Mercurial > repos > trinity_ctat > ctat_genome_ref_lib_data_manager_test2
comparison data_manager/add_ctat_ref_lib.xml @ 10:acff55f2d70a draft
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author | trinity_ctat |
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date | Tue, 12 Dec 2017 15:39:20 -0500 |
parents | |
children | 1d8ffed7a312 |
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9:a2dc68c7fef6 | 10:acff55f2d70a |
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1 <tool id="ctat_genome_ref_lib_data_manager" | |
2 name="CTAT Genome Reference Library Data Manager" | |
3 version="1.0.0" tool_type="manage_data"> | |
4 <description>Retrieve, and/or Specify the location of, a CTAT Genome Reference Library. | |
5 </description> | |
6 <requirements> | |
7 <requirement type="package" version="2.7">python</requirement> | |
8 </requirements> | |
9 <command detect_errors="default"> | |
10 <![CDATA[ | |
11 echo "Current directory and contents" && pwd && ls -la . && | |
12 echo "Tool directory and contents are" && echo "$__tool_directory__" && ls -la "$__tool_directory__" && | |
13 python add_ctat_ref_lib.py ${download} | |
14 --ref_genome "${genome_name}" | |
15 --destination_path "${destination}" | |
16 -o "${out_file}" | |
17 ]]> | |
18 </command> | |
19 <inputs> | |
20 <param name="download" type="boolean" checked="false" | |
21 truevalue="--download" falsevalue="" label="Need to Download? (yes/no)" /> | |
22 <param name="genome_name" type="text" label="Reference Genome name" /> | |
23 <param name="destination" type="text" label="Local Destination (full path)" /> | |
24 </inputs> | |
25 <outputs> | |
26 <data name="out_file" format="data_manager_json" /> | |
27 </outputs> | |
28 <help> | |
29 Retrieve, and/or specify the location of, a CTAT Genome Reference Library. | |
30 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. | |
31 Specify the Full Path of the location where the CTAT Reference Library should be placed. | |
32 You will need approximately 30GB of space for this library. | |
33 If you already have the library, specify the full path of the location where it exists and leave the download box unchecked. | |
34 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. | |
35 For more information on CTAT Genome Reference Libraries, see <a http="https://github.com/FusionFilter/FusionFilter/wiki">FusionFilter</a> | |
36 </help> | |
37 </tool> |