changeset 4:425e63adcc5d draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/yahs commit be65e1846c9d4d63e80c01625e6e5f0d613948fe

--- a/yahs.xml	Wed Sep 28 09:41:02 2022 +0000
+++ b/yahs.xml	Thu Mar 09 21:59:34 2023 +0000
@@ -2,7 +2,7 @@
     <description>yet another HI-C scaffolding tool</description>
     <macros>
         <token name="@VERSION@">1.2a.2</token>
-        <token name="@VERSION_SUFFIX@">0</token>
+        <token name="@VERSION_SUFFIX@">1</token>
     </macros>
     <requirements>
         <requirement type="package" version="@VERSION@">yahs</requirement>
@@ -39,8 +39,10 @@
                     -e 'GATC'
                 #else if $function.enzyme_conditional.preconfigured_enzymes == 'arima1'
                     -e 'GATC,GANTC'
-                #else
+                #else if $function.enzyme_conditional.preconfigured_enzymes == 'arima2'
                     -e 'GATC,GANTC,CTNAG,TTAA'
+                #else if $function.enzyme_conditional.preconfigured_enzymes == 'omnic'
+
                 #end if
             #else if $function.enzyme_conditional.enzyme_options == 'specific':
                 -e '${function.enzyme_conditional.manual_enzyme}'
@@ -101,6 +103,7 @@
                             <option value="dovetail">Dovetail Chicago, Dovetail Hi-C or Phase: GATC</option>
                             <option value="arima1">Arima Hi-C 1.0: GATC, GANTC</option>
                             <option value="arima2">Arima Hi-C 2.0: GATC, GANTC, CTNAG, TTAA</option>
+                            <option value="omnic">Dovetail Omni-C: enzyme-free prep</option>
                         </param>
                     </when>
                     <when value="specific">
@@ -248,6 +251,24 @@
             </output>
             <!-- COMMAND:   yahs test.fasta test.bed -r 50000,100000,150000,2000000,1000000 -a test.agp -o test_1 -->
         </test>
+        <!-- TEST 7: omnic prep -->
+        <test expect_num_outputs="6">
+            <conditional name="function">
+                <param name="function_select" value="yahs"/>
+                <param name="fasta" value="test.fasta"/>
+                <param name="bfile" value="test.bed"/>
+            </conditional>
+            <conditional name="enzyme_conditional">
+                <param name="enzyme_options" value="preconfigured"/>
+                <param name="preconfigured_enzymes" value="omnic"/>
+            </conditional>
+            <param name="log_out" value="yes"/>
+            <output name="log_file" ftype="txt">
+                <assert_contents>
+                    <not_has_text text="-e"/>
+                </assert_contents>
+            </output>
+        </test>
     </tests>
     <help><![CDATA[
         YaHS is scaffolding tool using Hi-C data. It relies on a new algothrim for contig joining detection which considers the topological distribution of Hi-C signals aiming to distingush real interaction signals from mapping nosies. YaHS has been tested in a wide range of genome assemblies. Compared to other Hi-C scaffolding tools, it usually generates more contiguous scaffolds - especially with a higher N90 and L90 statistics. It is also super fast - takes less than 5 minutes to reconstruct the human genome from an assembly of 5,483 contigs with ~45X Hi-C data.