--- a/progressivemauve.xml	Wed Oct 13 11:56:19 2021 +0000
+++ b/progressivemauve.xml	Sat Nov 27 12:13:25 2021 +0000
@@ -1,5 +1,5 @@
 <?xml version="1.0"?>
-<tool id="progressivemauve" name="progressiveMauve" version="@WRAPPER_VERSION@.0">
+<tool id="progressivemauve" name="progressiveMauve" version="@WRAPPER_VERSION@.1">
   <description>constructs multiple genome alignments</description>
   <macros>
     <import>macros.xml</import>
@@ -35,6 +35,9 @@
 #end if
 
 $collinear
+#if $input_guide_tree
+    --input-guide-tree='$input_guide_tree'
+#end if
 --scoring-scheme=$scoring_scheme
 $no_weight_scaling
 
@@ -50,7 +53,7 @@
 #if $gap_open:
     --gap-open=$gap_open
 #end if
-
+--repeat-penalty=$repeat_penalty
 #if $gap_extend:
     --gap-extend=$gap_extend
 #end if
@@ -79,7 +82,7 @@
     --output-guide-tree=$output_guide_tree_file
 #end if
 
-#if $output_backbone:
+#if $backbone_output:
     --backbone-output=$output_backbone_file
 #end if
 
@@ -89,141 +92,144 @@
 #end for
 
 ]]></command>
-  <inputs>
-      <param type="data" format="fasta" name="sequences" multiple="True"
-          label="Select sequences to align" help="in fasta format" />
-      <param type="data" format="xmfa" label="Apply Backbone" name="apply_backbone" optional="True"
-          help="Read an existing sequence alignment in XMFA format and apply backbone statistics to it (--apply-backbone)" />
+    <inputs>
+        <param type="data" format="fasta" name="sequences" multiple="true"
+            label="Select sequences to align" help="in fasta format" />
+        <param type="data" format="xmfa" label="Apply Backbone" name="apply_backbone" optional="true"
+            help="Read an existing sequence alignment in XMFA format and apply backbone statistics to it (--apply-backbone)" />
 
-      <param type="integer" label="Island gap size" value="20" name="island_gap_size"
-          help="Alignment gaps above this size in nucleotides are considered to be islands (--island-gap-size)"/>
+        <param type="integer" label="Island gap size" value="20" argument="--island-gap-size"
+            help="Alignment gaps above this size in nucleotides are considered to be islands"/>
 
-      <param type="boolean" truevalue="--disable-backbone" falsevalue="" name="disable_backbone"
-          label="Disable backbone" help="Disable backbone detection (--disable-backbone)" />
+        <param type="boolean" truevalue="--disable-backbone" falsevalue="" argument="--disable-backbone"
+            label="Disable backbone" help="Disable backbone detection" />
 
-      <param type="boolean" truevalue="True" falsevalue="" name="output_guide_tree"
-          label="Output Guide Tree" help="Write out the guide tree used for alignment to a file (--output-guide-tree)" />
+        <param type="boolean" truevalue="true" falsevalue="" argument="--output-guide-tree"
+            label="Output Guide Tree" help="Write out the guide tree used for alignment to a file" />
 
-      <param type="boolean" truevalue="True" falsevalue="" name="output_backbone"
-          label="Output Backbone" help="Write out the backbone to a file (--backbone-output)" />
+        <param type="boolean" truevalue="true" falsevalue="" argument="--backbone-output"
+            label="Output Backbone" help="Write out the backbone to a file" />
 
-      <param type="boolean" truevalue="--mums" falsevalue="" label="MUMs" name="mums"
-          help="Find MUMs only, do not attempt to determine locally collinear blocks (LCBs) (--mums)" />
+        <param type="boolean" truevalue="--mums" falsevalue="" label="MUMs" argument="--mums"
+            help="Find MUMs only, do not attempt to determine locally collinear blocks (LCBs)" />
 
-      <param type="integer" label="Seed weight" name="seed_weight" value="0" optional="True"
-          help="Use the specified seed weight for calculating initial anchors (--seed-weight)" />
+        <param type="integer" label="Seed weight" argument="--seed-weight" value="0" optional="true"
+            help="Use the specified seed weight for calculating initial anchors" />
 
-      <param type="data" format="tabular" label="Match Input" name="match_input" optional="True"
-          help="Use specified match file instead of searching for matches (--match-input)" />
+        <param type="data" format="tabular" label="Match Input" argument="--match-input" optional="true"
+            help="Use specified match file instead of searching for matches" />
 
-    <!--<param type="file" label="input-id-matrix" help="An identity matrix describing similarity among all pairs of input sequences/alignments (- -input-id-matrix)" />-->
-    <param type="integer" label="Max gapped aligner length" value="0" optional="True" name="max_gapped_aligner_length"
-        help="Maximum number of base pairs to attempt aligning with the gapped aligner (--max-gapped-aligner-length)" />
+        <!--<param type="file" label="input-id-matrix" help="An identity matrix describing similarity among all pairs of input sequences/alignments (- -input-id-matrix)" />-->
+        <param type="integer" label="Max gapped aligner length" value="0" optional="true" argument="--max-gapped-aligner-length"
+            help="Maximum number of base pairs to attempt aligning with the gapped aligner" />
 
-    <param type="data" format="nhx" label="input-guide-tree" optional="True" name="input_guide_tree"
-        help="A phylogenetic guide tree in Newick format that describes the order in which sequences will be aligned (--input-guide-tree)" />
+        <param type="data" format="nhx" label="input-guide-tree" optional="true" argument="--input-guide-tree"
+            help="A phylogenetic guide tree in Newick format that describes the order in which sequences will be aligned" />
 
-    <param type="boolean" truevalue="--collinear" falsevalue="" label="Collinear inputs" name="collinear"
-        help="Assume that input sequences are collinear--they have no rearrangements (--collinear)" />
+        <param type="boolean" truevalue="--collinear" falsevalue="" label="Collinear inputs" argument="--collinear"
+            help="Assume that input sequences are collinear--they have no rearrangements" />
 
-    <param type="select" label="Scoring scheme" name="scoring_scheme" help="Selects the anchoring score function. (--scoring-scheme)" >
-        <option value="sp" selected="True">Extant sum-of-pairs (sp)</option>
-        <option value="ancestral_sp">Sum-of-pairs + Ancestral (ancestral_sp)</option>
-        <option value="ancestral">Ancestral (ancestral)</option>
-    </param>
+        <param type="select" label="Scoring scheme" argument="--scoring-scheme" help="Selects the anchoring score function" >
+            <option value="sp" selected="true">Extant sum-of-pairs (sp)</option>
+            <option value="ancestral_sp">Sum-of-pairs + Ancestral (ancestral_sp)</option>
+            <option value="ancestral">Ancestral (ancestral)</option>
+        </param>
 
-    <param type="boolean" truevalue="--no-weight-scaling" falsevalue="" label="No weight scaling" name="no_weight_scaling"
-        help="Don't scale LCB weights by conservation distance and breakpoint distance (--no-weight-scaling)" />
+        <param type="boolean" truevalue="--no-weight-scaling" falsevalue="" label="No weight scaling" argument="--no-weight-scaling"
+            help="Don't scale LCB weights by conservation distance and breakpoint distance" />
 
-    <param type="float" min="0" max="1" label="max-breakpoint-distance-scale" value="0.5" name="max_breakpoint_distance_scale"
-        help="Set the maximum weight scaling by breakpoint distance. (--max-breakpoint-distance-scale)" />
+        <param type="float" min="0" max="1" label="max-breakpoint-distance-scale" value="0.5" argument="--max-breakpoint-distance-scale"
+            help="Set the maximum weight scaling by breakpoint distance" />
 
-    <param type="float" min="0" max="1"  label="conservation-distance-scale" value="0.5" name="conservation_distance_scale"
-        help="Scale conservation distances by this amount. (--conservation-distance-scale)" />
+        <param type="float" min="0" max="1"  label="conservation-distance-scale" value="0.5" argument="--conservation-distance-scale"
+            help="Scale conservation distances by this amount" />
 
-    <param type="boolean" truevalue="--skip-refinement" falsevalue="" label="Skip refinement" name="skip_refinement"
-        help="Do not perform iterative refinement (--skip-refinement)" />
-    <param type="boolean" truevalue="--skip-gapped-alignment" falsevalue="" label="Skip gapped alignment" name="skip_gapped_alignment"
-        help="Do not perform gapped alignment (--skip-gapped-alignment)" />
-    <param type="integer" label="BP dist estimate min score" name="bp_dist_estimate_min_score" value="0" optional="True"
-        help="Minimum LCB score for estimating pairwise breakpoint distance (--bp-dist-estimate-min-score)" />
+        <param type="boolean" truevalue="--skip-refinement" falsevalue="" label="Skip refinement" argument="--skip-refinement"
+            help="Do not perform iterative refinement" />
+        <param type="boolean" truevalue="--skip-gapped-alignment" falsevalue="" label="Skip gapped alignment" argument="--skip-gapped-alignment"
+            help="Do not perform gapped alignment" />
+        <param type="integer" label="BP dist estimate min score" argument="--bp-dist-estimate-min-score" value="0" optional="true"
+            help="Minimum LCB score for estimating pairwise breakpoint distance" />
 
-    <param type="integer" label="Gap open" name="gap_open" value="0" optional="True"
-        help="Gap open penalty (--gap-open)" />
+        <param type="integer" label="Gap open" argument="--gap-open" value="0" optional="true"
+            help="Gap open penalty" />
 
-    <param type="select" label="Repeat penalty" name="repeat_penalty"
-        help="Sets whether the repeat scores go negative or go to zero for highly repetitive sequences. (--repeat-penalty)">
-        <option value="negative" selected="True">Negative</option>
-        <option value="zero">Zero</option>
-    </param>
+        <param type="select" label="Repeat penalty" argument="--repeat-penalty"
+            help="Sets whether the repeat scores go negative or go to zero for highly repetitive sequences">
+            <option value="negative" selected="true">Negative</option>
+            <option value="zero">Zero</option>
+        </param>
 
-    <param type="integer" label="Gap extend" name="gap_extend" value="0" optional="True"
-        help="Gap extend penalty (--gap-extend)" />
+        <param type="integer" label="Gap extend" argument="--gap-extend" value="0" optional="true"
+            help="Gap extend penalty" />
 
-    <!--<param type="data" label="Substitution matrix" -->
-        <!--help="Nucleotide substitution matrix in NCBI format (- -substitution-matrix)" />-->
+        <!--<param type="data" label="Substitution matrix" -->
+            <!--help="Nucleotide substitution matrix in NCBI format (- -substitution-matrix)" />-->
 
-    <param type="integer" label="Weight" name="weight" value="0" optional="True"
-        help="Minimum pairwise LCB score (--weight)" />
-    <param type="integer" label="Min scaled penalty" name="min_scaled_penalty" value="0" optional="True"
-        help="Minimum breakpoint penalty after scaling the penalty by expected divergence (--min-scaled-penalty)" />
+        <param type="integer" label="Weight" argument="--weight" value="0" optional="true"
+            help="Minimum pairwise LCB score" />
+        <param type="integer" label="Min scaled penalty" argument="--min-scaled-penalty" value="0" optional="true"
+            help="Minimum breakpoint penalty after scaling the penalty by expected divergence" />
 
-    <param type="float" label="HMM p go homologous" name="hmm_p_go_homologous" min="0" max="1" value="0.00001"
-        help="Probability of transitioning from the unrelated to the homologous state (--hmm-p-go-homologous)" />
-    <param type="float" label="HMM p go unrelated" name="hmm_p_go_unrelated" min="0" max="1" value="0.000000001"
-        help="Probability of transitioning from the homologous to the unrelated state (--hmm-p-go-unrelated)" />
-    <param type="float" label="HMM identity" name="hmm_identity" min="0" max="1" value="0.7"
-        help="Expected level of sequence identity among pairs of sequences(--hmm-identity)" />
+        <param type="float" label="HMM p go homologous" argument="--hmm-p-go-homologous" min="0" max="1" value="0.00001"
+            help="Probability of transitioning from the unrelated to the homologous state" />
+        <param type="float" label="HMM p go unrelated" argument="--hmm-p-go-unrelated" min="0" max="1" value="0.000000001"
+            help="Probability of transitioning from the homologous to the unrelated state" />
+        <param type="float" label="HMM identity" argument="--hmm-identity" min="0" max="1" value="0.7"
+            help="Expected level of sequence identity among pairs of sequences" />
 
-    <param type="boolean" truevalue="--seed-family" falsevalue="" label="Seed family" name="seed_family"
-        help="Use a family of spaced seeds to improve sensitivity (--seed-family)" />
-    <param type="boolean" truevalue="--solid-seeds" falsevalue="" label="Solid seeds" name="solid_seeds"
-        help="Use solid seeds. Do not permit substitutions in anchor matches. (--solid-seeds)" />
-    <param type="boolean" truevalue="--coding-seeds" falsevalue="" label="Coding seeds" name="coding_seeds"
-        help="Use coding pattern seeds. Useful to generate matches coding regions with 3rd codon position degeneracy. (--coding-seeds)" />
-    <param type="boolean" truevalue="--no-recursion" falsevalue="" label="No recursion" name="no_recursion"
-        help="Disable recursive anchor search (--no-recursion)" />
-  </inputs>
-  <outputs>
-    <data format="xmfa" name="output" label="${tool.name} alignment of ${on_string}">
-       <change_format>
-           <when input="mums" value="--mums" format="tabular" />
-       </change_format>
-    </data>
-    <data format="nhx" name="output_guide_tree_file" label="${tool.name} alignment of ${on_string}: Guide tree">
-        <filter>output_guide_tree</filter>
-    </data>
-    <data format="tabular" name="output_backbone_file" label="${tool.name} alignment of ${on_string}: Backbone">
-        <filter>output_backbone</filter>
-    </data>
-  </outputs>
-  <tests>
-      <test>
-          <param name="sequences" value="phagey.fa,karma.fa" />
-          <output name="output" file="1.xmfa" lines_diff="20"/>
-      </test>
-      <test>
-          <param name="sequences" value="merged.fa" />
-          <output name="output" file="2.xmfa" lines_diff="20"/>
-      </test>
-      <test>
-          <param name="sequences" value="merged.fa" />
-          <param name="output_guide_tree" value="True" />
-          <output name="output" file="2.xmfa" lines_diff="20"/>
-          <output name="output_guide_tree_file" file="1.nhx" />
-      </test>
-      <test>
-          <param name="sequences" value="merged.fa" />
-          <param name="mums" value="True" />
-          <output name="output" file="1.mums" compare="sim_size" delta="1000"/>
-      </test>
-      <test>
-          <param name="sequences" value="merged.fa" />
-          <param name="match_input" value="1.mums" ftype="tabular"/>
-          <output name="output" file="2.xmfa" lines_diff="24"/>
-      </test>
-  </tests>
-  <help><![CDATA[
+        <param type="boolean" truevalue="--seed-family" falsevalue="" label="Seed family" argument="--seed-family"
+            help="Use a family of spaced seeds to improve sensitivity" />
+        <param type="boolean" truevalue="--solid-seeds" falsevalue="" label="Solid seeds" argument="--solid-seeds"
+            help="Use solid seeds. Do not permit substitutions in anchor matches" />
+        <param type="boolean" truevalue="--coding-seeds" falsevalue="" label="Coding seeds" argument="--coding-seeds"
+            help="Use coding pattern seeds. Useful to generate matches coding regions with 3rd codon position degeneracy" />
+        <param type="boolean" truevalue="--no-recursion" falsevalue="" label="No recursion" argument="--no-recursion"
+            help="Disable recursive anchor search" />
+    </inputs>
+    <outputs>
+        <data format="xmfa" name="output" label="${tool.name} alignment of ${on_string}">
+           <change_format>
+               <when input="mums" value="--mums" format="tabular" />
+           </change_format>
+        </data>
+        <data format="nhx" name="output_guide_tree_file" label="${tool.name} alignment of ${on_string}: Guide tree">
+            <filter>output_guide_tree and not mums</filter>
+        </data>
+        <data format="tabular" name="output_backbone_file" label="${tool.name} alignment of ${on_string}: Backbone">
+            <filter>backbone_output and not mums</filter>
+        </data>
+    </outputs>
+    <tests>
+        <test expect_num_outputs="1">
+            <param name="sequences" value="phagey.fa,karma.fa" />
+            <output name="output" file="1.xmfa" lines_diff="20" ftype="xmfa"/>
+        </test>
+        <test expect_num_outputs="1">
+            <param name="sequences" value="merged.fa" />
+            <output name="output" file="2.xmfa" lines_diff="20" ftype="xmfa"/>
+        </test>
+        <test expect_num_outputs="3">
+            <param name="sequences" value="merged.fa" />
+            <param name="output_guide_tree" value="true" />
+            <param name="backbone_output" value="true" />
+            <output name="output" file="2.xmfa" lines_diff="20" ftype="xmfa"/>
+            <output name="output_guide_tree_file" file="1.nhx" />
+            <output name="output_backbone_file" file="1.backbone" />
+        </test>
+        <test expect_num_outputs="1">
+            <param name="sequences" value="merged.fa" />
+            <param name="output_guide_tree" value="true" />
+            <param name="mums" value="true" />
+            <output name="output" file="1.mums" compare="sim_size" delta="1000" ftype="tabular"/>
+        </test>
+        <test expect_num_outputs="1">
+            <param name="sequences" value="merged.fa" />
+            <param name="match_input" value="1.mums" ftype="tabular"/>
+            <output name="output" file="2.xmfa" lines_diff="24" ftype="xmfa"/>
+        </test>
+    </tests>
+    <help><![CDATA[
 What it does
 ============
 
@@ -434,6 +440,6 @@
 the command line, you'll need to pass these flags with their "default" values.
 
 @ATTRIBUTION@
-]]></help>
-  <expand macro="citation" />
+    ]]></help>
+    <expand macro="citation" />
 </tool>