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https://github.com/galaxyproject/galaxy.git
synced 2026-10-16 07:19:13 +08:00
Daniel Blankenberg
11a2c767c3
MAF tool interfaces now support the use of index species and all species existing in cached alignment sets. Until main is updated and the old maf_location files can be overwritten, these symbolic links are required: maf_index.loc -> /depot/data2/galaxy/maf_index_new.loc maf_pairwise.loc -> /depot/data2/galaxy/maf_pairwise_new.loc
115 lines
5.0 KiB
XML
115 lines
5.0 KiB
XML
<tool id="Extract_features1" name="Extract features">
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<description> from GFF file</description>
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<command interpreter="python">extract_GFF_Features.py $input1 $out_file1 ${column_choice.col} ${column_choice.feature}</command>
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<inputs>
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<param format="gff" name="input1" type="data" label="Select GFF data"/>
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<conditional name="column_choice">
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<param name="col" type="select" label="From">
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<option value="0" selected="true">Column 1 / Sequence name</option>
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<option value="1">Column 2 / Source</option>
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<option value="2">Column 3 / Feature</option>
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<option value="6">Column 7 / Strand</option>
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<option value="7">Column 8 / Frame</option>
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</param>
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<when value="0">
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<param name="feature" type="select" multiple="true" label="Extract features" help="Multi-select list - hold the appropriate key while clicking to select multiple columns">
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<options from_dataset="input1">
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<column name="name" index="0"/>
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<column name="value" index="0"/>
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<filter type="unique_value" name="unique" column="0"/>
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</options>
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</param>
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</when>
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<when value="1">
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<param name="feature" type="select" multiple="true" label="Extract features" help="Multi-select list - hold the appropriate key while clicking to select multiple columns">
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<options from_dataset="input1">
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<column name="name" index="1"/>
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<column name="value" index="1"/>
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<filter type="unique_value" name="unique" column="1"/>
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</options>
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</param>
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</when>
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<when value="2">
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<param name="feature" type="select" multiple="true" label="Extract features" help="Multi-select list - hold the appropriate key while clicking to select multiple columns">
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<options from_dataset="input1">
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<column name="name" index="2"/>
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<column name="value" index="2"/>
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<filter type="unique_value" name="unique" column="2"/>
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</options>
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</param>
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</when>
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<when value="6">
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<param name="feature" type="select" multiple="true" label="Extract features" help="Multi-select list - hold the appropriate key while clicking to select multiple columns">
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<options from_dataset="input1">
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<column name="name" index="6"/>
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<column name="value" index="6"/>
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<filter type="unique_value" name="unique" column="6"/>
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</options>
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</param>
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</when>
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<when value="7">
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<param name="feature" type="select" multiple="true" label="Extract features" help="Multi-select list - hold the appropriate key while clicking to select multiple columns">
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<options from_dataset="input1">
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<column name="name" index="7"/>
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<column name="value" index="7"/>
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<filter type="unique_value" name="unique" column="7"/>
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</options>
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</param>
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</when>
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</conditional>
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</inputs>
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<outputs>
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<data format="gff" name="out_file1" />
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</outputs>
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<tests>
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<test>
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<param name="input1" value="5.gff"/>
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<param name="col" value="0" />
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<param name="feature" value="chr5,chr6,chr7,chr8" />
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<output name="out_file1" file="Extract_features1_out.gff"/>
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</test>
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</tests>
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<help>
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**What it does**
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This tool extracts selected features from GFF data.
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-----
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**Example**
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Selecting **promoter** from the following GFF data::
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chr22 GeneA enhancer 10000000 10001000 500 + . TGA
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chr22 GeneA promoter 10010000 10010100 900 + . TGA
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chr22 GeneB promoter 10020000 10025000 400 - . TGB
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chr22 GeneB CCDS2220 10030000 10065000 800 - . TGB
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will produce the following output::
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chr22 GeneA promoter 10010000 10010100 900 + . TGA
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chr22 GeneB promoter 10020000 10025000 400 - . TGB
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----
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.. class:: infomark
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**About formats**
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**GFF format** General Feature Format is a format for describing genes and other features associated with DNA, RNA and Protein sequences. GFF lines have nine tab-separated fields::
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1. seqname - Must be a chromosome or scaffold.
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2. source - The program that generated this feature.
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3. feature - The name of this type of feature. Some examples of standard feature types are "CDS", "start_codon", "stop_codon", and "exon".
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4. start - The starting position of the feature in the sequence. The first base is numbered 1.
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5. end - The ending position of the feature (inclusive).
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6. score - A score between 0 and 1000. If there is no score value, enter ".".
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7. strand - Valid entries include '+', '-', or '.' (for don't know/care).
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8. frame - If the feature is a coding exon, frame should be a number between 0-2 that represents the reading frame of the first base. If the feature is not a coding exon, the value should be '.'.
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9. group - All lines with the same group are linked together into a single item.
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</help>
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</tool>
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