diff data_manager/data_manager_fetch_and_index_maf.xml @ 0:475b10cd2ae8 draft default tip

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/data_manager/data_manager_fetch_and_index_maf.xml	Tue Jun 09 14:27:06 2020 -0400
@@ -0,0 +1,35 @@
+<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 NCBI</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'
+        --alignments '$alignments' --name '$name' --output '$output'
+    ]]></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"/>
+    </outputs>
+    <tests>
+        <test />
+    </tests>
+    <help>
+**What it does**
+
+Fetches a multiple alignment from UCSC's FTP server and indexes it with bx-python.
+
+------
+
+.. class:: infomark
+
+**Notice:** If you leave name, description, or id blank, it will be generated automatically.
+    </help>
+</tool>