Mercurial > repos > diodupima > coast_search_blast
changeset 3:9da41e56d579 draft
"planemo upload commit 5a255cfbba89d13ea62aeaaabd2801ac618cbb6b-dirty"
| author | diodupima |
|---|---|
| date | Thu, 08 Jul 2021 00:20:07 +0000 |
| parents | 82744218dd47 |
| children | 5528e73e6178 |
| files | macros.xml tool-data/coast_taxonomic_filters.loc.sample tool_data_table_conf.xml.sample |
| diffstat | 3 files changed, 8 insertions(+), 26 deletions(-) [+] |
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--- a/macros.xml Wed Jul 07 16:33:11 2021 +0000 +++ b/macros.xml Thu Jul 08 00:20:07 2021 +0000 @@ -44,7 +44,7 @@ <xml name="protein_db"> <param name="db" type="select" optional="false" label="BLAST-Ready protein sequences database."> - <options from_data_table="blastdb_p" /> + <options from_data_table="blastdb" /> </param> </xml> <token name="@DB@"><![CDATA[
--- a/tool-data/coast_taxonomic_filters.loc.sample Wed Jul 07 16:33:11 2021 +0000 +++ b/tool-data/coast_taxonomic_filters.loc.sample Thu Jul 08 00:20:07 2021 +0000 @@ -1,28 +1,10 @@ #This is a sample file distributed with Galaxy that enables tools #to use a directory of Samtools indexed sequences data files. You will need -#to create these data files and then create a sam_fa_indices.loc file +#to create these data files and then create a coast_taxonomic_filters.loc file #similar to this one (store it in this directory) that points to -#the directories in which those files are stored. The sam_fa_indices.loc +#the directories in which those files are stored. The coast_taxonomic_filters.loc #file has this format (white space characters are TAB characters): # -#index <seq> <location> -# -#So, for example, if you had hg18 indexed stored in -#/depot/data2/galaxy/sam/, -#then the sam_fa_indices.loc entry would look like this: -# -#index hg18 /depot/data2/galaxy/sam/hg18.fa -# -#and your /depot/data2/galaxy/sam/ directory -#would contain hg18.fa and hg18.fa.fai files: +#value <name> <node_name> <path> # -#-rw-r--r-- 1 james universe 830134 2005-09-13 10:12 hg18.fa -#-rw-r--r-- 1 james universe 527388 2005-09-13 10:12 hg18.fa.fai -# -#Your coast_taxonomic_filters.loc file should include an entry per line for -#each index set you have stored. The file in the path does actually -#exist, but it should never be directly used. Instead, the name serves -#as a prefix for the index file. For example: -# -#index hg18 /depot/data2/galaxy/sam/hg18.fa -#index hg19 /depot/data2/galaxy/sam/hg19.fa \ No newline at end of file +#2_2021_07_08_00_33_22 bac (taxid - 2) (date - 2021_07_08_00) bac /depot/data2/galaxy/sam/hg18.fa
--- a/tool_data_table_conf.xml.sample Wed Jul 07 16:33:11 2021 +0000 +++ b/tool_data_table_conf.xml.sample Thu Jul 08 00:20:07 2021 +0000 @@ -4,8 +4,8 @@ <columns>value, name, node_name, path</columns> <file path="tool-data/coast_taxonomic_filters.loc" /> </table> - <table name="blastdb_p" comment_char="#" allow_duplicate_entries="False"> - <columns>value, name, node_name, path</columns> - <file path="tool-data/coast_taxonomic_filters.loc" /> + <table name="blastdb" comment_char="#"> + <columns>value, name, path</columns> + <file path="tool-data/blastdb.loc" /> </table> </tables> \ No newline at end of file