--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/data_manager/salmon_index_builder.xml	Tue Aug 14 11:19:49 2018 -0400
@@ -0,0 +1,38 @@
+<tool id="salmon_index_builder_data_manager" name="Salmon" tool_type="manage_data" version="0.9.1">
+    <description>index builder</description>
+    <requirements>
+        <requirement type="package" version="0.9.1">salmon</requirement>
+    </requirements>
+    <command detect_errors="exit_code"><![CDATA[
+        python '$__tool_directory__/salmon_index_builder.py' --output '${out_file}'
+            --fasta_filename '${all_fasta_source.fields.path}'
+            --fasta_dbkey '${all_fasta_source.fields.dbkey}'
+            --fasta_description '${all_fasta_source.fields.name}'
+            --kmer_size "${kmer_size}"
+            --data_table_name salmon_indexes
+        ]]>
+    </command>
+    <inputs>
+        <param label="Source FASTA Sequence" name="all_fasta_source" type="select">
+            <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" />
+        <param name="kmer_size" type="integer" optional='true' value="21" max="32" label="The size of the k-mer on which the index is built"
+                    help="There is a tradeoff here between the distinctiveness of the k-mers and their robustness to errors. The shorter the k-mers, the more robust they will be to errors in the reads, but the longer the k-mers, the more distinct they will be.  We generally recommend using a k-mer size of at least 20. MUST BE AN ODD VALUE "/>
+
+
+
+    </inputs>
+    <outputs>
+        <data name="out_file" format="data_manager_json" />
+    </outputs>
+    <help>
+<![CDATA[
+.. class:: infomark
+
+**Notice:** If you leave name, description, or id blank, it will be generated automatically.
+]]>
+    </help>
+</tool>
+