Update minimap2.xml

tools/minimap2/macros.xml

@@ -1,6 +1,6 @@
 <macros>
     <token name="@TOOL_VERSION@">2.28</token>
-    <token name="@VERSION_SUFFIX@">0</token>
+    <token name="@VERSION_SUFFIX@">1</token>
     <xml name="edam_ontology">
         <edam_topics>                                                                                  
             <edam_topic>topic_0102</edam_topic>

tools/minimap2/minimap2.xml

@@ -141,6 +141,9 @@
     #if $io_options.K:
         -K $io_options.K
     #end if
+    #if $io_options.eqx:
+        --eqx
+    #end if
     -t \${GALAXY_SLOTS:-4}
     reference.fa
     #if $fastq_input.fastq_input_selector in ['single', 'paired_iv']:
@@ -164,7 +167,6 @@
         -T "\${TMPDIR:-.}"
         -@\${GALAXY_SLOTS:-2}
         -O $io_options.output_format
-        $io_options.eqx
         --reference reference.fa
         --output-fmt-option no_ref
         -o '$alignment_output'

tools/mummer4/macros.xml

@@ -11,7 +11,7 @@
         </citations>
     </xml>
     <token name="@TOOL_VERSION@">4.0.0</token>
-    <token name="@VERSION_SUFFIX@">0</token>
+    <token name="@VERSION_SUFFIX@">1</token>
     <token name="@PROFILE@">20.05</token>
     <xml name="gnuplot_requirement">
         <requirement type="package" version="5.4.10">gnuplot</requirement>

tools/mummer4/show-coords.xml

@@ -9,6 +9,7 @@
         <![CDATA[
         show-coords
             $merge
+            $direction
             -c
             -H
             -I '$identity'
@@ -17,39 +18,60 @@
             $annotate
             $sort
             -T
-            '${delta}' > '${output}'
+            '${delta}' 
+            #if $direction:
+                >  '${output_extend}'
+            #else:
+               >  '${output}'
+            #end if
         ]]>
     </command>
     <inputs>
         <param name="delta" type="data" format="tabular" label="Match file from Nucmer" />
         <param name="merge" type="boolean" argument="-b" truevalue="-b" falsevalue="" label="Merge"
             help="Merges overlapping alignments regardless of match dir or frame and does not display any idenitity information. (-b)" />
         <param name="identity" type="float" argument="-I" value="75.0" label="Identity" help="Set minimum percent identity to display (-I)" />
+
+        <param name="direction" type="boolean" argument="-d"  truevalue="-d" falsevalue="" label="Direction"  help="Display the alignment direction in the additional FRM columns (-d)" />
         <param name="min_alignment_length" type="integer" argument="-L" value="100" label="Minimum Alignment Length" help="Set minimum alignment length to display (-L)" />
         <param name="annotate" type="boolean" argument="-o" truevalue="-o" falsevalue="" label="Annotate"
             help="Annotate maximal alignments between two sequences, i.e. overlaps between reference and query sequences (-o)" />
         <param name="sort" type="select" label="Sorting strategy for output" >
             <option value="-q">Sort output by query IDs and coordinates (-q)</option>
             <option value="-r">Sort output by reference IDs and coordinates (-r)</option>
         </param>
+
     </inputs>
     <outputs>
-        <data name="output" format="tabular" from_work_dir="show-coords.txt" >
+        <data name="output" format="tabular" from_work_dir="show-coords.txt"   label="${tool.name} on ${on_string} default format)">
+            <filter>direction is False</filter>
             <actions>
                 <action name="column_names" type="metadata" default="[S1], [E1], [S2], [E2], [LEN 1], [LEN 2], [% IDY], [LEN R], [LEN Q], [COV R], [COV Q], [REF TAG], [QUERY TAG]" />
             </actions>
         </data>
+        <data name="output_extend" format="tabular" from_work_dir="show-coords_extend.txt"   label="${tool.name} on ${on_string} extend format)" >
+            <filter>direction is True</filter>
+            <actions>
+                <action name="column_names" type="metadata" default="[S1], [E1], [S2], [E2], [LEN 1], [LEN 2], [% IDY], [LEN R], [LEN Q], [COV R], [COV Q], [FRM R], [FRM Q], [REF TAG], [QUERY TAG]" />
+            </actions>
+        </data>
     </outputs>
     <tests>
-        <test>
+        <test expect_num_outputs="1">
             <param name="delta" ftype="tabular" value="nucmer.txt" />
+            <param name="direction" value="False" />
             <output name="output" ftype="tabular" compare="diff" value="show-coords.txt" />
         </test>
+        <test expect_num_outputs="1">
+            <param name="delta" ftype="tabular" value="nucmer.txt" />
+            <param name="direction" value="True" />
+            <output name="output_extend" ftype="tabular" compare="diff" value="show-coords_extend.txt" />
+        </test>
     </tests>
     <help><![CDATA[
 This program parses the delta alignment output of nucmer and displays the coordinates, and other useful information about the alignments.
 
-Output is tabular. Below is a description of each column:
+Output is tabular. Below is a description of each column (Default):
     * **[S1]** Start of the alignment region in the reference sequence
     * **[E1]** End of the alignment region in the reference sequence
     * **[S2]** Start of the alignment region in the query sequence
@@ -61,6 +83,8 @@ Output is tabular. Below is a description of each column:
     * **[LEN Q]** Length of the query sequence
     * **[COV R]** Percent coverage of the alignment on the reference sequence, calculated as [LEN 1] / [LEN R]
     * **[COV Q]** Percent coverage of the alignment on the query sequence, calculated as [LEN 2] / [LEN Q]
+    * **[FRM R]** Reading frame for the reference sequence (only with -d)
+    * **[FRM Q]** Reading frame for the query sequence (only with -d)
     * **[REF TAG]** The reference FastA ID
     * **[QUERY TAG]** The query FastA ID
 
@@ -72,7 +96,7 @@ The Percent Coverage and Sequence Length options are useful when comparing two s
 
     -b      Merges overlapping alignments regardless of match dir or frame and does not display any 
             identity information.
-
+    -d      Display the alignment direction in the additional FRM columns
     -I      Set minimum percent identity to display
 
     -L      Set minimum alignment length to display

tools/mummer4/test-data/show-coords_extend.txt

@@ -0,0 +1,2 @@
+74	223	43	194	150	152	87.50	6480	5460	2.31	2.78	1	1	NG_007476.1:4960-11439	NC_000070.6:c41098183-41092724
+5080	5599	4148	4658	520	511	86.18	6480	5460	8.02	9.36	1	1	NG_007476.1:4960-11439	NC_000070.6:c41098183-41092724