[2] | 1 | <tool id="liftOver1" name="Convert genome coordinates" version="1.0.2">
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| 2 | <description> between assemblies and genomes</description>
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| 3 | <command interpreter="python">liftOver_wrapper.py $input "$out_file1" "$out_file2" $dbkey $to_dbkey $minMatch</command>
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| 4 | <inputs>
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| 5 | <param format="interval" name="input" type="data" label="Convert coordinates of">
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| 6 | <validator type="unspecified_build" /> |
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| 7 | <validator type="dataset_metadata_in_file" filename="liftOver.loc" metadata_name="dbkey" metadata_column="0" message="Liftover mappings are currently not available for the specified build." />
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| 8 | </param> |
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| 9 | <param name="to_dbkey" type="select" label="To">
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| 10 | <options from_file="liftOver.loc">
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| 11 | <column name="name" index="1"/>
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| 12 | <column name="value" index="2"/>
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| 13 | <column name="dbkey" index="0"/>
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| 14 | <filter type="data_meta" ref="input" key="dbkey" column="0" />
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| 15 | </options> |
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| 16 | </param> |
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| 17 | <param name="minMatch" size="10" type="float" value="0.95" label="Minimum ratio of bases that must remap" /> |
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| 18 | </inputs>
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| 19 | <outputs>
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| 20 | <data format="input" name="out_file1" label="${tool.name} on ${on_string} [ MAPPED COORDINATES ]">
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| 21 | <actions>
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| 22 | <action type="metadata" name="dbkey">
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| 23 | <option type="from_file" name="liftOver.loc" column="1" offset="0">
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| 24 | <filter type="param_value" column="0" value="#" compare="startswith" keep="False"/>
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| 25 | <filter type="param_value" ref="to_dbkey" column="2"/>
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| 26 | </option>
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| 27 | </action>
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| 28 | </actions>
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| 29 | </data>
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| 30 | <data format="input" name="out_file2" label="${tool.name} on ${on_string} [ UNMAPPED COORDINATES ]" />
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| 31 | </outputs>
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| 32 | <requirements>
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| 33 | <requirement type="package">ucsc_tools</requirement>
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| 34 | </requirements>
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| 35 | <tests>
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| 36 | <test>
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| 37 | <param name="input" value="5.bed" dbkey="hg18" ftype="bed" />
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| 38 | <param name="to_dbkey" value="panTro2" />
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| 39 | <param name="minMatch" value="0.95" />
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| 40 | <output name="out_file1" file="5_liftover_mapped.bed"/>
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| 41 | <output name="out_file2" file="5_liftover_unmapped.bed"/>
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| 42 | </test>
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| 43 | </tests>
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| 44 | <help>
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| 45 | .. class:: warningmark
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| 46 |
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| 47 | 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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| 48 |
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| 49 | .. class:: warningmark
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| 50 |
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| 51 | This tool will only work on interval datasets with chromosome in column 1, |
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| 52 | start co-ordinate in column 2 and end co-ordinate in column 3. BED comments |
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| 53 | and track and browser lines will be ignored, but if other non-interval lines |
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| 54 | are present the tool will return empty output datasets.
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| 55 |
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| 56 | -----
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| 57 |
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| 58 | .. class:: infomark
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| 59 |
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| 60 | **What it does**
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| 61 |
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| 62 | 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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| 63 |
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| 64 | -----
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| 65 |
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| 66 | **Example**
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| 67 |
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| 68 | Converting the following hg16 intervals to hg18 intervals::
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| 69 |
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| 70 | chrX 85170 112199 AK002185 0 +
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| 71 | chrX 110458 112199 AK097346 0 +
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| 72 | chrX 112203 121212 AK074528 0 -
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| 73 |
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| 74 | will produce the following hg18 intervals::
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| 75 |
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| 76 | chrX 132991 160020 AK002185 0 +
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| 77 | chrX 158279 160020 AK097346 0 +
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| 78 | chrX 160024 169033 AK074528 0 -
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| 79 |
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| 80 | </help>
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| 81 | </tool>
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