--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/kraken_taxonomy_report.xml	Wed Jun 01 17:25:40 2016 -0400
@@ -0,0 +1,242 @@
+<?xml version="1.0"?>
+<tool id="kraken_taxonomy_report" name="Kraken taxonomic report" version="0.0.1">
+    <description>view report of classification for multiple samples</description>
+    <requirements>
+        <requirement type="package" version="1.66">biopython</requirement>
+    </requirements>
+    <stdio>
+        <exit_code range="1:" />
+        <exit_code range=":-1" />
+    </stdio>
+    <version_command>python ${__tool_directory__}/kraken_taxonomy_report.py --version</version_command>
+    <command>
+<![CDATA[
+
+#for $input_classification in $classification:
+    ln -s "${input_classification}" "${input_classification.element_identifier}" &&
+#end for
+
+export KRAKEN_DB_PATH="${kraken_database.fields.path}" && 
+python ${__tool_directory__}/kraken_taxonomy_report.py
+
+--db "${kraken_database.fields.name}"
+${show_zeros}
+${header_line}
+${otu_name}
+${taxonomy}
+${show_rank}
+${intermediate}
+${sanitize_names}
+#if str( $cluster.cluster ):
+    --cluster "${cluster.cluster}"
+#else:
+    ${cluster.summation}
+#end if
+
+--output "${output_report}"
+
+#if $output_tree:
+    --output-tree "${output_tree}"
+#end if
+
+#for $input_classification in $classification:
+    "${input_classification.element_identifier}"
+#end for
+
+]]>
+    </command>
+    <inputs>
+        <param format="tabular" label="Kraken output" multiple="True" name="classification" type="data" />
+        <param checked="False" falsevalue="" argument="--show-zeros" label="Display taxa even if they lack a read in any sample" name="show_zeros" truevalue="--show-zeros" type="boolean" />
+        <param checked="True" falsevalue="" argument="--header-line" label="Display a header line indicating sample IDs" name="header_line" truevalue="--header-line" type="boolean" />
+        <param label="Select a Kraken database" name="kraken_database" type="select" help="Select the same database used to classify reads">
+            <options from_data_table="kraken_databases">
+                <validator message="No Kraken databases are available" type="no_options" />
+            </options>
+        </param>
+        <param label="How to name OTUs" name="otu_name" type="select" multiple="False">
+            <option value="" selected="True">Node name only</option>
+            <option value="--name-long">Taxonified Name</option>
+            <option value="--name-id">Node ID</option>
+        </param>
+        <param checked="True" falsevalue="" argument="--sanitize-names" label="Sanitize Names" name="sanitize_names" truevalue="--sanitize-names" type="boolean" help="Replace special chars (\t| |\||\.;) with underscore (_)" />
+        <param checked="False" falsevalue="" argument="--show-rank" label="Output Rank Name in (second to) last column" name="show_rank" truevalue="--show-rank" type="boolean" />
+        <param checked="False" falsevalue="" argument="--taxonomy" label="Output taxonomy in last column" name="taxonomy" truevalue="--taxonomy" type="boolean" />
+        <param checked="False" falsevalue="" argument="--intermediate" label="Display intermediate ranks" name="intermediate" truevalue="--intermediate" type="boolean" />
+        <conditional name="cluster">
+            <param argument="--cluster" help="Combines rows under the selected taxon and reports only selected rank." label="Cluster by taxonomic rank" name="cluster" type="select">
+                <option value="Superkingdom">Superkingdom</option>
+                <option value="Kingdom">Kingdom</option>
+                <option value="Subkingdom">Subkingdom</option>
+                <option value="Superphylum">Superphylum</option>
+                <option value="Phylum">Phylum</option>
+                <option value="Subphylum">Subphylum</option>
+                <option value="Superclass">Superclass</option>
+                <option value="Class">Class</option>
+                <option value="Subclass">Subclass</option>
+                <option value="Infraclass">Infraclass</option>
+                <option value="Superorder">Superorder</option>
+                <option value="Order">Order</option>
+                <option value="Suborder">Suborder</option>
+                <option value="Infraorder">infraorder</option>
+                <option value="Parvorder">Parvorder</option>
+                <option value="Superfamily">Superfamily</option>
+                <option value="Family">Family</option>
+                <option value="Subfamily">Subfamily</option>
+                <option value="Tribe">Tribe</option>
+                <option value="Subtribe">Subtribe</option>
+                <option value="Genus">Genus</option>
+                <option value="Subgenus">Subgenus</option>
+                <option value="Species Group">Species Group</option>
+                <option value="Species Subgroup">Species Subgroup</option>
+                <option value="Species">Species</option>
+                <option value="Subspecies">Subspecies</option>
+                <option value="Varietas">Varietas</option>
+                <option value="Forma">Forma</option>
+                <option value="" selected="True">No Clustering</option>
+            </param>
+            <when value="">
+                <param checked="False" falsevalue="" argument="--summation" label="Summation of lower ranks into higher ranks" name="summation" truevalue="--summation" type="boolean" />
+            </when>
+            <when value="Superkingdom"/>
+            <when value="Kingdom"/>
+            <when value="Subkingdom"/>
+            <when value="Superphylum"/>
+            <when value="Phylum"/>
+            <when value="Subphylum"/>
+            <when value="Superclass"/>
+            <when value="Class"/>
+            <when value="Subclass"/>
+            <when value="Infraclass"/>
+            <when value="Superorder"/>
+            <when value="Order"/>
+            <when value="Suborder"/>
+            <when value="Infraorder"/>
+            <when value="Parvorder"/>
+            <when value="Superfamily"/>
+            <when value="Family"/>
+            <when value="Subfamily"/>
+            <when value="Tribe"/>
+            <when value="Subtribe"/>
+            <when value="Genus"/>
+            <when value="Subgenus"/>
+            <when value="Species Group"/>
+            <when value="Species Subgroup"/>
+            <when value="Species"/>
+            <when value="Subspecies"/>
+            <when value="Varietas"/>
+            <when value="Forma"/>
+        </conditional>
+        <param checked="False" falsevalue="" label="Output a newick tree" name="tree" truevalue="true" type="boolean" help="Trees are pruned at specified rank when clustering"/>
+    </inputs>
+    <outputs>
+        <data format="tabular" name="output_report" label="${tool.name} on ${on_string} (Abundances)"/>
+        <data format="txt" name="output_tree" label="${tool.name} on ${on_string} (Newick Tree)">
+            <filter>tree</filter>
+        </data>
+    </outputs>
+    <tests>
+        <test>
+            <param name="classification" value="input_kraken_1.tabular" ftype="tabular"/>
+            <param name="show_zeros" value="True"/>
+            <param name="header_line" value="True"/>
+            <param name="kraken_database" value="test_db"/>
+            <param name="otu_name" value=""/>
+            <param name="sanitize_names" value="True"/>
+            <param name="show_rank" value="True"/>
+            <param name="taxonomy" value="True"/>
+            <param name="intermediate" value="True"/>
+            <conditional name="cluster">
+                <param name="cluster" value=""/>
+                <param name="summation" value="True"/>
+            </conditional>
+            <param name="tree" value="True"/>
+            <output name="output_report" file="output_abundance_1.tabular" ftype="tabular"/>
+            <output name="output_tree" file="output_tree_1.newick" />
+        </test>
+        <test>
+            <param name="classification" value="input_kraken_1.tabular" ftype="tabular"/>
+            <param name="show_zeros" value="True"/>
+            <param name="header_line" value="True"/>
+            <param name="kraken_database" value="test_db"/>
+            <param name="otu_name" value=""/>
+            <param name="sanitize_names" value="True"/>
+            <param name="show_rank" value="True"/>
+            <param name="taxonomy" value="True"/>
+            <param name="intermediate" value="True"/>
+            <conditional name="cluster">
+                <param name="cluster" value=""/>
+                <param name="summation" value="False"/>
+            </conditional>
+            <param name="tree" value="True"/>
+            <output name="output_report" file="output_abundance_2.tabular" ftype="tabular"/>
+            <output name="output_tree" file="output_tree_1.newick" />
+        </test>
+        <test>
+            <param name="classification" value="input_kraken_1.tabular" ftype="tabular"/>
+            <param name="show_zeros" value="True"/>
+            <param name="header_line" value="True"/>
+            <param name="kraken_database" value="test_db"/>
+            <param name="otu_name" value=""/>
+            <param name="sanitize_names" value="True"/>
+            <param name="show_rank" value="True"/>
+            <param name="taxonomy" value="True"/>
+            <param name="intermediate" value="False"/>
+            <conditional name="cluster">
+                <param name="cluster" value="Species"/>
+            </conditional>
+            <param name="tree" value="True"/>
+            <output name="output_report" file="output_abundance_3.tabular" ftype="tabular"/>
+            <output name="output_tree" file="output_tree_3.newick" />
+        </test>
+        <test>
+            <param name="classification" value="input_kraken_1.tabular,input_kraken_2.tabular" ftype="tabular"/>
+            <param name="show_zeros" value="True"/>
+            <param name="header_line" value="True"/>
+            <param name="kraken_database" value="test_db"/>
+            <param name="otu_name" value=""/>
+            <param name="sanitize_names" value="True"/>
+            <param name="show_rank" value="True"/>
+            <param name="taxonomy" value="True"/>
+            <param name="intermediate" value="False"/>
+            <conditional name="cluster">
+                <param name="cluster" value="Species"/>
+            </conditional>
+            <param name="tree" value="True"/>
+            <output name="output_report" file="output_abundance_4.tabular" ftype="tabular"/>
+            <output name="output_tree" file="output_tree_3.newick" />
+        </test>
+    </tests>
+    <help>
+<![CDATA[
+
+.. class:: warningmark
+
+**Note**: the database used must be the same as the one used in the original Kraken run
+
+-----
+
+**What is Does**
+
+Summarizes read counts across taxonomic ranks for multiple samples. This is convenient for comparing results across multiple experiments, conditions, locations, etc.
+
+-----
+
+**Output**
+
+The output is tab-delimited, with one line per taxon.
+
+Will optionally output a newick tree built from the kraken database taxonomy using the specified options. Tree branch lengths will be set to "1.00000".
+
+
+]]>
+    </help>
+    <citations>
+        <citation type="bibtex">@unpublished{Kraken-Taxonomy-Report:2016,
+          title  = "Kraken Taxonomy Report",
+          author = "Daniel Blankenberg",
+          url    = "https://github.com/blankenberg/Kraken-Taxonomy-Report",
+          year   = "2016 (accessed June 1, 2016)"
+        }</citation>
+    </citations>
+</tool>