Mercurial > repos > iuc > bedtools

annotate tool-data/all_gff.loc.sample @ 36:0a5c785ac6db draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 833a0b5510d91226c1b0b94550cebfd44243b8d4"
author iuc
date Mon, 15 Jun 2020 16:55:13 -0400
parents b73962f8fcbf
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b73962f8fcbf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit c5007eff737fcabb28fa726ac40f13a1cd4893c1
iuc
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1 #This file lists the locations and dbkeys of all the GFF files
b73962f8fcbf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit c5007eff737fcabb28fa726ac40f13a1cd4893c1
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2 #This file has the format (white space characters are
b73962f8fcbf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit c5007eff737fcabb28fa726ac40f13a1cd4893c1
iuc
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3 #TAB characters):
b73962f8fcbf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit c5007eff737fcabb28fa726ac40f13a1cd4893c1
iuc
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4 #
b73962f8fcbf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit c5007eff737fcabb28fa726ac40f13a1cd4893c1
iuc
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5 #<unique_build_id> <dbkey> <display_name> <file_path>
b73962f8fcbf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit c5007eff737fcabb28fa726ac40f13a1cd4893c1
iuc
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6 #
b73962f8fcbf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit c5007eff737fcabb28fa726ac40f13a1cd4893c1
iuc
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7 #So, all_gff.loc could look something like this:
b73962f8fcbf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit c5007eff737fcabb28fa726ac40f13a1cd4893c1
iuc
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8 #
b73962f8fcbf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit c5007eff737fcabb28fa726ac40f13a1cd4893c1
iuc
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9 #apiMel3 apiMel3 Honeybee (Apis mellifera): apiMel3 /path/to/annotation/apiMel3/apiMel3.gff
b73962f8fcbf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit c5007eff737fcabb28fa726ac40f13a1cd4893c1
iuc
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10 #hg19canon hg19 Human (Homo sapiens): hg19 Canonical /path/to/annotation/hg19/hg19canon.gff
b73962f8fcbf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit c5007eff737fcabb28fa726ac40f13a1cd4893c1
iuc
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11 #hg19full hg19 Human (Homo sapiens): hg19 Representative transcripts /path/to/annotation/hg19/hg19_representative_tx.gff
b73962f8fcbf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit c5007eff737fcabb28fa726ac40f13a1cd4893c1
iuc
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12 #
b73962f8fcbf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit c5007eff737fcabb28fa726ac40f13a1cd4893c1
iuc
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13 #Your all_gff.loc file should contain an entry for each different annotation.
b73962f8fcbf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit c5007eff737fcabb28fa726ac40f13a1cd4893c1
iuc
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14 #So there can be multiple gff files for each build, such as with hg19 above.