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https://github.com/galaxyproject/galaxy.git
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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
68 lines
3.2 KiB
XML
68 lines
3.2 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 ${GALAXY_DATA_INDEX_DIR}</command>
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<inputs>
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<display>
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<p><div class="toolFormTitle">hg17 (most recent datasets in bold)</div>$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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<column name="name" index="2"/>
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<column name="value" index="3"/>
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<column name="dbkey" index="1"/>
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<column name="encode_group" index="0"/>
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<column name="uid" index="3"/>
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<filter type="static_value" name="encode_group" value="MSA" column="0"/>
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<filter type="static_value" name="dbkey" value="hg17" column="1"/>
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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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<column name="name" index="2"/>
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<column name="value" index="3"/>
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<column name="dbkey" index="1"/>
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<column name="encode_group" index="0"/>
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<column name="uid" index="3"/>
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<filter type="static_value" name="encode_group" value="MSA" column="0"/>
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<filter type="static_value" name="dbkey" value="hg16" column="1"/>
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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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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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