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