diff data_manager/bowtie_color_space_index_builder.xml @ 0:0a0c648498e2 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie_index_builder commit 418f745190d77983c3fb09badb6298493bccf4e0

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/data_manager/bowtie_color_space_index_builder.xml	Tue Jan 05 12:57:11 2016 -0500
@@ -0,0 +1,32 @@
+<tool id="bowtie_color_space_index_builder_data_manager" name="Bowtie Color index" tool_type="manage_data" version="0.0.2">
+    <description>builder</description>
+    <requirements>
+        <requirement type="package" version="0.12.7">bowtie</requirement>
+    </requirements>
+    <command interpreter="python">
+        bowtie_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 "bowtie_indexes_color"
+            --color_space
+    </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>