Mercurial > repos > yhoogstrate > featurecounts_valid_gff
changeset 40:4850787ee1d9
Uploaded
| author | yhoogstrate |
|---|---|
| date | Mon, 24 Feb 2014 08:19:34 -0500 |
| parents | 0abd1de08703 |
| children | c55c0c51b634 |
| files | featurecounts_valid_gff.xml tool-data/gene_sets.loc.sample tool_data_table_conf.xml.sample |
| diffstat | 3 files changed, 17 insertions(+), 11 deletions(-) [+] |
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--- a/featurecounts_valid_gff.xml Fri Feb 21 04:23:38 2014 -0500 +++ b/featurecounts_valid_gff.xml Mon Feb 24 08:19:34 2014 -0500 @@ -93,7 +93,7 @@ </param> <when value="indexed_filtered"> <param name="reference_gene_sets" type="select" label="Reference Gene Sets used during alignment (GFF/GTF)" > - <options from_file="gene_sets.loc"> + <options from_data_table="gene_sets"><!-- replaces 'from_file="gene_sets"' - more strict --> <column name="name" index="0"/> <column name="dbkey" index="1"/> <column name="value" index="2"/> @@ -104,7 +104,7 @@ </when> <when value="indexed_all"> <param name="reference_gene_sets" type="select" label="Reference Gene Sets used during alignment (GFF/GTF)" > - <options from_file="gene_sets.loc"> + <options from_data_table="gene_sets"><!-- replaces 'from_file="gene_sets"' - more strict --> <column name="name" index="0"/> <column name="dbkey" index="1"/> <column name="value" index="2"/>
--- a/tool-data/gene_sets.loc.sample Fri Feb 21 04:23:38 2014 -0500 +++ b/tool-data/gene_sets.loc.sample Mon Feb 24 08:19:34 2014 -0500 @@ -1,15 +1,18 @@ -# Because of this file, galaxy tools can access gene annotations +# This is a sample file distributed with Galaxy that enables tools +# to use gene/exon annotations in the GFF/GTF format. You will need +# to add all the gene set annotations in this configuration file. +# Because of this file, galaxy tools are able to access gene annotations # provided as GFF / GTF files by selecting on: -# - Priorty (order in the file) +# - Priorty (defined by the order in the file) # - Provider # - dbkey (reference genome id) # # The gene_sets.loc file syntax is: # <name/UID> <dbkey> <path> <provider> <URL/reference*> -# -# *optional +# *optional # # Please ensure maximally one TAB (\t) between two columns! +# --------------------------------------------------------- # # In case you have TWO or MORE providers PER dbkey, the one mentioned # first in the file, should have the "default" priority.
--- a/tool_data_table_conf.xml.sample Fri Feb 21 04:23:38 2014 -0500 +++ b/tool_data_table_conf.xml.sample Mon Feb 24 08:19:34 2014 -0500 @@ -1,5 +1,8 @@ -<?xml version="1.0"?> -<table name="gene_sets" comment_char="#"> - <columns>name, dbkey, value, provider, reference</columns> - <file path="tool-data/gene_sets.loc.sample" /> -</table> \ No newline at end of file +<!-- Use the file tool_data_table_conf.xml.oldlocstyle if you don't want to update your loc files as changed in revision 4550:535d276c92bc--> +<tables> + <!-- Location of all GFF/GTF files --> + <table name="gene_sets" comment_char="#"> + <columns>name, dbkey, value, provider, reference</columns> + <file path="tool-data/gene_sets.loc" /> + </table> +</tables> \ No newline at end of file