Mercurial > repos > greg > draw_amr_matrix
changeset 5:46d31ec5d24c draft
Uploaded
| author | greg |
|---|---|
| date | Tue, 21 Feb 2023 20:36:37 +0000 |
| parents | 33a0ea992043 |
| children | caf554e039b2 |
| files | .shed.yml all_fasta.loc.sample test-data/all_fasta.loc tool_data_table_conf.xml.sample tool_data_table_conf.xml.test |
| diffstat | 5 files changed, 36 insertions(+), 2 deletions(-) [+] |
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--- a/.shed.yml Tue Feb 21 19:55:42 2023 +0000 +++ b/.shed.yml Tue Feb 21 20:36:37 2023 +0000 @@ -1,7 +1,7 @@ name: draw_amr_matrix owner: greg -description: Accepts a tabular AMR gene drugs file and a collection of best feature hits and draws an AMR matrix. -long_description: Accepts a tabular AMR gene drugs file and a collection of best feature hits and draws an AMR matrix. +description: Accepts a collection of best AMR feature hits, an optional AMR deletions BED file, an optional AMR mutations TSV file and a AMR gene drug mappings file and draws an AMR matrix. +long_description: Accepts a collection of best AMR feature hits, an optional AMR deletions BED file, an optional AMR mutations TSV file and a AMR gene drug mappings file and draws an AMR matrix. categories: - Visualization remote_repository_url: https://github.com/gregvonkuster/galaxy_tools/tree/master/tools/pima/draw_amr_matrix
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/all_fasta.loc.sample Tue Feb 21 20:36:37 2023 +0000 @@ -0,0 +1,18 @@ +#This file lists the locations and dbkeys of all the fasta files +#under the "genome" directory (a directory that contains a directory +#for each build). The script extract_fasta.py will generate the file +#all_fasta.loc. This file has the format (white space characters are +#TAB characters): +# +#<unique_build_id> <dbkey> <display_name> <file_path> +# +#So, all_fasta.loc could look something like this: +# +#apiMel3 apiMel3 Honeybee (Apis mellifera): apiMel3 /path/to/genome/apiMel3/apiMel3.fa +#hg19canon hg19 Human (Homo sapiens): hg19 Canonical /path/to/genome/hg19/hg19canon.fa +#hg19full hg19 Human (Homo sapiens): hg19 Full /path/to/genome/hg19/hg19full.fa +# +#Your all_fasta.loc file should contain an entry for each individual +#fasta file. So there will be multiple fasta files for each build, +#such as with hg19 above. +#
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/all_fasta.loc Tue Feb 21 20:36:37 2023 +0000 @@ -0,0 +1,1 @@ +ref_genome ref_genome ref_genome ${__HERE__}/ref_genome.fasta
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_data_table_conf.xml.sample Tue Feb 21 20:36:37 2023 +0000 @@ -0,0 +1,7 @@ +<tables> + <!-- Locations of all fasta files under genome directory --> + <table name="all_fasta" comment_char="#" allow_duplicate_entries="False"> + <columns>value, dbkey, name, path</columns> + <file path="tool-data/all_fasta.loc" /> + </table> +</tables>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_data_table_conf.xml.test Tue Feb 21 20:36:37 2023 +0000 @@ -0,0 +1,8 @@ +<tables> + <!-- Locations of all fasta files under genome directory --> + <table name="all_fasta" comment_char="#" allow_duplicate_entries="False"> + <columns>value, dbkey, name, path</columns> + <file path="${__HERE__}/test-data/all_fasta.loc" /> + </table> +</tables> +