/tools/extract/extract_genomic_dna.xml
XML | 189 lines | 161 code | 24 blank | 4 comment | 0 complexity | b320d4e4bf1691e981095771738afc15 MD5 | raw file
1<tool id="Extract genomic DNA 1" name="Extract Genomic DNA" version="2.2.3"> 2 <description>using coordinates from assembled/unassembled genomes</description> 3 <command interpreter="python"> 4 extract_genomic_dna.py $input $out_file1 -o $out_format -d $dbkey 5 6 #if str( $interpret_features ) == "yes": 7 -I 8 #end if 9 10 ## Columns to use in input file. 11 #if isinstance( $input.datatype, $__app__.datatypes_registry.get_datatype_by_extension('gff').__class__): 12 -1 1,4,5,7 --gff 13 #else: 14 -1 ${input.metadata.chromCol},${input.metadata.startCol},${input.metadata.endCol},${input.metadata.strandCol},${input.metadata.nameCol} 15 #end if 16 17 #if $seq_source.index_source == "cached": 18 ## Genomic data from cache. 19 -g ${GALAXY_DATA_INDEX_DIR} 20 #else: 21 ## Genomic data from history. 22 -F $seq_source.ref_file 23 #end if 24 </command> 25 <inputs> 26 <param format="interval,gff" name="input" type="data" label="Fetch sequences for intervals in"/> 27 <param name="interpret_features" type="select" label="Interpret features when possible" help="Only meaningful for GFF, GTF datasets."> 28 <option value="yes">Yes</option> 29 <option value="no">No</option> 30 </param> 31 <conditional name="seq_source"> 32 <param name="index_source" type="select" label="Source for Genomic Data"> 33 <option value="cached">Locally cached</option> 34 <option value="history">History</option> 35 </param> 36 <when value="cached"> 37 </when> 38 <when value="history"> 39 <param name="ref_file" type="data" format="fasta" label="Using reference file" /> 40 </when> 41 </conditional> 42 <param name="out_format" type="select" label="Output data type"> 43 <option value="fasta">FASTA</option> 44 <option value="interval">Interval</option> 45 </param> 46 </inputs> 47 <outputs> 48 <data format="input" name="out_file1" metadata_source="input"> 49 <change_format> 50 <when input="out_format" value="fasta" format="fasta" /> 51 </change_format> 52 </data> 53 </outputs> 54 <requirements> 55 <requirement type="package">ucsc_tools</requirement> 56 <requirement type="binary">faToTwoBit</requirement> 57 </requirements> 58 <tests> 59 <test> 60 <param name="input" value="1.bed" dbkey="hg17" ftype="bed" /> 61 <param name="interpret_features" value="yes"/> 62 <param name="index_source" value="cached"/> 63 <param name="out_format" value="fasta"/> 64 <output name="out_file1"> 65 <assert_contents> 66 <!-- First few lines... --> 67 <has_text text=">hg17_chr1_147962192_147962580_- CCDS989.1_cds_0_0_chr1_147962193_r" /> 68 <has_text text="ACTTGATCCTGCTCCCTCGGTGTCTGCATTGACTCCTCATGCTGGGACTG" /> 69 <has_text text="GACCCGTCAACCCCCCTGCTCGCTGCTCACGTACCTTCATCACTTTTAGT" /> 70 <has_text text="GATGATGCAACTTTCGAGGAATGGTTCCCCCAAGGGCGGCCCCCAAAAGT" /> 71 <!-- Last few lines... --> 72 <has_text text="GCTGTGGCACAGAACATGGACTCTGTGTTTAAGGAGCTCTTGGGAAAGAC" /> 73 <has_text text="CTCTGTCCGCCAGGGCCTTGGGCCAGCATCTACCACCTCTCCCAGTCCTG" /> 74 <has_text text="GGCCCCGAAGCCCAAAGGCCCCGCCCAGCAGCCGCCTGGGCAGGAACAAA" /> 75 <has_text text="GGCTTCTCCCGGGGCCCTGGGGCCCCAGCCTCACCCTCAGCTTCCCACCC" /> 76 <has_text text="CCAGGGCCTAGACACGACCCCCAAGCCACACTGA" /> 77 </assert_contents> 78 </output> 79 </test> 80 <test> 81 <param name="input" value="droPer1.bed" dbkey="droPer1" ftype="bed" /> 82 <param name="interpret_features" value="yes"/> 83 <param name="index_source" value="cached"/> 84 <param name="out_format" value="fasta"/> 85 <output name="out_file1" file="extract_genomic_dna_out2.fasta" /> 86 </test> 87 <test> 88 <param name="input" value="1.bed" dbkey="hg17" ftype="bed" /> 89 <param name="interpret_features" value="yes"/> 90 <param name="index_source" value="cached"/> 91 <param name="out_format" value="interval"/> 92 <output name="out_file1" file="extract_genomic_dna_out3.interval" /> 93 </test> 94 <!-- Test GFF file support. --> 95 <test> 96 <param name="input" value="gff_filter_by_attribute_out1.gff" dbkey="mm9" ftype="gff" /> 97 <param name="interpret_features" value="no"/> 98 <param name="index_source" value="cached"/> 99 <param name="out_format" value="interval"/> 100 <output name="out_file1" file="extract_genomic_dna_out4.gff" /> 101 </test> 102 <test> 103 <param name="input" value="gff_filter_by_attribute_out1.gff" dbkey="mm9" ftype="gff" /> 104 <param name="interpret_features" value="no"/> 105 <param name="out_format" value="fasta"/> 106 <param name="index_source" value="cached"/> 107 <output name="out_file1" file="extract_genomic_dna_out5.fasta" /> 108 </test> 109 <!-- Test custom sequences support and GFF feature interpretation. --> 110 <test> 111 <param name="input" value="cufflinks_out1.gtf" dbkey="mm9" ftype="gff" /> 112 <param name="interpret_features" value="no"/> 113 <param name="index_source" value="history"/> 114 <param name="ref_file" value="tophat_in1.fasta"/> 115 <param name="out_format" value="fasta"/> 116 <output name="out_file1" file="extract_genomic_dna_out6.fasta" /> 117 </test> 118 <test> 119 <param name="input" value="cufflinks_out1.gtf" dbkey="mm9" ftype="gff" /> 120 <param name="interpret_features" value="yes"/> 121 <param name="index_source" value="history"/> 122 <param name="ref_file" value="tophat_in1.fasta"/> 123 <param name="out_format" value="fasta"/> 124 <output name="out_file1" file="extract_genomic_dna_out7.fasta" /> 125 </test> 126 </tests> 127 <help> 128 129.. class:: warningmark 130 131This tool requires interval or gff (special tabular formatted data). If your data is not TAB delimited, first use *Text Manipulation->Convert*. 132 133.. class:: warningmark 134 135Make sure that the genome build is specified for the dataset from which you are extracting sequences (click the pencil icon in the history item if it is not specified). 136 137.. class:: warningmark 138 139All of the following will cause a line from the input dataset to be skipped and a warning generated. The number of warnings and skipped lines is documented in the resulting history item. 140 - Any lines that do not contain at least 3 columns, a chromosome and numerical start and end coordinates. 141 - Sequences that fall outside of the range of a line's start and end coordinates. 142 - Chromosome, start or end coordinates that are invalid for the specified build. 143 - Any lines whose data columns are not separated by a **TAB** character ( other white-space characters are invalid ). 144 145.. class:: infomark 146 147 **Extract genomic DNA using coordinates from ASSEMBLED genomes and UNassembled genomes** previously were achieved by two separate tools. 148 149----- 150 151**What it does** 152 153This tool uses coordinate, strand, and build information to fetch genomic DNAs in FASTA or interval format. 154 155If strand is not defined, the default value is "+". 156 157----- 158 159**Example** 160 161If the input dataset is:: 162 163 chr7 127475281 127475310 NM_000230 0 + 164 chr7 127485994 127486166 NM_000230 0 + 165 chr7 127486011 127486166 D49487 0 + 166 167Extracting sequences with **FASTA** output data type returns:: 168 169 >hg17_chr7_127475281_127475310_+ NM_000230 170 GTAGGAATCGCAGCGCCAGCGGTTGCAAG 171 >hg17_chr7_127485994_127486166_+ NM_000230 172 GCCCAAGAAGCCCATCCTGGGAAGGAAAATGCATTGGGGAACCCTGTGCG 173 GATTCTTGTGGCTTTGGCCCTATCTTTTCTATGTCCAAGCTGTGCCCATC 174 CAAAAAGTCCAAGATGACACCAAAACCCTCATCAAGACAATTGTCACCAG 175 GATCAATGACATTTCACACACG 176 >hg17_chr7_127486011_127486166_+ D49487 177 TGGGAAGGAAAATGCATTGGGGAACCCTGTGCGGATTCTTGTGGCTTTGG 178 CCCTATCTTTTCTATGTCCAAGCTGTGCCCATCCAAAAAGTCCAAGATGA 179 CACCAAAACCCTCATCAAGACAATTGTCACCAGGATCAATGACATTTCAC 180 ACACG 181 182Extracting sequences with **Interval** output data type returns:: 183 184 chr7 127475281 127475310 NM_000230 0 + GTAGGAATCGCAGCGCCAGCGGTTGCAAG 185 chr7 127485994 127486166 NM_000230 0 + GCCCAAGAAGCCCATCCTGGGAAGGAAAATGCATTGGGGAACCCTGTGCGGATTCTTGTGGCTTTGGCCCTATCTTTTCTATGTCCAAGCTGTGCCCATCCAAAAAGTCCAAGATGACACCAAAACCCTCATCAAGACAATTGTCACCAGGATCAATGACATTTCACACACG 186 chr7 127486011 127486166 D49487 0 + TGGGAAGGAAAATGCATTGGGGAACCCTGTGCGGATTCTTGTGGCTTTGGCCCTATCTTTTCTATGTCCAAGCTGTGCCCATCCAAAAAGTCCAAGATGACACCAAAACCCTCATCAAGACAATTGTCACCAGGATCAATGACATTTCACACACG 187 188</help> 189</tool>