diff data_manager/mummer4_index_builder.xml @ 0:a2a04db1bbf3 draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/data_manager/mummer4_index_builder.xml	Thu May 24 21:11:29 2018 -0400
@@ -0,0 +1,30 @@
+<tool id="mummer4_index_builder_data_manager" name="Mummer 4 index" tool_type="manage_data" version="0.0.3">
+    <description>builder</description>
+    <requirements>
+        <requirement type="package" version="4.0.0beta2">mummer4</requirement>
+    </requirements>
+    <command detect_errors="exit_code"><![CDATA[
+        python '$__tool_directory__/mummer4_index_builder.py'
+        '${out_file}'
+        --fasta_filename '${all_fasta_source.fields.path}'
+        --fasta_dbkey '${all_fasta_source.fields.dbkey}'
+        --fasta_description '${all_fasta_source.fields.name}'
+        --data_table_name mummer4_indexes
+    ]]></command>
+    <inputs>
+        <param name="all_fasta_source" type="select" label="Source FASTA Sequence">
+            <options from_data_table="all_fasta"/>
+        </param>
+        <param name="sequence_name" type="text" value="" label="Name of sequence" />
+        <param name="sequence_id" type="text" value="" label="ID for sequence" />
+    </inputs>
+    <outputs>
+        <data name="out_file" format="data_manager_json"/>
+    </outputs>
+
+    <help>
+.. class:: infomark
+
+**Notice:** If you leave name, description, or id blank, it will be generated automatically.
+    </help>
+</tool>