diff data_manager/data_manager_gatk_picard_index_builder.xml @ 0:619dd9e9c09c draft

Imported from capsule None

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/data_manager/data_manager_gatk_picard_index_builder.xml	Tue Apr 01 10:48:03 2014 -0400
@@ -0,0 +1,33 @@
+<tool id="gatk_picard_index_builder" name="Generate GATK-sorted Picard indexes" tool_type="manage_data" version="0.0.1">
+    <description>builder</description>
+    <requirements>
+        <requirement type="package" version="0.1.18">samtools</requirement>
+        <requirement type="package" version="1.56.0">picard</requirement>
+    </requirements>
+    <command interpreter="python">
+        data_manager_gatk_picard_index_builder.py "${out_file}" \
+            --jar "\$JAVA_JAR_PATH/CreateSequenceDictionary.jar" \
+            --fasta_filename "${all_fasta_source.fields.path}" \
+            --fasta_dbkey "${all_fasta_source.fields.dbkey}" \
+            --fasta_description "${all_fasta_source.fields.name}" \
+            --data_table_name "gatk_picard_indexes"
+    </command>
+    <inputs>
+        <param name="all_fasta_source" type="select" label="Source FASTA Sequence">
+            <options from_data_table="all_fasta"/>
+        </param>
+        <param type="text" name="sequence_name" value="" label="Name of sequence" />
+        <param type="text" name="sequence_id" 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>