Mercurial > repos > fubar > microsatbedfubar
changeset 5:d30190825002 draft
planemo upload for repository https://github.com/fubar2/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty
| author | fubar |
|---|---|
| date | Sun, 14 Jul 2024 03:56:55 +0000 |
| parents | e2e1e48a2e56 |
| children | c5324bf8a52c |
| files | README.md all_fasta.loc.sample microsatbed.xml test-data/all_fasta.loc tool_data_table_conf.xml.sample tool_data_table_conf.xml.test |
| diffstat | 6 files changed, 45 insertions(+), 4 deletions(-) [+] |
line wrap: on
line diff
--- a/README.md Sun Jul 14 02:22:32 2024 +0000 +++ b/README.md Sun Jul 14 03:56:55 2024 +0000 @@ -1,5 +1,6 @@ ## microsatellites to bed features + **Convert short repetitive sequences to bed features** Microsatellites refer to short DNA patterns that are repeated.
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/all_fasta.loc.sample Sun Jul 14 03:56:55 2024 +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. +#
--- a/microsatbed.xml Sun Jul 14 02:22:32 2024 +0000 +++ b/microsatbed.xml Sun Jul 14 03:56:55 2024 +0000 @@ -1,4 +1,4 @@ -<tool name="STR to bed" id="microsatbedfubar" version="1.3.0" profile="22.05"> +<tool name="strtobed" id="microsatbedfubar" version="1.3.0" profile="22.05"> <description>Short Tandem Repeats to bed features from fasta</description> <requirements> <requirement version="3.12.3" type="package">python</requirement>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/all_fasta.loc Sun Jul 14 03:56:55 2024 +0000 @@ -0,0 +1,22 @@ +#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. +#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. +# +hgtest hgtest hgtest ${__HERE__}/humsamp.fa
--- a/tool_data_table_conf.xml.sample Sun Jul 14 02:22:32 2024 +0000 +++ b/tool_data_table_conf.xml.sample Sun Jul 14 03:56:55 2024 +0000 @@ -2,6 +2,6 @@ <!-- Locations of all fasta files under genome directory --> <table name="all_fasta" comment_char="#"> <columns>value, dbkey, name, path</columns> - <file path="tool-data/all_fasta.loc.sample" /> + <file path="test-data/all_fasta.loc" /> </table> </tables>
--- a/tool_data_table_conf.xml.test Sun Jul 14 02:22:32 2024 +0000 +++ b/tool_data_table_conf.xml.test Sun Jul 14 03:56:55 2024 +0000 @@ -1,7 +1,7 @@ <tables> <!-- Locations of dbkeys and len files under genome directory --> - <table name="__dbkeys__" comment_char="#" allow_duplicate_entries="False"> + <table name="all_fasta" comment_char="#"> <columns>value, dbkey, name, path</columns> - <file path="${__HERE__}/tool-data/all_fasta.loc.sample" /> + <file path="${__HERE__}/test-data/all_fasta.loc" /> </table> </tables>