--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/macros.xml	Wed Nov 10 23:33:13 2021 +0000
@@ -0,0 +1,97 @@
+<macros>
+    <token name="@TOOL_VERSION@">2.1.0</token>
+    <token name="@VERSION_SUFFIX@">0</token>
+    <xml name="xrefs">
+      <xrefs>
+        <xref type="bio.tools">ragtag</xref>
+      </xrefs>
+    </xml>
+    <xml name="requirements">
+        <requirements>
+            <requirement type="package" version="@TOOL_VERSION@">ragtag</requirement>
+        </requirements>
+    </xml>
+    <xml name="citations">
+        <citations>
+            <citation type="doi">10.1186/s13059-019-1829-6</citation>
+        </citations>
+    </xml>
+    <xml name="input_options">
+        <param name="reference" type="data" format="fasta" label="Reference FASTA file"/>
+        <param name="query" type="data" format="fasta" label="Query FASTA file" />
+    </xml>
+    <xml name="common_parameters">
+        <param argument="-e" type="data" format="txt" optional="true" label="List of reference headers to ignore" 
+            help="Use this parameter to provide a single column file listing any reference.fa headers that should 
+                be ignored (e.g. chr0/chrUn or alt contigs)"/>
+        <param argument="-j" type="data" format="txt" optional="true" label="List of query headers to leave uncorrected" 
+            help="use this parameter to provide a single column file listing any query.fa headers that shall not be broken"/>
+        <param argument="-f" type="integer" min="0" value="1000" label="Minimum unique single length" 
+            help="If an alignment is not entirely unique, at least -f bp of the alignment must be unique to be considered 
+                for scaffolding. By default, entirely unique alignments are considered regardless of their length, but 
+                this can be disabled with --remove-small. Doing so ensures that only alignments at least -f bp in length 
+                are considered for correction"/>
+        <param argument="--remove-small" type="boolean" truevalue="--remove-small" 
+            falsevalue="" checked="false" label="Remove unique alignments" 
+            help="Remove unique alignments shorter than the minimum unique alignment length" />
+        <param argument="-q" type="integer" min="0" value="10" label="Minimum mappping quality" 
+            help="Mapping quality scores quantify the probability that a read is misplaced" />
+        <param argument="-d" type="integer" min="0" value="100000" label="Maximum alignment merge distance" 
+            help="For each query sequence, syntenic alignments within -d bp of each other are merged into longer alignments"/>        
+        <conditional name="mapping_conditional">
+            <param name="mapping_option" type="select" label="Aligner tool">
+                <option value="nucmer">Nucmer</option>
+                <!--Unimap is not included because according the minimap2 developers, minimap2 backports unimap features https://github.com/lh3/minimap2/releases/tag/v2.19
+                <option value="unimap">Unimap</option>
+                -->
+                <option value="minimap2" selected="true">Minimap2</option>
+            </param>
+            <when value="nucmer">
+                <param name="anchor_mode" type="select" label="Anchoring mode">
+                    <option value="--mum">Use anchor matches that are unique in both the reference and query (--mum)</option>
+                    <option value="--mumreference">Use anchor matches that are unique in in the reference but not necessarily unique in the query (--mumreference)</option>
+                    <option value="--maxmatch" selected="true">Use all anchor matches regardless of their uniqueness (--maxmatch)</option>
+                </param>
+                <param argument="-l" type="integer" min="0" value="100" label="Minimun length of a single match"/>
+                <param argument="-c" type="integer" min="0" value="500" label="Minimum length of a cluster of matches"/>
+            </when>
+            <when value="minimap2">
+                <param argument="--mm2-params" type="select"
+                    label="Select a profile of preset options"
+                    help="Each profile comes with the preconfigured settings mentioned in parentheses" >
+                        <option value="asm5">Asm5: the alignment will not extend to regions with 5% or higher sequence divergence (-k19 -w19 -A1 -B19 -O39,81 -E3,1 -s200 -z200 --min-occ-floor=100)</option>
+                        <option value="asm10">Asm10: up to 10% sequence divergence (-k19 -w19 -A1 -B9 -O16,41 -E2,1 -s200 -z200 --min-occ-floor=100)</option>
+                        <option value="asm20">Asm20: up to 20% sequence divergence (-k19 -w10 -A1 -B6 -O6,26 -E2,1 -s200 -z200 --min-occ-floor=100)</option>
+                </param>
+            </when>
+        </conditional>
+    </xml>
+    <token name="@INPUTS@"><![CDATA[
+        $mode_conditional.reference
+        $mode_conditional.query
+    ]]></token>
+    <token name="@COMMON_PARAMETERS@"><![CDATA[
+        --aligner $mode_conditional.advanced_options.mapping_conditional.mapping_option 
+        #if $mode_conditional.advanced_options.mapping_conditional.mapping_option == 'nucmer'
+            --nucmer-params '$nucmer_params'
+        #else
+            #if $mode_conditional.advanced_options.mapping_conditional.mm2_params == 'asm5'
+                --mm2-params '-k19 -w19 -A1 -B19 -O39,81 -E3,1 -s200 -z200 --min-occ-floor=100'
+            #else if $mode_conditional.advanced_options.mapping_conditional.mm2_params == 'asm10'
+                --mm2-params '-k19 -w19 -A1 -B9 -O16,41 -E2,1 -s200 -z200 --min-occ-floor=100'
+            #else
+                --mm2-params '-k19 -w10 -A1 -B6 -O6,26 -E2,1 -s200 -z200 --min-occ-floor=100'
+            #end if
+        #end if
+        #if $mode_conditional.advanced_options.e 
+            -e '${mode_conditional.advanced_options.e}'
+        #end if
+        #if $mode_conditional.advanced_options.j
+            -j '${mode_conditional.advanced_options.j}'
+        #end if 
+        -f $mode_conditional.advanced_options.f 
+        --remove-small $mode_conditional.advanced_options.remove_small 
+        -q $mode_conditional.advanced_options.q
+        -d $mode_conditional.advanced_options.d
+    ]]></token>
+</macros>