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Greg Von Kuster
e190e6e2b0
We're still supporting the current dynamic_options functionality. This is a first pass and will be cleaned up as we continue to evolve more tools to use this new approach. Within tool configs, SelectToolParameter types now include a <select_options> tag set. Several tools have been altered to use this new approach. Other tools we enhanced to use the ColumnListParameter type.
51 lines
2.5 KiB
XML
51 lines
2.5 KiB
XML
<tool id="encode_import_multi-species_sequence_analysis1" name="Multi-species Sequence Analysis">
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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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<select_options from_file="/depot/data2/galaxy/encode_datasets.loc" func="get_options_for_encode">
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<func_param name="encode_group" value="MSA" />
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<func_param name="build" value="hg17" />
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</select_options>
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</param>
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<param name="hg16" type="select" display="checkboxes" multiple="true">
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<select_options from_file="/depot/data2/galaxy/encode_datasets.loc" func="get_options_for_encode">
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<func_param name="encode_group" value="MSA" />
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<func_param name="build" value="hg16" />
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</select_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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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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