Mercurial > repos > trinity_ctat > ctat_genome_ref_lib_data_manager_test2
changeset 10:acff55f2d70a draft
Uploaded
author | trinity_ctat |
---|---|
date | Tue, 12 Dec 2017 15:39:20 -0500 |
parents | a2dc68c7fef6 |
children | 1d8ffed7a312 |
files | data_manager/add_ctat_ref_lib.xml |
diffstat | 1 files changed, 37 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/data_manager/add_ctat_ref_lib.xml Tue Dec 12 15:39:20 2017 -0500 @@ -0,0 +1,37 @@ +<tool id="ctat_genome_ref_lib_data_manager" + name="CTAT Genome Reference Library Data Manager" + version="1.0.0" tool_type="manage_data"> + <description>Retrieve, and/or Specify the location of, a CTAT Genome Reference Library. + </description> + <requirements> + <requirement type="package" version="2.7">python</requirement> + </requirements> + <command detect_errors="default"> + <![CDATA[ + echo "Current directory and contents" && pwd && ls -la . && + echo "Tool directory and contents are" && echo "$__tool_directory__" && ls -la "$__tool_directory__" && + python add_ctat_ref_lib.py ${download} + --ref_genome "${genome_name}" + --destination_path "${destination}" + -o "${out_file}" + ]]> + </command> + <inputs> + <param name="download" type="boolean" checked="false" + truevalue="--download" falsevalue="" label="Need to Download? (yes/no)" /> + <param name="genome_name" type="text" label="Reference Genome name" /> + <param name="destination" type="text" label="Local Destination (full path)" /> + </inputs> + <outputs> + <data name="out_file" format="data_manager_json" /> + </outputs> + <help> + Retrieve, and/or specify the location of, a CTAT Genome Reference Library. + When download is true, the file retrieved and processed is https://data.broadinstitute.org/Trinity/CTAT_RESOURCE_LIB/GRCh38_gencode_v26_CTAT_lib_Nov012017.plug-n-play.tar.gz. + Specify the Full Path of the location where the CTAT Reference Library should be placed. + You will need approximately 30GB of space for this library. + If you already have the library, specify the full path of the location where it exists and leave the download box unchecked. + The Reference Genome name may be left empty if downloading. The name will be used as the selector text of the entry in the data table. + For more information on CTAT Genome Reference Libraries, see <a http="https://github.com/FusionFilter/FusionFilter/wiki">FusionFilter</a> + </help> +</tool> \ No newline at end of file