--- a/snp-sites.xml	Fri Jun 30 16:43:26 2017 -0400
+++ b/snp-sites.xml	Sat Nov 02 11:12:17 2019 -0400
@@ -1,30 +1,140 @@
 <?xml version='1.0' encoding='UTF-8'?>
-<tool id='snp_sites' name='Finds SNP sites' version='0.1.0'>
+<tool id='snp_sites' name='Finds SNP sites' version='@TOOL_VERSION@+galaxy0'>
    <description>from a multi-FASTA alignment file</description>	
+   <macros>
+      <token name="@TOOL_VERSION@">2.5.1</token>
+   </macros>
    <requirements>
-      <requirement type='package' version='2.3.2'>snp-sites</requirement>
+      <requirement type='package' version='@TOOL_VERSION@'>snp-sites</requirement>
    </requirements>
    <version_command>snp-sites -V</version_command>
    <command detect_errors='aggressive'><![CDATA[
+#if str($out_type.ot_select) == "alignment"
+    #if str($out_type.formats) == 'None'
+        echo "Error, no output format specified" >&2 && exit 1 ;
+        #set outputs=""
+    #else
+        #set outputs=" ".join(str($out_type.formats).split(","))
+    #end if
+#end if
+
 snp-sites 
--mvp 
--o output 
-'$input_fasta'
+#if str($out_type.ot_select) == "alignment"
+    $outputs
+    $out_type.b
+    $out_type.c
+#else if str($out_type.ot_select) == "counts"
+    -C
+#end if
+    -o output 
+    '$input_fasta'
+
+#if str($out_type.ot_select) == "counts"
+   && mv output $output_counts
+#else if ',' in str($out_type.formats)
+   #if '-m' in str($out_type.formats)
+      && mv 'output.snp_sites.aln' '$output_fasta'
+   #end if
+   #if '-v' in str($out_type.formats)
+      && mv 'output.vcf' '$output_vcf'
+   #end if
+   #if '-p' in str($out_type.formats)
+      && mv 'output.phylip' '$output_phylip'
+   #end if
+#else
+   #if str($out_type.formats) == '-m'
+      && mv 'output' '$output_fasta'
+   #else if str($out_type.formats) == '-v'
+      && mv 'output' '$output_vcf'
+   #else if str($out_type.formats) == '-p'
+      && mv 'output' '$output_phylip'
+   #end if
+#end if
 ]]></command>
    <inputs>
+
         <param name='input_fasta' format='fasta' type='data' label='FASTA file' />
+        <conditional name="out_type" label="Output type">
+            <param type="select" name="ot_select" label="Output">
+                <option value="alignment" selected="true">Sequence alignment / VCF</option>
+                <option value="counts">Constant site count (suitable for IQ-TREE -fconst)</option>
+            </param>
+        <when value="alignment">
+            <param type='select' multiple='true' name='formats' label='Output formats' help='Output format to use if not counting constant sites'>
+            <option value="-m"  selected="true">Multi-FASTA alignment file</option>
+            <option value="-v">VCF</option>
+            <option value="-p">Phylip</option>
+            </param>
+            <param argument="-b" label="Output constant sites (suitable for use in BEAST)" truevalue="-b" falsevalue="" 
+            type="boolean" help="Output monomorphic (constant) as opposed to polymorphic (variable) sites"/>
+            <param argument="-c" label="Only output columns containing exclusively ACTG" truevalue="-c" falsevalue=""
+            type="boolean" help="Ignore columns containing ambiguous characters and gaps"/>
+        </when>
+        <when value="counts">
+        </when>
+        </conditional>
    </inputs>
    <outputs>
-        <data name='output_fasta' format='fasta' label='${tool.name} on ${on_string}: FASTA' from_work_dir='output.snp_sites.aln'/>
-        <data name='output_vcf' format='vcf' label='${tool.name} on ${on_string}: VCF' from_work_dir='output.vcf'/>
-        <data name='output_phylip' format='phylip' label='${tool.name} on ${on_string}: phylip' from_work_dir='output.phylip'/>
+      <data name='output_fasta' format='fasta' label='${tool.name} on ${on_string}: FASTA'>
+	      <!-- this becomes a catch-all for when no format is specified. if no format is specified the job ends with an error but shows 1 red dataset output -->
+         <filter>(out_type["ot_select"] == "alignment" and out_type["formats"] is not None and '-m' in out_type["formats"]) or (out_type["ot_select"] == "alignment" and out_type.formats is None)</filter>
+      </data>
+      <data name='output_vcf' format='vcf' label='${tool.name} on ${on_string}: VCF' from_work_dir='output.vcf'>
+         <filter>out_type["ot_select"] == "alignment" and out_type["formats"] is not None and '-v' in out_type["formats"]</filter>
+      </data>
+      <data name='output_phylip' format='phylip' label='${tool.name} on ${on_string}: phylip'>
+         <filter>out_type["ot_select"] == "alignment" and out_type["formats"] is not None and '-p' in out_type["formats"]</filter>
+      </data>
+      <data name='output_counts' format='tabular' label='${tool.name} on ${on_string}: constant site counts'>
+         <filter>out_type["ot_select"] == "counts"</filter>
+      </data>
    </outputs>
    <tests>
-      <test>
+      <test expect_num_outputs="3">
+         <param name='input_fasta' value='input.fasta' ftype='fasta' />
+         <conditional name="out_type">
+            <param name="ot_select" value="alignment" />
+            <param name='formats' value='-m,-p,-v' />
+         </conditional>
+        <output name='output_fasta' value='output.fasta' ftype='fasta' />
+        <output name='output_vcf' value='output.vcf' ftype='vcf' />
+        <output name='output_phylip' value='output.phylip' ftype='phylip' />
+      </test>
+      <test expect_num_outputs="1">
+         <param name='input_fasta' value='input.fasta' ftype='fasta' />
+         <conditional name="out_type">
+            <param name="ot_select" value="alignment" />
+            <param name='formats' value='-m' />
+            <param name='b' value='True' />
+         </conditional>
+         <output name='output_fasta' value='output_monomorphic.fasta' ftype='fasta' />
+      </test>
+      <test expect_num_outputs="1">
          <param name='input_fasta' value='input.fasta' ftype='fasta' />
-         <output name='output_fasta' value='output.fasta' ftype='fasta' />
-         <output name='output_vcf' value='output.vcf' ftype='vcf' />
-         <output name='output_phylip' value='output.phylip' ftype='phylip' />
+         <conditional name="out_type">
+            <param name="ot_select" value="alignment" />
+            <param name='formats' value='-m' />
+            <param name='c' value='True' />
+         </conditional>
+         <output name='output_fasta' value='output_actg.fasta' ftype='fasta' />
+      </test>
+      <test expect_num_outputs="1">
+         <param name='input_fasta' value='input.fasta' ftype='fasta' />
+         <conditional name="out_type">
+            <param name="ot_select" value="alignment" />
+            <param name='formats' value='-m' />
+            <param name='b' value='True' />
+            <param name="c" value="True" />
+         </conditional>
+         <output name='output_fasta' value='output_monomorphic_actg.fasta' ftype='fasta' />
+      </test>
+      <test expect_num_outputs="1">
+         <param name='input_fasta' value='input.fasta' ftype='fasta' />
+         <conditional name="out_type">
+            <param name="ot_select" value="counts" />
+            <param name='C' value='True' />
+         </conditional>
+         <output name='output_counts' value='output_counts.tabular' ftype='tabular' />
       </test>
    </tests>
    <help>
@@ -32,7 +142,11 @@
    
 **SNP-sites**
 
-This tool can rapidly extract SNPs from a multi-FASTA alignment using modest resources and can output results in multiple formats for downstream analysis. SNPs can be extracted from a 8.3 GB alignment file (1,842 taxa, 22,618 sites) in 267 seconds using 59 MB of RAM and 1 CPU core, making it feasible to run on modest computers. SNP-sites is implemented in C and is available under the open source license GNU GPL version 3.
+This tool can rapidly extract SNPs from a multi-FASTA alignment using modest resources and can output results in multiple formats for downstream analysis. SNPs can be extracted from a 8.3 GB alignment file (1,842 taxa, 22,618 sites) in 267 seconds using 59 MB of RAM and 1 CPU core, making it feasible to run on modest computers. 
+SNP-sites is implemented in C and is available under the open source license GNU GPL version 3.
+
+Alternatively it can report on the number of constant sites in an alignment in a format (A count, C count, G count, T count) suitable for passing
+to IQ-TREE's `-fconst` option.
 
 **Input FASTA format:**
 
@@ -49,6 +163,16 @@
   >sample1
   AAACGCATTCAN
 
+**Options** 
+
+In addition to the default output mode, this tool supports three other options:
+
+1. Output only constant (monomorphic) (i.e. not polymorphic) sites (useful for input to BEAST)
+
+2. Output only columns that have purely ACTGs in them (i.e. no gaps or ambiguous nucleotides). This can be used together with the previous option. 
+
+3. Output only a count of constant sites, in a format suitable for use with IQ-TREE `-fconst`. This option cannot be used together with the previously mentioned options.
+
 **Output files:**
 
 The output of the tool are three different files in following format:
@@ -56,6 +180,7 @@
 - a multi fasta alignment,
 - relaxed phylip format and,
 - VCF.
+- alternatively constant site counts (As, Cs, Gs and Ts).
 
 The VCF file for the above specified input is