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https://github.com/galaxyproject/galaxy.git
synced 2026-09-21 13:50:20 +08:00
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
57 lines
2.3 KiB
XML
57 lines
2.3 KiB
XML
<tool id="random_intervals1" name="Random Intervals">
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<description>create a random set of intervals</description>
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<command interpreter="python">random_intervals_no_bits.py $regions $input2 $input1 $out_file1 $input2_chromCol $input2_startCol $input2_endCol $input1_chromCol $input1_startCol $input1_endCol $input1_strandCol $use_mask $strand_overlaps ${GALAXY_DATA_INDEX_DIR}</command>
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<inputs>
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<param name="input1" type="data" format="interval" label="File to Mimick">
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<validator type="unspecified_build" message="Unspecified build, this tool works with data from genome builds hg16 or hg17. Click the pencil icon in your history item to set the genome build."/>
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</param>
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<param name="input2" type="data" format="interval" label="Intervals to Mask"/>
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<param name="use_mask" type="select" label="Use mask">
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<option value="no_mask">No</option>
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<option value="use_mask">Yes</option>
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</param>
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<param name="strand_overlaps" type="select" label="Allow overlaps">
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<option value="all">Any</option>
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<option value="strand">Across Strands</option>
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<option value="none">None</option>
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</param>
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<param name="regions" type="select" label="Regions to use">
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<options from_file="regions.loc">
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<column name="name" index="2"/>
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<column name="value" index="1"/>
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<column name="dbkey" index="0"/>
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<filter type="data_meta" ref="input1" key="dbkey" column="0" />
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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 name="out_file1" format="input"/>
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</outputs>
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<help>
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.. class:: warningmark
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This tool currently only works with data from genome builds hg16 or hg17.
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-----
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.. class:: infomark
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**Note:** If you do not wish to mask a set of intervals, change the Use Mask option to No, this option will override any Mask files selected.
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-----
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**Syntax**
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This tool will attempt to create a random set of intervals that mimic those found within your source file. You may also specify a set of intervals to mask.
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**Allow overlaps** options
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* **Across Strands** - random regions are allowed to overlap only if they are on different strands.
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* **Any** - all overlaps are allowed.
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* **None** - no overlapping regions are allowed.
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**Regions to use** options
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* Bounding region of interest based on the dataset build.
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</help>
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</tool> |