--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/data_manager/salmon_index_builder.xml	Wed Jul 24 07:17:00 2019 -0400
@@ -0,0 +1,50 @@
+<tool id="salmon_index_builder_data_manager" name="Salmon" tool_type="manage_data" version="0.11.3" profile_version="19.01">
+    <description>index builder</description>
+    <requirements>
+        <requirement type="package" version="0.11.3">salmon</requirement>
+        <requirement type="package" version="3.7">python</requirement>
+    </requirements>
+   <macros>
+       <token name="@IDX_VERSION@">q5</token>
+   </macros>
+    <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_versioned
+            --index_version @IDX_VERSION@
+        ]]>
+    </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>
+    <tests>
+        <test>
+            <param name="all_fasta_source" value="phiX174"/>
+            <param name="sequence_name" value="sequence_name"/>
+            <param name="sequence_id" value="sequence_id"/>
+            <output name="out_file" file="salmon_phiX174.data_manager_json"/>
+        </test>
+    </tests>
+    <help>
+<![CDATA[
+.. class:: infomark
+
+**Notice:** If you leave name, description, or id blank, it will be generated automatically.
+]]>
+    </help>
+    <citations>
+        <citation type="doi">https://doi.org/10.1038/nmeth.4197</citation>
+    </citations>
+</tool>