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122 <option value="--mutations=TC">T->C mutations</option>
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123 <option value="--mutations=allmuts">all mutations</option>
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124 <option value="--mutations=nomuts">no mutations</option>
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125 </param>
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126 <param format="integer" name="align_quality" type="integer" label="Align Quality --align_quality " value="0" size="5" >
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127 <validator type="in_range" min="0" message="Please enter a value >= 0"/>
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128 </param>
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129 <param format="integer" name="align_score" type="integer" label="Align Score --align_score " value="0" size="5" >
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130 <validator type="in_range" min="0" message="Please enter a value >= 0"/>
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131 </param>
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132 <param format="integer" name="max" type="integer" label="Mapped reads to read from input file --max" help="Set to 0 to align all reads." value="0" size="10" >
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133 <validator type="in_range" min="0" max="100000000" message="Please enter a value between 1 and 100000000 or 0 to align all reads"/>
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134 </param>
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135 <param format="integer" name="d" type="integer" label="Distance --distance " value="1000" size="6" help="Set the maximum number of bp allowed between two non-overlapping paired reads">
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136 <validator type="in_range" min="1" message="Please enter a value >= 0"/>
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137 </param>
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138 <param format="integer" name="length" type="integer" label="Set the maximum length of reads --length" value="1000" size="7" help="Set the read length threshold between 15 and 1000">
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139 <validator type="in_range" min="15" max="1000" message="Please enter a value between 15 and 1000"/>
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140 </param>
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141 <param name="unique" type="select" label="Remove reads with multiple alignment locations --unique">
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142 <option value="" selected="true">OFF</option>
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143 <option value="--unique">ON</option>
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144 </param>
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145 <param name="blocks" type="select" label="Only count reads with same start and end coords once --blocks">
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146 <option value="" selected="true">OFF</option>
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147 <option value="--blocks">ON</option>
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148 </param>
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149 </when>
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150 <when value="default">
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151 </when>
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152 </conditional>
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153 </when>
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154 <when value="novo">
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155 <param format="tabular" name="input" type="data" label="Input File -f" help="Alignment file of type .novo" />
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156 <conditional name="disc">
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157 <param name="discard" type="select" label="Print discarded reads to a separate file">
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158 <option value="" selected="true">OFF</option>
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159 <option value="discard">ON</option>
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160 </param>
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161 <when value="discard">
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162 </when>
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163 <when value="">
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164 </when>
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165 </conditional>
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166 <conditional name="addAlignOpt">
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167 <param name="alignoptions" type="select" label="Alignment Options">
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168 <option value="default" selected="true">Default</option>
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169 <option value="edit">Edit</option>
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170 </param>
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171 <when value="edit">
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172 <param name="mutations" type="select" label="Filter reads by mutations --mutations" help="cross-linking sites are often
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173 highlighted by deletions and/or substitutions in the reads. You can use this option to filter reads based on whether they have mutations or not.">
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174 <option value="" selected="true">Off</option>
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175 <option value="--mutations=delsonly">deletions</option>
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176 <option value="--mutations=subsonly">substitutions</option>
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177 <option value="--mutations=TC">T->C mutations</option>
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178 <option value="--mutations=allmuts">all mutations</option>
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179 <option value="--mutations=nomuts">no mutations</option>
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180 </param>
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181 <param format="integer" name="align_quality" type="integer" label="Align Quality --align_quality " value="0" size="5" >
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182 <validator type="in_range" min="0" message="Please enter a value >= 0"/>
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183 </param>
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184 <param format="integer" name="align_score" type="integer" label="Align Score --align_score " value="0" size="5" >
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185 <validator type="in_range" min="0" message="Please enter a value >= 0"/>
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186 </param>
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187 <param format="integer" name="max" type="integer" label="Mapped reads to read from input file --max" help="Set to 0 to align all reads." value="0" size="10" >
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188 <validator type="in_range" min="0" max="100000000" message="Please enter a value between 1 and 100000000 or 0 to align all reads"/>
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189 </param>
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190 <param format="integer" name="d" type="integer" label="Distance --distance " value="1000" size="6" help="Set the maximum number of bp allowed between two non-overlapping paired reads">
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191 <validator type="in_range" min="1" message="Please enter a value >= 0"/>
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192 </param>
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193 <param format="integer" name="length" type="integer" label="Set the maximum length of reads --length" value="1000" size="7" help="Set the read length threshold between 15 and 1000">
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194 <validator type="in_range" min="15" max="1000" message="Please enter a value between 15 and 1000"/>
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195 </param>
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196 <param name="unique" type="select" label="Remove reads with multiple alignment locations --unique">
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197 <option value="" selected="true">OFF</option>
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198 <option value="--unique">ON</option>
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199 </param>
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200 <param name="blocks" type="select" label="Only count reads with same start and end coords once --blocks">
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201 <option value="" selected="true">OFF</option>
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202 <option value="--blocks">ON</option>
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203 </param>
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204 </when>
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205 <when value="default">
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206 </when>
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207 </conditional>
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208 </when>
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209 <when value="gtf">
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210 <param format="gtf" name="input" type="data" label="Input File -f" help="File of type .gtf" />
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211 </when>
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212 </conditional>
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213
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214 <conditional name="addOpt">
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215 <param name="options" type="select" label="Standard Options">
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216 <option value="default" selected="true">Default</option>
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217 <option value="edit">Edit</option>
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218 </param>
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219 <when value="edit">
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220 <param format="integer" name="range" type="integer" label="Range --range" value="0" size="5" help="Manually set the length of the 5' and 3' UTRs 0>50000">
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221 <validator type="in_range" min="0" max="50000" message="Please enter a value between 0 and 50000"/>
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222 </param>
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223 <param name="ignore" type="select" label="Ignore strand information? --ignorestrand">
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224 <option value="" selected="true">No</option>
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225 <option value="--ignorestrand">Yes</option>
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226 </param>
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227 <param format="integer" name="overlap" type="integer" label="Overlap --overlap" value="1" size="5" help="Sets the number of nucleotides a read has to overlap with a gene before it is considered a hit. ">
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228 <validator type="in_range" min="1" message="Please enter a positive integer"/>
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229 </param>
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230 <param name="sequence" type="select" label="Align reads to --sequence">
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231 <option value="genomic" selected="true">Genomic Sequence</option>
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232 <option value="coding">Coding Sequence</option>
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233 </param>
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234 <param name="iclip" type="select" label="iCLIP mode --iCLIP">
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235 <option value="" selected="true">OFF</option>
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236 <option value="--iCLIP">ON</option>
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237 </param>
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238 <param format="integer" name="limit" type="integer" label="Limit number of reads to count that map to a particular region --limit" value="0" size="15" help="Set to 0 for unlimited reads" >
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239 <validator type="in_range" min="0" message="Please enter a value greater than 1 or set to 0 for unlimited reads"/>
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240 </param>
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241 </when>
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242 <when value="default">
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243 </when>
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244 </conditional>
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245 <param name="label" type="text" format="txt" size="30" value="pyPileup" label="Enter output file label -o" />
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246 </inputs>
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247 <outputs>
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248 <data format="tabular" name="output" label="${label.value}.pileup"/>
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249 <data format="txt" name="discarded" label="${label.value}_discarded.txt">
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250 <filter>(ftype['file_type'] == "novo" or ftype['file_type'] == "sam") and ftype['disc']['discard'] == "discard"</filter>
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251 </data>
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252 </outputs>
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253 <help>
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254
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255
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256 .. class:: infomark
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257
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258 **pyPileup**
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259
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260 pyPileup is part of the pyCRAC_ package. Produces pileups containing the number of hits, substitutions and deletions for each nucleotide covered by
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261 reads in specific genes or genomic regions
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262
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263 .. _pyCRAC: http://sandergranneman.bio.ed.ac.uk/Granneman_Lab/pyCRAC_software.html
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264
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265 ------
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266
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267 **Parameter list**
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268
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269 File input options::
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270
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271 -f FILE, --input_file=FILE
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272 As input files you can use Novoalign native output,
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273 SAM, pyMotif or pyReadCounters GTF files as input
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274 file. By default it expects data from the standard
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275 input. Make sure to specify the file type of the file
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276 you want to have analyzed using the --file_type
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277 option!
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278 -o OUTPUT_FILE, --output_file=OUTPUT_FILE
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279 Use this flag to override the standard output file
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280 names. All pileups will be written to one output file.
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281 -g FILE, --genes_file=FILE
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282 here you need to type in the name of your gene list
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283 file (1 column) or the hittable file
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284 --chr=FILE
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285 if you simply would like to align reads against a
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286 genomic sequence you should generate a tab delimited
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287 file containing an identifyer, chromosome name, start
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288 position, end position and strand
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289 --gtf=annotation_file.gtf
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290 type the path to the gtf annotation file that you want
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291 to use
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292 --tab=tab_file.tab
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293 type the path to the tab file that contains the
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294 genomic reference sequence
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295 --file_type=FILE_TYPE
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296 use this option to specify the file type (i.e. 'novo',
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297 'sam', 'gtf'). This will tell the program which
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298 parsers to use for processing the files. Default =
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299 'novo'
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300
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301 pyPileup specific options::
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302
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303 --limit=500
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304 with this option you can select how many reads mapped
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305 to a particular gene/ORF/region you want to count.
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306 Default = All
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307 --iCLIP
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308 This turns on the iCLIP mode and the pileups will
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309 report cross-linking site frequencies in iCLIP data in
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310 reference sequences
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311
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312 Common options::
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313
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314 -v, --verbose
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315 prints all the status messages to a file rather than
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316 the standard output
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317 --ignorestrand
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318 this flag tells the program to ignore strand
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319 information and all overlapping reads will considered
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320 sense reads. Useful for analysing ChIP or RIP data
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321 --zip=FILE
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322 use this option to compress all the output files in a
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323 single zip file
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324 --overlap=1
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325 sets the number of nucleotides a read has to overlap
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326 with a gene before it is considered a hit. Default =
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327 1 nucleotide
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328 -s genomic, --sequence=genomic
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329 with this option you can select whether you want the
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330 reads aligned to the genomic or the coding sequence.
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331 Default = genomic
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332 -r 100, --range=100
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333 allows you to set the length of the UTR regions. If
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334 you set '-r 50' or '--range=50', then the program will
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335 set a fixed length (50 bp) regardless of whether the
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336 GTF file has genes with annotated UTRs.
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337
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338 Options for novo, SAM and BAM files::
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339
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340 --align_quality=100, --mapping_quality=100
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341 with these options you can set the alignment quality
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342 (Novoalign) or mapping quality (SAM) threshold. Reads
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343 with qualities lower than the threshold will be
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344 ignored. Default = 0
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345 --align_score=100
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346 with this option you can set the alignment score
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347 threshold. Reads with alignment scores lower than the
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348 threshold will be ignored. Default = 0
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349 -l 100, --length=100
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350 to set read length threshold. Default = 1000
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351 -m 100000, --max=100000
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352 maximum number of mapped reads that will be analyzed.
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353 Default = All
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354 --unique
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355 with this option reads with multiple alignment
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356 locations will be removed. Default = Off
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357 --blocks
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358 with this option reads with the same start and end
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359 coordinates on a chromosome will only be counted once.
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360 Default = Off
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361 --discarded=FILE
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362 prints the lines from the alignments file that were
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363 discarded by the parsers. This file contains reads
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364 that were unmapped (NM), of poor quality (i.e. QC) or
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365 paired reads that were mapped to different chromosomal
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366 locations or were too far apart on the same
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367 chromosome. Useful for debugging purposes
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368 -d 1000, --distance=1000
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369 this option allows you to set the maximum number of
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370 base-pairs allowed between two non-overlapping paired
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371 reads. Default = 1000
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372 --mutations=delsonly
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373 Use this option to only track mutations that are of
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374 interest. For CRAC data this is usually deletions
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375 (--mutations=delsonly). For PAR-CLIP data this is
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376 usually T-C mutations (--mutations=TC). Other options
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377 are: do not report any mutations: --mutations=nomuts.
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378 Only report specific base mutations, for example only
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379 in T's, C's and G's :--mutations=[TCG]. The brackets
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380 are essential. Other nucleotide combinations are also
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381 possible
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382
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383 </help>
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384 </tool>
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