Mercurial > repos > galaxyp > custom_pro_db_annotation_data_manager
changeset 1:4c77cf5a2977 draft
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/data_manager_customProDB commit 141369f97aa2804d2bbfd9ed620ea2a5574994c2-dirty
| author | galaxyp |
|---|---|
| date | Mon, 25 Jan 2016 18:00:15 -0500 |
| parents | 663ee21a8609 |
| children | 20a1b026b798 |
| files | data_manager/customProDB_annotation.xml tool-data/customProDB.loc.sample tool_data_table_conf.xml.sample |
| diffstat | 3 files changed, 26 insertions(+), 1 deletions(-) [+] |
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--- a/data_manager/customProDB_annotation.xml Thu Jan 21 18:19:52 2016 -0500 +++ b/data_manager/customProDB_annotation.xml Mon Jan 25 18:00:15 2016 -0500 @@ -15,7 +15,7 @@ </param> <param type="text" name="sequence_name" value="" label="Name of sequence" /> <param type="text" name="sequence_id" value="" label="ID for sequence" />--> - <param type="text" name="dbkey" value="" label="UCSC dbKey for reference genome" /> + <param type="genomebuild" name="dbkey" value="" label="UCSC dbKey for reference genome" /> </inputs> <outputs> <data name="out_file" format="data_manager_json"/>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool-data/customProDB.loc.sample Mon Jan 25 18:00:15 2016 -0500 @@ -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/tool_data_table_conf.xml.sample Mon Jan 25 18:00:15 2016 -0500 @@ -0,0 +1,7 @@ +<tables> + <!-- Locations of all customProDB annotations under genome directory --> + <table name="customProDB" comment_char="#"> + <columns>value, dbkey, name, path</columns> + <file path="tool-data/customProDB.loc" /> + </table> +</tables>