--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/taxonomy_filter_refseq.xml	Wed Jan 16 08:30:47 2019 -0500
@@ -0,0 +1,117 @@
+<tool id="taxonomy_filter_refseq" name="Filter RefSeq by taxonomy" version="@TOOL_VERSION@+galaxy0">
+    <description>Only retain sequences that are descendants of a given taxonomic node.</description>
+    <macros>
+        <token name="@TOOL_VERSION@">0.1.4</token>
+    </macros>
+    <edam_topics>
+        <edam_topic>topic_0091</edam_topic>
+    </edam_topics>
+    <edam_operations>
+        <edam_operation>operation_3460</edam_operation>
+    </edam_operations>
+    <requirements>
+        <requirement type="package" version="@TOOL_VERSION@">rust-ncbitaxonomy</requirement>
+    </requirements>
+    <!-- current using redirect to output rather than output to file due to bug in pre-0.1.4 rust-ncbitaxonomy -->
+    <command detect_errors="aggressive"><![CDATA[
+        #if str($refseq.refseq_source) == 'cached':
+            #set $refseq_input = str( $refseq.cached_refseq.fields.path )
+        #else:
+            ln -s '$refseq.history_refseq' refseq.fasta &&
+            #set $refseq_input = "refseq.fasta"
+        #end if
+        #if str($taxonomy.taxonomy_source) == 'cached':
+            #set $taxonomy_dir = $taxonomy.taxonomy_table.fields.path
+        #else:
+            mkdir taxonomy && ln -s '$taxonomy.nodes' taxonomy/nodes.dmp && ln -s '$taxonomy.names' taxonomy/names.dmp &&
+            #set $taxonomy_dir = 'taxonomy'
+        #end if
+	    taxonomy_filter_refseq '$refseq_input' '$taxonomy_dir' '$ancestor_name' >'$refseq_output_fasta'
+    ]]></command>
+    <inputs>
+        <conditional name="taxonomy">
+            <param name="taxonomy_source" type="select" label="Choose source of NCBI Taxonomy">
+                <option value="cached" selected="true">Use built-in NCBI Taxonomy database</option>
+                <option value="history">Datasets from history</option>
+            </param>
+            <when value="cached">
+                <param type="select" name="taxonomy_table" label="NCBI Taxonomy database">
+                    <options from_data_table="ncbi_taxonomy">
+                        <filter type="sort_by" column="name" /> 
+                        <validator type="no_options" message="No NCBI Taxonomy downloads are available" />
+                    </options>
+                    <validator type="no_options" message="No NCBI Taxonomy database download is available" />
+                </param>
+            </when>
+            <when value="history">
+                <param name="nodes" type="data" format="txt" label="NCBI Taxonomy nodes.dmp file" />
+                <param name="names" type="data" format="txt" label="NCBI Taxonomy names.dmp file" />
+            </when>
+        </conditional>
+        <conditional name="refseq">
+            <param name="refseq_source" type="select" label="Choose source of RefSeq sequences">
+                <option value="cached" selected="true">Use a built-in RefSeq FASTA file</option>
+                <option value="history">History</option>
+            </param>
+            <when value="cached">
+                <param type="select" name="cached_refseq" label="Select RefSeq FASTA file">
+                    <options from_data_table="all_fasta">
+                        <filter type="sort_by" column="name" /> 
+                        <validator type="no_options" message="No FASTA data is available" />
+                    </options>
+                    <validator type="no_options" message="No FASTA data is available" />
+                </param>
+            </when>
+            <when value="history">
+                <param type="data" name="history_refseq" format="fasta" label="RefSeq FASTA file" />
+            </when>
+        </conditional>
+        <param name="ancestor_name" type="text" label="Ancestor taxon (scientific) name" />
+    </inputs>
+    <outputs>
+        <data name="refseq_output_fasta" format="fasta" label="${tool.name} on ${on_string}" />
+    </outputs>
+    <tests>
+        <test>
+            <param name="taxonomy_source" value="history" />
+            <param name="refseq_source" value="history" />
+            <param name="nodes" ftype="txt" value="sample_tree_nodes.dmp" />
+            <param name="names" ftype="txt" value="sample_tree_names.dmp" />
+            <param name="history_refseq" ftype="fasta" value="sample_refseq.fasta" />
+            <param name="ancestor_name" value="unclassified bacterial viruses" />
+            <output name="refseq_output_fasta" value="output1.fasta" />
+        </test>
+        <test>
+            <param name="taxonomy_source" value="cached" />
+            <param name="taxonomy_table" value="2019-01-01" />
+            <param name="refseq_source" value="cached" />
+            <param name="cached_refseq" value="refseq_sample" />
+            <param name="nodes" ftype="txt" value="sample_tree_nodes.dmp" />
+            <param name="names" ftype="txt" value="sample_tree_names.dmp" />
+            <param name="history_refseq" ftype="fasta" value="sample_refseq.fasta" />
+            <param name="ancestor_name" value="unclassified bacterial viruses" />
+            <output name="refseq_output_fasta" value="output1.fasta" />
+        </test>
+    </tests>
+    <help><![CDATA[
+        This tool allows NCBI RefSeq sequences to be filtered so that only those whose species name are 
+        descendants of a given taxon in the NCBI taxonomy are retained. For example, from the NCBI RefSeq
+        "other vertebrate" file only ray finned fishes can be retained by filtering for "Actinopterygii".
+
+        The NCBI RefSeq FASTA files can either be provided by the Galaxy administrator or from the user
+        history. The NCBI taxonomy should be provided by the Galaxy administrator but if that is not
+        possible the nodes.dmp and names.dmp files from the NCBI taxonomy can be provided in the history.
+    ]]></help>
+    <citations>
+       <citation type="bibtex">
+    @misc{vanHeusden2019,
+    author = {van Heusden, Peter},
+    year = {2019},
+    title = ncbitaxonomy Rust crate},
+    publisher = {crates.io},
+    journal = {Rust Package Registry},
+    url = {https://crates.io/crates/ncbitaxonomy},        
+    }
+        </citation>
+    </citations>
+</tool>