diff data_manager/add_ctat_ref_lib.xml @ 0:fcf82328f066 draft default tip

new version. Not tested yet.

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/data_manager/add_ctat_ref_lib.xml	Mon Jan 22 16:06:42 2018 -0500
@@ -0,0 +1,61 @@
+<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>
+        <requirement type="package" version="0.3.0">gmap-fusion</requirement>
+        <!-- gmap-fusion is required in order to process downloaded libraries 
+             to create all of the required files and indexes. It includes gmap
+             and FusionFilter, programs from both of which are needed.
+        -->
+    </requirements>
+    <command detect_errors="default">
+        <![CDATA[
+        python $__tool_directory__/add_ctat_ref_lib.py 
+            --genome_name "${genome_name}"
+            --destination_path "${destination}" 
+            --output_filename "${out_file}"
+            #if str(${download}) == "true":
+                --download "${filename}"
+            #end if
+        ]]>
+    </command>
+    <inputs>
+        <!--
+        <param name="download" type="boolean" checked="false"
+             truevalue="- -download" falsevalue="" label="Need to Download? (yes/no)" />
+            <param name="download" type="select" label="Need to Download?">
+                <option value="single" selected="true">Single Dataset</option>
+                <option value="paired_collection">Paired Collection</option>
+            <when value="paired_collection">
+                 <param name="fastq_input" format="fastqsanger" type="data_collection" collection_type="paired" label="Select dataset pair" help="Specify paired dataset collection containing paired reads"/>
+            </when>
+        -->
+        <conditional name="download_question">
+            <param name="download" type="boolean" checked="false" label="Need to Download? (yes/no)" />
+            </param>
+            <when value="true">
+                 <param name="filename" type="select" label="Select File" display="radio" 
+                     dynamic_options="get_ctat_genome_filenames()" help="Select a CTAT Genome Reference Library to Download." />
+            </when>
+        </conditional>
+
+        <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>
+    <code file="add_ctat_ref_lib.py"
+</tool>