diff data_manager/data_manager_fetch_and_index_maf.xml @ 0:de73b258a601 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_index_maf commit 21852ee28cf191d12b1ffe5583efaa5deeb1d80d-dirty"

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/data_manager/data_manager_fetch_and_index_maf.xml	Wed Jul 15 14:30:00 2020 -0400
@@ -0,0 +1,26 @@
+<tool id="data_manager_fetch_and_index_maf" name="Fetch and index" version="1.0.0" tool_type="manage_data" profile="19.01">
+    <description>multiple alignments from UCSC</description>
+    <requirements>
+        <requirement type="package" version="3.7">python</requirement>
+        <requirement type="package" version="0.8.8">bx-python</requirement>
+    </requirements>
+    <command detect_errors="exit_code"><![CDATA[
+        python '$__tool_directory__/data_manager_fetch_and_index_maf.py' --nexus '$nexus'
+        --name '$name' --output '$output' --dbkey '${dbkey.fields.dbkey}'
+    ]]></command>
+    <inputs>
+        <param name="dbkey" type="select" label="Species aligned against">
+            <options from_data_table="all_fasta"/>
+        </param>
+        <param name="nexus" type="text" label="FTP path to nexus file on UCSC." help="The MAF paths will be computed from this" />
+        <param name="name" type="text" label="Display name for this multi-alignment" />
+    </inputs>
+    <outputs>
+        <data name="output" format="data_manager_json" metadata_source="dbkey" />
+    </outputs>
+    <help>
+**What it does**
+
+This data manager fetches a multiple alignment from UCSC's FTP server and indexes it with bx-python.
+    </help>
+</tool>