diff data_manager/bowtie2_index_builder.xml @ 0:5515ee3559f0 draft default tip

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/data_manager/bowtie2_index_builder.xml	Tue Aug 20 11:58:27 2013 -0400
@@ -0,0 +1,25 @@
+<tool id="bowtie2_index_builder_data_manager" name="Bowtie2 index" tool_type="manage_data" version="0.0.1">
+    <description>bowtie2 index builder</description>
+    <requirements>
+        <requirement type="package" version="2.1.0">bowtie</requirement>
+    </requirements>
+    <command interpreter="python">bowtie2_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 "bowtie2_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" help="Leave blank to use all_fasta name" />
+        <param type="text" name="sequence_id" value="" label="ID for sequence" help="Leave blank to use all_fasta id" />
+    </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>