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annotate README.md @ 0:dabc1e7ca486 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 97a064489364118d108b0dd2cfb4d9bc53080837
author iuc
date Thu, 19 Nov 2015 14:54:54 -0500
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dabc1e7ca486 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 97a064489364118d108b0dd2cfb4d9bc53080837
iuc
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1 # bcftools (v1.2)
dabc1e7ca486 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 97a064489364118d108b0dd2cfb4d9bc53080837
iuc
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dabc1e7ca486 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 97a064489364118d108b0dd2cfb4d9bc53080837
iuc
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3 This aims to be a "faithful" rendering of the bcftool suite. I.e. options are
dabc1e7ca486 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 97a064489364118d108b0dd2cfb4d9bc53080837
iuc
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4 presented essentially as closely to the command line version as is useful.
dabc1e7ca486 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 97a064489364118d108b0dd2cfb4d9bc53080837
iuc
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dabc1e7ca486 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 97a064489364118d108b0dd2cfb4d9bc53080837
iuc
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6 This may not appeal to all, if you'd like to see smaller and more dedicated
dabc1e7ca486 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 97a064489364118d108b0dd2cfb4d9bc53080837
iuc
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7 tools (e.g. "intersect", "union" and "complement" being separate tools instead
dabc1e7ca486 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 97a064489364118d108b0dd2cfb4d9bc53080837
iuc
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8 of all of them included in the "isec" tool,) please feel free to file an issue.
dabc1e7ca486 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 97a064489364118d108b0dd2cfb4d9bc53080837
iuc
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dabc1e7ca486 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 97a064489364118d108b0dd2cfb4d9bc53080837
iuc
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10 ## TODO:
dabc1e7ca486 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 97a064489364118d108b0dd2cfb4d9bc53080837
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dabc1e7ca486 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 97a064489364118d108b0dd2cfb4d9bc53080837
iuc
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12 - Galaxy needs datatypes for bcf and vcf files, block-gzipped and uncompressed.
dabc1e7ca486 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 97a064489364118d108b0dd2cfb4d9bc53080837
iuc
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13 - Galaxy needs to automatically index those files with tabix
dabc1e7ca486 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 97a064489364118d108b0dd2cfb4d9bc53080837
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dabc1e7ca486 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 97a064489364118d108b0dd2cfb4d9bc53080837
iuc
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15 ## "Complete" Wrappers
dabc1e7ca486 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 97a064489364118d108b0dd2cfb4d9bc53080837
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dabc1e7ca486 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 97a064489364118d108b0dd2cfb4d9bc53080837
iuc
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17 The wrappers were automatically generated in bulk. That doesn't get them 100%
dabc1e7ca486 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 97a064489364118d108b0dd2cfb4d9bc53080837
iuc
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18 of the way there (e.g. meaningful test cases), so the rest of the process is a
dabc1e7ca486 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 97a064489364118d108b0dd2cfb4d9bc53080837
iuc
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19 bit slower.
dabc1e7ca486 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 97a064489364118d108b0dd2cfb4d9bc53080837
iuc
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dabc1e7ca486 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 97a064489364118d108b0dd2cfb4d9bc53080837
iuc
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21 - bcftools call