Mercurial > repos > iuc > bedtools
changeset 23:13400f3c3ec5 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 6418f2e58def1a81b3aa7c04cb5dc33decea1a96
| author | iuc |
|---|---|
| date | Fri, 09 Feb 2018 09:00:06 -0500 |
| parents | bd7721ad15aa |
| children | 33c3ddea63c5 |
| files | getfastaBed.xml tool-data/fasta_indexes.loc.sample tool_data_table_conf.xml.sample |
| diffstat | 3 files changed, 36 insertions(+), 2 deletions(-) [+] |
line wrap: on
line diff
--- a/getfastaBed.xml Sun Jan 21 07:17:19 2018 -0500 +++ b/getfastaBed.xml Fri Feb 09 09:00:06 2018 -0500 @@ -1,4 +1,4 @@ -<tool id="bedtools_getfastabed" name="GetFastaBed" version="@WRAPPER_VERSION@.0"> +<tool id="bedtools_getfastabed" name="GetFastaBed" version="@WRAPPER_VERSION@.1"> <description>use intervals to extract sequences from a FASTA file</description> <macros> <import>macros.xml</import> @@ -34,7 +34,7 @@ </when> <when value="preloaded"> <param name="fasta_id" type="select"> - <options from_data_table="all_fasta" /> + <options from_data_table="fasta_indexes" /> </param> </when> </conditional>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool-data/fasta_indexes.loc.sample Fri Feb 09 09:00:06 2018 -0500 @@ -0,0 +1,29 @@ +#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 fasta_indexes.loc file +#similar to this one (store it in this directory) that points to +#the directories in which those files are stored. The fasta_indexes.loc +#file has this format (white space characters are TAB characters): +# +# <unique_build_id> <dbkey> <display_name> <file_base_path> +# +#So, for example, if you had hg19 Canonical indexed stored in +# +# /depot/data2/galaxy/hg19/sam/, +# +#then the fasta_indexes.loc entry would look like this: +# +#hg19canon hg19 Human (Homo sapiens): hg19 Canonical /depot/data2/galaxy/hg19/sam/hg19canon.fa +# +#and your /depot/data2/galaxy/hg19/sam/ directory +#would contain hg19canon.fa and hg19canon.fa.fai files. +# +#Your fasta_indexes.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: +# +#hg18canon hg18 Human (Homo sapiens): hg18 Canonical /depot/data2/galaxy/hg18/sam/hg18canon.fa +#hg18full hg18 Human (Homo sapiens): hg18 Full /depot/data2/galaxy/hg18/sam/hg18full.fa +#hg19canon hg19 Human (Homo sapiens): hg19 Canonical /depot/data2/galaxy/hg19/sam/hg19canon.fa +#hg19full hg19 Human (Homo sapiens): hg19 Full /depot/data2/galaxy/hg19/sam/hg19full.fa
--- a/tool_data_table_conf.xml.sample Sun Jan 21 07:17:19 2018 -0500 +++ b/tool_data_table_conf.xml.sample Fri Feb 09 09:00:06 2018 -0500 @@ -4,6 +4,11 @@ <columns>value, dbkey, name, path</columns> <file path="tool-data/all_fasta.loc" /> </table> + <!-- Locations of all sam indexes under genome directory --> + <table name="fasta_indexes" comment_char="#"> + <columns>value, dbkey, name, path</columns> + <file path="tool-data/fasta_indexes.loc" /> + </table> <!-- Locations of all gff files with annotations of genome builds --> <table name="all_gff" comment_char="#"> <columns>value, dbkey, name, path</columns>