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Greg Von Kuster
cd52cabd48
Galaxy developers should execute the following commands in their $UNIVERSE_HOME/tool-data directories: ln -s /depot/data2/galaxy/alignseq.loc alignseq.loc ln -s /depot/data2/galaxy/binned_scores.loc binned_scores.loc ln -s /depot/data2/galaxy/blastdb.loc blastdb.loc ln -s /depot/data2/galaxy/encode_datasets.loc encode_datasets.loc ln -s /depot/data2/galaxy/liftOver.loc liftOver.loc ln -s /depot/data2/galaxy/maf_index.loc maf_index.loc ln -s /depot/data2/galaxy/maf_pairwise.loc maf_pairwise.loc ln -s /depot/data2/galaxy/microbes/microbial_data.loc microbial_data.loc ln -s /depot/data2/galaxy/phastOdds.loc phastOdds.loc ln -s /depot/data2/galaxy/quality_scores.loc quality_scores.loc ln -s /depot/data2/galaxy/regions.loc regions.loc ln -s /depot/data2/galaxy/twobit.loc twobit.loc
59 lines
2.7 KiB
XML
59 lines
2.7 KiB
XML
<tool id="encode_import_gencode1" name="Gencode Datasets">
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<command interpreter="python">encode_import.py $hg17,$hg16 $output</command>
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<inputs>
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<display>
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<p><div class="toolFormTitle">hg17 (most recent datasets in bold)</div>$hg17</p>
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<p><div class="toolFormTitle">hg16 (most recent datasets in bold)</div>$hg16</p>
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</display>
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<param name="hg17" type="select" display="checkboxes" multiple="true">
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<options from_file="encode_datasets.loc">
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<filter type="param" name="encode_group" value="GENCODE" />
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<filter type="param" name="dbkey" value="hg17" />
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</options>
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</param>
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<param name="hg16" type="select" display="checkboxes" multiple="true">
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<options from_file="encode_datasets.loc">
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<filter type="param" name="encode_group" value="GENCODE" />
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<filter type="param" name="dbkey" value="hg16" />
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</options>
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</param>
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</inputs>
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<outputs>
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<data format="bed" name="output"/>
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</outputs>
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<code file="encode_import_code.py"/>
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<help>
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.. class:: warningmark
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The data in this section is intended as a supplement for this manuscript_. Use the **Get Data->UCSC Main** tool for current ENCODE data.
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.. _manuscript: http://www.genome.org/cgi/content/full/17/6/960
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These are the datasets used for partitioning files.
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For detailed information about data deposition and partitioning, click here_.
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.. _here: http://genome.imim.es/gencode/wiki/index.php/Collecting_Feature_Sets_from_All_Analysis_Groups
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*[gencode_partitioned]* means that the dataset was partitioned according to the protocol below:
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A partition scheme has been defined that is similar to what has previously been done with TARs/TRANSFRAGs such that any feature can be classified as falling into one of the following 6 categories:
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1. **Coding** -- coding exons defined from the GENCODE experimentally verified coding set (coding in any transcript)
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2. **5UTR** -- 5' UTR exons defined from the GENCODE experimentally verified coding set (5' UTR in some transcript but never coding in any other)
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3. **3UTR** -- 3' UTR exons defined from the GENCODE experimentally verified coding set (3' UTR in some transcript but never coding in any other)
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4. **Intronic Proximal** -- intronic and no more than 5kb away from an exon.
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5. **Intergenic Proximal** -- between genes and no more than 5kb away from an exon.
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6. **Intronic Distal** -- intronic and greater than 5kb away from an exon.
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7. **Intergenic Distal** -- between genes and greater than 5kb away from an exon.
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-----
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.. class:: infomark
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**Note:** Features overlapping more than one partition will take the identity of the lower-numbered partition.
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</help>
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</tool>
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