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https://github.com/galaxyproject/galaxy.git
synced 2026-09-17 16:41:31 +08:00
Nicola Soranzo
2515267ca5
instead of relying on `lib/galaxy/tools/deps/resolvers/default_conda_mapping.yml` . Follow-up on https://github.com/galaxyproject/galaxy/pull/5544 . See https://github.com/galaxyproject/galaxy/pull/5544/files#r183909746 for an explanation why that's preferrable for future-proof reproducibility. Also, small fixes to `tools/evolution/codingSnps.xml` .
187 lines
8.5 KiB
XML
187 lines
8.5 KiB
XML
<tool id="Extract genomic DNA 1" name="Extract Genomic DNA" version="2.2.4">
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<description>using coordinates from assembled/unassembled genomes</description>
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<requirements>
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<requirement type="package" version="357">ucsc-fatotwobit</requirement>
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</requirements>
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<command>
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python '$__tool_directory__/extract_genomic_dna.py' '${input}' '${out_file1}' -o ${out_format} -d '${dbkey}'
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#if str( $interpret_features ) == "yes":
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-I
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#end if
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## Columns to use in input file.
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#if isinstance( $input.datatype, $__app__.datatypes_registry.get_datatype_by_extension('gff').__class__):
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-1 "1,4,5,7" --gff
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#else:
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-1 "${input.metadata.chromCol},${input.metadata.startCol},${input.metadata.endCol},${input.metadata.strandCol},${input.metadata.nameCol}"
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#end if
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#if $seq_source.index_source == "cached":
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## Genomic data from cache.
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-g '${GALAXY_DATA_INDEX_DIR}'
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#else:
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## Genomic data from history.
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-F '${seq_source.ref_file}'
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#end if
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</command>
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<inputs>
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<param format="interval,gff" name="input" type="data" label="Fetch sequences for intervals in"/>
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<param name="interpret_features" type="select" label="Interpret features when possible" help="Only meaningful for GFF, GTF datasets.">
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<option value="yes">Yes</option>
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<option value="no">No</option>
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</param>
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<conditional name="seq_source">
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<param name="index_source" type="select" label="Source for Genomic Data" help="If 'Locally cached' is selected, it will use a genomic reference file that matches the input file's dbkey. First it looks whether there are corresponding *.nib files in alignseq.loc. If that is not available, it searches for a corresponding *.2bit in twobit.loc.">
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<option value="cached">Locally cached</option>
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<option value="history">History</option>
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</param>
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<when value="cached">
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</when>
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<when value="history">
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<param name="ref_file" type="data" format="fasta" label="Using reference file" />
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</when>
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</conditional>
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<param name="out_format" type="select" label="Output data type">
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<option value="fasta">FASTA</option>
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<option value="interval">Interval</option>
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</param>
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</inputs>
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<outputs>
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<data format_source="input" name="out_file1" metadata_source="input">
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<change_format>
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<when input="out_format" value="fasta" format="fasta" />
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</change_format>
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</data>
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</outputs>
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<tests>
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<test>
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<param name="input" value="1.bed" dbkey="hg17" ftype="bed" />
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<param name="interpret_features" value="yes"/>
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<param name="index_source" value="cached"/>
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<param name="out_format" value="fasta"/>
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<output name="out_file1">
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<assert_contents>
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<!-- First few lines... -->
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<has_text text=">hg17_chr1_147962192_147962580_- CCDS989.1_cds_0_0_chr1_147962193_r" />
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<has_text text="ACTTGATCCTGCTCCCTCGGTGTCTGCATTGACTCCTCATGCTGGGACTG" />
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<has_text text="GACCCGTCAACCCCCCTGCTCGCTGCTCACGTACCTTCATCACTTTTAGT" />
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<has_text text="GATGATGCAACTTTCGAGGAATGGTTCCCCCAAGGGCGGCCCCCAAAAGT" />
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<!-- Last few lines... -->
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<has_text text="GCTGTGGCACAGAACATGGACTCTGTGTTTAAGGAGCTCTTGGGAAAGAC" />
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<has_text text="CTCTGTCCGCCAGGGCCTTGGGCCAGCATCTACCACCTCTCCCAGTCCTG" />
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<has_text text="GGCCCCGAAGCCCAAAGGCCCCGCCCAGCAGCCGCCTGGGCAGGAACAAA" />
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<has_text text="GGCTTCTCCCGGGGCCCTGGGGCCCCAGCCTCACCCTCAGCTTCCCACCC" />
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<has_text text="CCAGGGCCTAGACACGACCCCCAAGCCACACTGA" />
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</assert_contents>
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</output>
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</test>
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<test>
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<param name="input" value="droPer1.bed" dbkey="droPer1" ftype="bed" />
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<param name="interpret_features" value="yes"/>
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<param name="index_source" value="cached"/>
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<param name="out_format" value="fasta"/>
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<output name="out_file1" file="extract_genomic_dna_out2.fasta" />
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</test>
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<test>
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<param name="input" value="1.bed" dbkey="hg17" ftype="bed" />
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<param name="interpret_features" value="yes"/>
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<param name="index_source" value="cached"/>
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<param name="out_format" value="interval"/>
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<output name="out_file1" file="extract_genomic_dna_out3.interval" />
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</test>
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<!-- Test GFF file support. -->
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<test>
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<param name="input" value="gff_filter_by_attribute_out1.gff" dbkey="mm9" ftype="gff" />
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<param name="interpret_features" value="no"/>
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<param name="index_source" value="cached"/>
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<param name="out_format" value="interval"/>
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<output name="out_file1" file="extract_genomic_dna_out4.gff" />
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</test>
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<test>
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<param name="input" value="gff_filter_by_attribute_out1.gff" dbkey="mm9" ftype="gff" />
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<param name="interpret_features" value="no"/>
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<param name="out_format" value="fasta"/>
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<param name="index_source" value="cached"/>
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<output name="out_file1" file="extract_genomic_dna_out5.fasta" />
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</test>
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<!-- Test custom sequences support and GFF feature interpretation. -->
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<test>
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<param name="input" value="cufflinks_out1.gtf" dbkey="mm9" ftype="gff" />
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<param name="interpret_features" value="no"/>
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<param name="index_source" value="history"/>
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<param name="ref_file" value="tophat_in1.fasta"/>
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<param name="out_format" value="fasta"/>
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<output name="out_file1" file="extract_genomic_dna_out6.fasta" />
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</test>
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<test>
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<param name="input" value="cufflinks_out1.gtf" dbkey="mm9" ftype="gff" />
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<param name="interpret_features" value="yes"/>
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<param name="index_source" value="history"/>
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<param name="ref_file" value="tophat_in1.fasta"/>
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<param name="out_format" value="fasta"/>
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<output name="out_file1" file="extract_genomic_dna_out7.fasta" />
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</test>
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</tests>
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<help>
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.. class:: warningmark
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This tool requires interval or gff (special tabular formatted data). If your data is not TAB delimited, first use *Text Manipulation->Convert*.
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.. class:: warningmark
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Make 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).
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.. class:: warningmark
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All 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.
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- Any lines that do not contain at least 3 columns, a chromosome and numerical start and end coordinates.
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- Sequences that fall outside of the range of a line's start and end coordinates.
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- Chromosome, start or end coordinates that are invalid for the specified build.
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- Any lines whose data columns are not separated by a **TAB** character ( other white-space characters are invalid ).
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.. class:: infomark
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**Extract genomic DNA using coordinates from ASSEMBLED genomes and UNassembled genomes** previously were achieved by two separate tools.
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-----
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**What it does**
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This tool uses coordinate, strand, and build information to fetch genomic DNAs in FASTA or interval format.
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If strand is not defined, the default value is "+".
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-----
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**Example**
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If the input dataset is::
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chr7 127475281 127475310 NM_000230 0 +
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chr7 127485994 127486166 NM_000230 0 +
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chr7 127486011 127486166 D49487 0 +
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Extracting sequences with **FASTA** output data type returns::
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>hg17_chr7_127475281_127475310_+ NM_000230
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GTAGGAATCGCAGCGCCAGCGGTTGCAAG
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>hg17_chr7_127485994_127486166_+ NM_000230
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GCCCAAGAAGCCCATCCTGGGAAGGAAAATGCATTGGGGAACCCTGTGCG
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GATTCTTGTGGCTTTGGCCCTATCTTTTCTATGTCCAAGCTGTGCCCATC
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CAAAAAGTCCAAGATGACACCAAAACCCTCATCAAGACAATTGTCACCAG
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GATCAATGACATTTCACACACG
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>hg17_chr7_127486011_127486166_+ D49487
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TGGGAAGGAAAATGCATTGGGGAACCCTGTGCGGATTCTTGTGGCTTTGG
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CCCTATCTTTTCTATGTCCAAGCTGTGCCCATCCAAAAAGTCCAAGATGA
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CACCAAAACCCTCATCAAGACAATTGTCACCAGGATCAATGACATTTCAC
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ACACG
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Extracting sequences with **Interval** output data type returns::
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chr7 127475281 127475310 NM_000230 0 + GTAGGAATCGCAGCGCCAGCGGTTGCAAG
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chr7 127485994 127486166 NM_000230 0 + GCCCAAGAAGCCCATCCTGGGAAGGAAAATGCATTGGGGAACCCTGTGCGGATTCTTGTGGCTTTGGCCCTATCTTTTCTATGTCCAAGCTGTGCCCATCCAAAAAGTCCAAGATGACACCAAAACCCTCATCAAGACAATTGTCACCAGGATCAATGACATTTCACACACG
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chr7 127486011 127486166 D49487 0 + TGGGAAGGAAAATGCATTGGGGAACCCTGTGCGGATTCTTGTGGCTTTGGCCCTATCTTTTCTATGTCCAAGCTGTGCCCATCCAAAAAGTCCAAGATGACACCAAAACCCTCATCAAGACAATTGTCACCAGGATCAATGACATTTCACACACG
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</help>
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</tool>
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