--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/macros.xml	Fri Oct 11 18:24:47 2019 -0400
@@ -0,0 +1,22 @@
+<macros>
+    <token name="@TOOL_VERSION@">2.7.0</token>
+    <token name="@INTYPES@">
+        fasta,fasta.gz,fastq,fastq.gz,fastqsanger,fastqsanger.gz
+    </token>
+    <xml name="citations">
+        <citations>
+          <citation type="bibtex">
+	    @article{ezewudo2018integrating,
+              title={Integrating standardized whole genome sequence analysis with a global Mycobacterium tuberculosis antibiotic resistance knowledgebase},
+              author={Ezewudo, Matthew and Borens, Amanda and Chiner-Oms, {\'A}lvaro and Miotto, Paolo and Chindelevitch, Leonid and Starks, Angela M and Hanna, Debra and Liwski, Richard and Zignol, Matteo and Gilpin, Christopher and others},
+              journal={Scientific reports},
+              volume={8},
+              number={1},
+              pages={15382},
+              year={2018},
+              publisher={Nature Publishing Group}
+            }
+	  </citation>
+        </citations>
+    </xml>
+</macros>

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/uvp.xml	Fri Oct 11 18:24:47 2019 -0400
@@ -0,0 +1,68 @@
+<tool id="uvp" name="Unified Variant analysis Pipeline for M. tuberculosis complex" version="@TOOL_VERSION@+galaxy0">
+    <description></description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <requirements>
+        <requirement type="package" version="@TOOL_VERSION@">uvp</requirement>
+    </requirements>
+    <version_command>uvp --version</version_command>
+    <command detect_errors="exit_code">
+        <![CDATA[
+        uvp
+            --threads \${GALAXY_SLOTS:-1}
+            #if $single_paired.single_paired_selector == 'yes'
+                -n '${single_paired.forward_input.element_identifier}'
+                -q '${single_paired.forward_input}' 
+                -q2 '${single_paired.reverse_input}'
+            #elif $single_paired.single_paired_selector == "collection":
+                -n '${single_paired.input_pair.forward.element_identifier}'
+                -q '${single_paired.input_pair.forward}'
+                -q2 '${single_paired.input_pair.reverse}'
+            #else:
+                -n '${single_paired.input_sequences.element_identifier}'
+                -q '${single_paired.input_sequences}'
+            #end if
+            --krakendb '${kraken_database.fields.path}'
+            -r '${reference}'
+            ${annotate}
+            --outdir outdir
+	]]>
+    </command>
+    <inputs>
+        <conditional name="single_paired">
+            <param name="single_paired_selector" type="select" label="Single or paired reads" help="--paired">
+                <option value="collection">Collection</option>
+                <option value="yes">Paired</option>
+                <option selected="True" value="no">Single</option>
+            </param>
+            <when value="collection">
+                <param format="fasta,fastq" name="input_pair" type="data_collection" collection_type="paired" label="Collection of paired reads" help="FASTA or FASTQ datasets" />
+            </when>
+            <when value="yes">
+                <param format="fasta,fastq" name="forward_input" type="data" label="Forward strand" help="FASTA or FASTQ dataset"/>
+                <param format="fasta,fastq" name="reverse_input" type="data" label="Reverse strand" help="FASTA or FASTQ dataset"/>
+            </when>
+            <when value="no">
+                <param format="fasta,fastq" label="Input sequences" name="input_sequences" type="data" help="FASTA or FASTQ datasets"/>
+            </when>
+        </conditional>
+	<param name="kraken_database" type="select">
+	    <options from_data_table="kraken_databases">
+	        <validator type="no_options" message="No Kraken databases are available" />
+            </options>
+        </param>
+	<param name="reference" type="data" format="fasta" label="Reference Sequence" />
+	<param name="annotate" type="boolean" truevalue="--annotate" falsevalue="" />
+    </inputs>
+    <outputs>
+        <data name="low_quals" label="Low-quality" format="tabular" from_work_dir="outdir/QC/low_quals.txt"/>
+    </outputs>
+    <tests>
+    </tests>
+    <help>
+      <![CDATA[
+      ]]>
+    </help>
+    <expand macro="citations" />
+</tool>