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82 lines
3.2 KiB
XML
82 lines
3.2 KiB
XML
<tool id="liftOver1" name="Convert genome coordinates" version="1.0.2">
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<description> between assemblies and genomes</description>
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<command interpreter="python">liftOver_wrapper.py $input "$out_file1" "$out_file2" $dbkey $to_dbkey $minMatch</command>
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<inputs>
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<param format="interval" name="input" type="data" label="Convert coordinates of">
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<validator type="unspecified_build" />
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<validator type="dataset_metadata_in_file" filename="liftOver.loc" metadata_name="dbkey" metadata_column="0" message="Liftover mappings are currently not available for the specified build." />
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</param>
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<param name="to_dbkey" type="select" label="To">
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<options from_file="liftOver.loc">
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<column name="name" index="1"/>
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<column name="value" index="2"/>
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<column name="dbkey" index="0"/>
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<filter type="data_meta" ref="input" key="dbkey" column="0" />
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</options>
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</param>
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<param name="minMatch" size="10" type="float" value="0.95" label="Minimum ratio of bases that must remap" />
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</inputs>
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<outputs>
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<data format="input" name="out_file1" label="${tool.name} on ${on_string} [ MAPPED COORDINATES ]">
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<actions>
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<action type="metadata" name="dbkey">
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<option type="from_file" name="liftOver.loc" column="1" offset="0">
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<filter type="param_value" column="0" value="#" compare="startswith" keep="False"/>
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<filter type="param_value" ref="to_dbkey" column="2"/>
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</option>
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</action>
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</actions>
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</data>
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<data format="input" name="out_file2" label="${tool.name} on ${on_string} [ UNMAPPED COORDINATES ]" />
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</outputs>
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<requirements>
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<requirement type="package">ucsc_tools</requirement>
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</requirements>
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<tests>
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<test>
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<param name="input" value="5.bed" dbkey="hg18" ftype="bed" />
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<param name="to_dbkey" value="panTro2" />
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<param name="minMatch" value="0.95" />
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<output name="out_file1" file="5_liftover_mapped.bed"/>
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<output name="out_file2" file="5_liftover_unmapped.bed"/>
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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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Make sure that the genome build of the input dataset is specified (click the pencil icon in the history item to set it if necessary).
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.. class:: warningmark
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This tool will only work on interval datasets with chromosome in column 1,
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start co-ordinate in column 2 and end co-ordinate in column 3. BED comments
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and track and browser lines will be ignored, but if other non-interval lines
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are present the tool will return empty output datasets.
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-----
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.. class:: infomark
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**What it does**
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This tool converts coordinates and annotations between assemblies and genomes. It produces 2 files, one containing all the mapped coordinates and the other containing the unmapped coordinates, if any.
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-----
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**Example**
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Converting the following hg16 intervals to hg18 intervals::
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chrX 85170 112199 AK002185 0 +
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chrX 110458 112199 AK097346 0 +
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chrX 112203 121212 AK074528 0 -
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will produce the following hg18 intervals::
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chrX 132991 160020 AK002185 0 +
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chrX 158279 160020 AK097346 0 +
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chrX 160024 169033 AK074528 0 -
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</help>
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</tool>
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