--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/data_manager/kallisto_index_builder.xml	Sat Aug 05 04:02:01 2017 -0400
@@ -0,0 +1,51 @@
+<tool id="kallisto_index_builder_data_manager" name="Kallisto" tool_type="manage_data" version="0.43.1">
+    <description>index builder</description>
+    <requirements>
+        <requirement type="package" version="0.43.1">kallisto</requirement>
+    </requirements>
+    <command detect_errors="exit_code"><![CDATA[
+        python '$__tool_directory__/kallisto_index_builder.py' --output '${out_file}'
+            --fasta_filename '${all_fasta_source.fields.path}'
+            --fasta_dbkey '${all_fasta_source.fields.dbkey}'
+            --fasta_description '${all_fasta_source.fields.name}'
+            --data_table_name kallisto_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" />
+    </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.
+
+What is Kallisto?
+---------------
+
+`kallisto <https://pachterlab.github.io/kallisto/about>`__ is a program for
+quantifying abundances of transcripts from RNA-Seq data, or more generally of
+target sequences using high-throughput sequencing reads. It is based on the
+novel idea of pseudoalignment for rapidly determining the compatibility of
+reads with targets, without the need for alignment. On benchmarks with standard
+RNA-Seq data, kallisto can quantify 30 million human reads in less than 3
+minutes on a Mac desktop computer using only the read sequences and a
+transcriptome index that itself takes less than 10 minutes to build.
+Pseudoalignment of reads preserves the key information needed for
+quantification, and kallisto is therefore not only fast, but also as accurate
+as existing quantification tools. In fact, because the pseudoalignment
+procedure is robust to errors in the reads, in many benchmarks kallisto
+significantly outperforms existing tools.
+]]>
+    </help>
+    <citations>
+        <citation type="doi">10.1038/nmeth.3317</citation>
+    </citations>
+</tool>