--- a/slamdunk.xml	Thu Oct 11 20:33:07 2018 -0400
+++ b/slamdunk.xml	Sun Jan 20 06:51:15 2019 -0500
@@ -1,8 +1,9 @@
-<tool id="slamdunk" name="Slamdunk" version="0.3.3">
+<tool id="slamdunk" name="Slamdunk" version="@TOOL_VERSION@+galaxy1">
     <description>- streamlining SLAM-seq analysis with ultra-high sensitivity</description>
-    <requirements>
-        <requirement type="package" version="0.3.3">slamdunk</requirement>
-    </requirements>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements" />
     <version_command>slamdunk --version</version_command>
     <command detect_errors="exit_code"><![CDATA[
     #if $reference_source.reference_source_selector == 'history':
@@ -30,26 +31,8 @@
         '$Reads'
     ]]></command>
     <inputs>
-        <conditional name="reference_source">
-            <param name="reference_source_selector" type="select" label="Genome" help="Select a built-in FASTA file (if available) or one from the history">
-                <option value="cached">Use a built-in FASTA</option>
-                <option value="history">Use a FASTA from history</option>
-            </param>
-            <when value="cached">
-                <param name="ref_file" type="select" label="Use built-in FASTA" help="Select genome from the list">
-                    <options from_data_table="all_fasta">
-                        <filter type="sort_by" column="2" />
-                        <validator type="no_options" message="No reference genomes are available" />
-                    </options>
-                    <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file"/>
-                </param>
-            </when>
-            <when value="history">
-                <param name="ref_file" type="data" format="fasta" label="Use the following dataset as the FASTA" help="You can upload a FASTA sequence to the history and use it as reference" />
-            </when>
-        </conditional>
-        <param name="Reference" type="data" format="bed" />
-        <param name="Reads" type="data" format="fastqsanger,fastqsanger.gz" />
+        <expand macro="reference_files" />
+        <param name="Reads" type="data" format="fastqsanger,fastqsanger.gz" label="FASTQ files"/>
         <section name="multimapper" title="Multimapper recovery"
             expanded="false">
             <section name="filterbed"
@@ -79,8 +62,6 @@
             <param name="minMQ" type="integer" min="0" value="2"
                 label="Minimum mapping quality"
                 help="Minimum mapping quality to consider alignments (default: 2)." />
-            <param name="minMQ" type="integer" label="Minimum mapping quality" min="0" value="2"
-                help="Minimum mapping quality to consider alignments (default: 2)." />
             <param name="minID" type="float" min="0" value="0.95"
                 label="Minimum alignment identity"
                 help="Minimum alignment-identity to consider alignments (default: 0.95)." />
@@ -105,11 +86,13 @@
             help="Maximum read length (before trimming)." />
     </inputs>
     <outputs>
-        <data name="outputBam" format="bam" from_work_dir="./out/filter/*.bam" />
-        <data name="outputTsv" format="tabular" from_work_dir="./out/count/*_tcount.tsv" />
+        <data name="outputBam" format="bam" from_work_dir="./out/filter/*.bam" label="${tool.name} on ${on_string}: BAM"/>
+        <data name="outputTsv" format="tabular" from_work_dir="./out/count/*_tcount.tsv" label="${tool.name} on ${on_string}: Count TSV"/>
+        <data name="outputVcf" format="vcf" from_work_dir="./out/snp/*vcf" label="${tool.name} on ${on_string}: VCF"/>
     </outputs>
     <tests>
         <test>
+            <!--Ensure default outputs work -->
             <param name="reference_source_selector" value="history" />
             <param name="ref_file" value="ref.fa" />
             <param name="Reference" value="actb.bed" />
@@ -121,11 +104,13 @@
             <section name="advanced">
                 <param name="minBaseQual" value="27" />
             </section>
-            <output name="outputTsv" file="reads_slamdunk_mapped_filtered_tcount.tsv"
+            <output name="outputBam" ftype="bam" file="reads1.bam" compare="sim_size"/>
+            <output name="outputTsv" ftype="tabular" file="reads_slamdunk_mapped_filtered_tcount.tsv"
                 lines_diff="2" />
+            <output name="outputVcf" ftype="vcf" file="reads1_snp.vcf" compare="sim_size"/>
         </test>
         <test>
-            <!-- test built-in fasta -->
+            <!--Ensure built-in fasta works -->
             <param name="reference_source_selector" value="cached" />
             <param name="Reference" value="actb.bed" />
             <param name="Reads" ftype="fastqsanger" dbkey="hg38" value="reads.fq" />
@@ -136,8 +121,10 @@
             <section name="advanced">
                 <param name="minBaseQual" value="27" />
             </section>
-            <output name="outputTsv" file="reads_slamdunk_mapped_filtered_tcount.tsv"
+            <output name="outputBam" ftype="bam" file="reads1.bam" compare="sim_size"/>
+            <output name="outputTsv" ftype="tabular" file="reads_slamdunk_mapped_filtered_tcount.tsv"
                 lines_diff="2" />
+            <output name="outputVcf" ftype="vcf" file="reads1_snp.vcf" compare="sim_size"/>
         </test>
     </tests>
     <help><![CDATA[
@@ -162,10 +149,13 @@
 **Read length**  Maximum length of reads (usually 50, 100, 150).
 ===============  ==========================================================================================================================================================
 
-This will run the entire *slamdunk* analysis with the most relevant output files being:
+This will run the entire *slamdunk* analysis (`slamdunk all`) with the most relevant output files being:
 
-* Tab-separated *tcount* file containing the SLAM-seq statistics per UTR
-* BAM-file with the final mapped reads for visualization and further processing
+* Tab-separated *tcount* file (Count TSV) containing the SLAM-seq statistics per UTR
+* BAM-file with the final filtered mapped reads
+* VCF file of variants called on the final filtered alignments
+
+These files can be input to the **Alleyoop** tool for visualization and further processing. See the `Slamdunk documentation`_ for more information.
 
 ------------------------------------------------------
 
@@ -198,18 +188,10 @@
 **T>C conversion threshold**  Minimum number of T>C conversions to consider a read as T>C read.
 ============================  ================================================================================
 
+.. _`Slamdunk documentation`: http://t-neumann.github.io/slamdunk/docs.html
 
     ]]></help>
     <citations>
-        <citation type="bibtex">
- @misc{Neumann2018,
-  author = {Neumann, Tobias},
-  year = {2018},
-  title = Slamdunk},
-  publisher = {GitHub},
-  journal = {GitHub repository},
-  url = {https://github.com/t-neumann/slamdunk},
-}
-        </citation>
+        <expand macro="citations" />
     </citations>
 </tool>