Mercurial > repos > chrisw > monorail_test
changeset 21:1ec6238425ac draft
Uploaded
| author | chrisw |
|---|---|
| date | Thu, 14 Nov 2019 05:04:56 +0000 |
| parents | f158bf75c44c |
| children | e66c08660de6 |
| files | monorail.xml tool-data/monorail_index.loc.sample tool_data_table_conf.xml.sample |
| diffstat | 3 files changed, 1 insertions(+), 29 deletions(-) [+] |
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--- a/monorail.xml Wed Nov 13 23:55:04 2019 +0000 +++ b/monorail.xml Thu Nov 14 05:04:56 2019 +0000 @@ -70,7 +70,7 @@ <!-- Genome source. --> <conditional name="refGenomeSource"> - <param name="genomeDir" argument="--genomeDir" type="select" label="Select reference genome index set" help="If your genome of interest is not listed, contact the Galaxy team"> + <param name="genomeDir" type="select" label="Select reference genome index set" help="If your genome of interest is not listed, contact the Galaxy team"> <options from_data_table="monorail_index"> <validator type="no_options" message="No indexes are available for the selected input dataset"/> </options>
--- a/tool-data/monorail_index.loc.sample Wed Nov 13 23:55:04 2019 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,22 +0,0 @@ -#This is a sample file distributed with Galaxy that enables tools -#to use a directory of rna-star indexed sequences data files. You will -#need to create these data files and then create a rnastar_index2.loc -#file similar to this one (store it in this directory) that points to -#the directories in which those files are stored. The rnastar_index2.loc -#file has this format (longer white space characters are TAB characters): -# -#<unique_build_id> <dbkey> <display_name> <file_base_path> <withGTF> -# -#The <with_gtf> column should be 1 or 0, indicating whether the index was made -#with an annotation (i.e., --sjdbGTFfile and --sjdbOverhang were used) or not, -#respecively. -# -#Note that STAR indices can become quite large. Consequently, it is only -#advisable to create indices with annotations if it's known ahead of time that -#(A) the annotations won't be frequently updated and (B) the read lengths used -#will also rarely vary. If either of these is not the case, it's advisable to -#create indices without annotations and then specify an annotation file and -#maximum read length (minus 1) when running STAR. -# -#hg19 hg19 hg19 full /mnt/galaxyIndices/genomes/hg19/rnastar 0 -#hg19Ensembl hg19Ensembl hg19 full with Ensembl annotation /mnt/galaxyIndices/genomes/hg19Ensembl/rnastar 1
--- a/tool_data_table_conf.xml.sample Wed Nov 13 23:55:04 2019 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,6 +0,0 @@ -<tables> - <table name="monorail_index" comment_char="#"> - <columns>value, dbkey, name, path</columns> - <file path="tool-data/monorail_index.loc" /> - </table> -</tables>