|
10
|
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> |
