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1 <tool id="Extract genomic DNA 1" name="Extract Genomic DNA" version="3.0.0">
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2 <description>using coordinates from assembled/unassembled genomes</description>
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1
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3 <requirements>
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4 <requirement type="package" version="35x1">faToTwoBit</requirement>
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5 </requirements>
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0
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6 <command>
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7 <![CDATA[
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2
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8 #set input_format = $input.ext
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1
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9 #set genome = $input.metadata.dbkey
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10 #set datatype = $input.datatype
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11 mkdir -p output_dir &&
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12 python $__tool_directory__/extract_genomic_dna.py
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13 --input_format $input_format
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14 --input "$input"
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1
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15 --genome "$genome"
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16 #if str($input_format) == "gff":
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1
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17 --interpret_features $interpret_features
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0
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18 #end if
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19 #if isinstance($datatype, $__app__.datatypes_registry.get_datatype_by_extension('gff').__class__):
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20 --columns "1,4,5,7"
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21 #else:
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22 --columns "${input.metadata.chromCol},${input.metadata.startCol},${input.metadata.endCol},${input.metadata.strandCol},${input.metadata.nameCol}"
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23 #end if
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24 --reference_genome_source $reference_genome_cond.reference_genome_source
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25 #if str($reference_genome_cond.reference_genome_source) == "cached"
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26 --reference_genome $reference_genome_cond.reference_genome.fields.path
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27 #else:
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28 --reference_genome $reference_genome_cond.reference_genome
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29 #end if
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30 --output_format $output_format
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31 --output $output
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32 ]]>
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33 </command>
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34 <inputs>
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1
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35 <param name="input" type="data" format="gff,interval" label="Fetch sequences for intervals in" help="Supported formats are gff, interval">
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36 <validator type="unspecified_build" />
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37 </param>
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38 <param name="interpret_features" type="select" label="Interpret features when possible" help="Applicable only when input dataset format is gff">
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39 <option value="yes">Yes</option>
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40 <option value="no">No</option>
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41 </param>
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0
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42 <conditional name="reference_genome_cond">
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43 <param name="reference_genome_source" type="select" label="Choose the source for the reference genome">
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44 <option value="cached">locally cached</option>
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45 <option value="history">from history</option>
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46 </param>
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47 <when value="cached">
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48 <param name="reference_genome" type="select" label="Using reference genome">
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1
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49 <options from_data_table="twobit">
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50 <filter type="data_meta" key="dbkey" ref="input" column="0"/>
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0
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51 </options>
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52 <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file"/>
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53 </param>
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54 </when>
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55 <when value="history">
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56 <param name="reference_genome" type="data" format="fasta" label="Using reference genome">
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57 <options>
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1
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58 <filter type="data_meta" key="dbkey" ref="input"/>
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0
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59 </options>
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60 <validator type="no_options" message="The current history does not include a fasta dataset with the build associated with the selected input file"/>
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61 </param>
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62 </when>
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63 </conditional>
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64 <param name="output_format" type="select" label="Select output format">
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65 <option value="fasta" selected="True">fasta</option>
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66 <option value="interval">interval</option>
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67 </param>
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68 </inputs>
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69 <outputs>
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70 <data name="output" format="gff">
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71 <change_format>
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72 <when output_format="interval" format="interval" />
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73 </change_format>
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74 </data>
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75 </outputs>
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76 <tests>
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77 <test>
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78 <param name="input" value="1.bed" dbkey="hg17" ftype="bed" />
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79 <param name="interpret_features" value="yes"/>
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80 <param name="index_source" value="cached"/>
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81 <param name="out_format" value="fasta"/>
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82 <output name="out_file1">
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83 <assert_contents>
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84 <!-- First few lines... -->
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85 <has_text text=">hg17_chr1_147962192_147962580_- CCDS989.1_cds_0_0_chr1_147962193_r" />
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86 <has_text text="ACTTGATCCTGCTCCCTCGGTGTCTGCATTGACTCCTCATGCTGGGACTG" />
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87 <has_text text="GACCCGTCAACCCCCCTGCTCGCTGCTCACGTACCTTCATCACTTTTAGT" />
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88 <has_text text="GATGATGCAACTTTCGAGGAATGGTTCCCCCAAGGGCGGCCCCCAAAAGT" />
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89 <!-- Last few lines... -->
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90 <has_text text="GCTGTGGCACAGAACATGGACTCTGTGTTTAAGGAGCTCTTGGGAAAGAC" />
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91 <has_text text="CTCTGTCCGCCAGGGCCTTGGGCCAGCATCTACCACCTCTCCCAGTCCTG" />
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92 <has_text text="GGCCCCGAAGCCCAAAGGCCCCGCCCAGCAGCCGCCTGGGCAGGAACAAA" />
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93 <has_text text="GGCTTCTCCCGGGGCCCTGGGGCCCCAGCCTCACCCTCAGCTTCCCACCC" />
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94 <has_text text="CCAGGGCCTAGACACGACCCCCAAGCCACACTGA" />
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95 </assert_contents>
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96 </output>
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97 </test>
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98 <test>
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99 <param name="input" value="droPer1.bed" dbkey="droPer1" ftype="bed" />
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100 <param name="interpret_features" value="yes"/>
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101 <param name="index_source" value="cached"/>
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102 <param name="out_format" value="fasta"/>
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103 <output name="out_file1" file="extract_genomic_dna_out2.fasta" />
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104 </test>
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105 <test>
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106 <param name="input" value="1.bed" dbkey="hg17" ftype="bed" />
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107 <param name="interpret_features" value="yes"/>
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108 <param name="index_source" value="cached"/>
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109 <param name="out_format" value="interval"/>
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110 <output name="out_file1" file="extract_genomic_dna_out3.interval" />
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111 </test>
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112 <!-- Test GFF file support. -->
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113 <test>
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114 <param name="input" value="gff_filter_by_attribute_out1.gff" dbkey="mm9" ftype="gff" />
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115 <param name="interpret_features" value="no"/>
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116 <param name="index_source" value="cached"/>
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117 <param name="out_format" value="interval"/>
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118 <output name="out_file1" file="extract_genomic_dna_out4.gff" />
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119 </test>
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120 <test>
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121 <param name="input" value="gff_filter_by_attribute_out1.gff" dbkey="mm9" ftype="gff" />
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122 <param name="interpret_features" value="no"/>
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123 <param name="out_format" value="fasta"/>
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124 <param name="index_source" value="cached"/>
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125 <output name="out_file1" file="extract_genomic_dna_out5.fasta" />
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126 </test>
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127 <!-- Test custom sequences support and GFF feature interpretation. -->
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128 <test>
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129 <param name="input" value="cufflinks_out1.gtf" dbkey="mm9" ftype="gff" />
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130 <param name="interpret_features" value="no"/>
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131 <param name="index_source" value="history"/>
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132 <param name="ref_file" value="tophat_in1.fasta"/>
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133 <param name="out_format" value="fasta"/>
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134 <output name="out_file1" file="extract_genomic_dna_out6.fasta" />
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135 </test>
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136 <test>
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137 <param name="input" value="cufflinks_out1.gtf" dbkey="mm9" ftype="gff" />
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138 <param name="interpret_features" value="yes"/>
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139 <param name="index_source" value="history"/>
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140 <param name="ref_file" value="tophat_in1.fasta"/>
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141 <param name="out_format" value="fasta"/>
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142 <output name="out_file1" file="extract_genomic_dna_out7.fasta" />
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143 </test>
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144 </tests>
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145 <help>
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146
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147 .. class:: warningmark
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148
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149 The following will cause a line from the input dataset to be skipped and a warning generated.
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150
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151 - Sequences that fall outside of the range of a line's start and end coordinates.
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152 - Chromosome start or end coordinates that are invalid for the specified build.
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153
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154 -----
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155
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156 **What it does**
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157
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158 This tool uses coordinate, strand, and build information to fetch genomic DNA from gff data, producing fasta data.
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159
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160 -----
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161
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162 **Example**
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163
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164 If the input dataset is::
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165
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166 chr7 127475281 127475310 NM_000230 0 +
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167 chr7 127485994 127486166 NM_000230 0 +
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168 chr7 127486011 127486166 D49487 0 +
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169
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170 Extracting sequences returns::
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171
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172 >hg17_chr7_127475281_127475310_+ NM_000230
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173 GTAGGAATCGCAGCGCCAGCGGTTGCAAG
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174 >hg17_chr7_127485994_127486166_+ NM_000230
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175 GCCCAAGAAGCCCATCCTGGGAAGGAAAATGCATTGGGGAACCCTGTGCG
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176 GATTCTTGTGGCTTTGGCCCTATCTTTTCTATGTCCAAGCTGTGCCCATC
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177 CAAAAAGTCCAAGATGACACCAAAACCCTCATCAAGACAATTGTCACCAG
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178 GATCAATGACATTTCACACACG
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179 >hg17_chr7_127486011_127486166_+ D49487
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180 TGGGAAGGAAAATGCATTGGGGAACCCTGTGCGGATTCTTGTGGCTTTGG
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181 CCCTATCTTTTCTATGTCCAAGCTGTGCCCATCCAAAAAGTCCAAGATGA
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182 CACCAAAACCCTCATCAAGACAATTGTCACCAGGATCAATGACATTTCAC
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183 ACACG
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184
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185 </help>
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186 <citations>
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187 <citation type="bibtex">
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188 @unpublished{None,
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189 author = {},
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190 title = {None},
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191 year = {None},
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192 eprint = {None},
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193 url = {http://www.bx.psu.edu/~anton/labSite/}
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194 }</citation>
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195 </citations>
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196 </tool>
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