diff hifiasm_meta.xml @ 2:fa35f1106d3e draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hifiasm_meta commit bc8759245f44924d0122276e42f02fc1f1190e50

--- a/hifiasm_meta.xml	Wed Jan 18 09:12:38 2023 +0000
+++ b/hifiasm_meta.xml	Mon Feb 06 12:20:38 2023 +0000
@@ -17,17 +17,26 @@
         #################
 
         hifiasm_meta 
-        --lowq-10 '$read_selection.lowq_10'
-        --lowq-3 '$read_selection.lowq_3'
-        --lowq-5 '$read_selection.lowq_5'
-        -a '$assembly.a'
+
+        ## bloom filter parameter
         #if $f:
             -f '$f'
         #end if
+
+        ## read selection parameters
+        #if $read_selection.forced_read_selection.force_rs == "yes":
+            --force-rs
+            --lowq-10 '$read_selection.forced_read_selection.lowq_10'
+            --lowq-3 '$read_selection.forced_read_selection.lowq_3'
+            --lowq-5 '$read_selection.forced_read_selection.lowq_5'
+        #else
+            $read_selection.forced_read_selection.S
+        #end if
+    
+        -a '$assembly.a'
         -k '$overlap_correction.k'
         -o asm
         -r '$overlap_correction.r'
-        $read_selection.S
         -t \${GALAXY_SLOTS:-4}
         '$reads_fn'
 
@@ -38,10 +47,20 @@
         <!-- See https://github.com/galaxyproject/tools-iuc/pull/5033#issuecomment-1382915060 -->
         <param type="hidden" optional="true" argument="-f" />
         <section name="read_selection" title="Read selection" expanded="false">
-            <param argument='-S' type="boolean" checked="true" truevalue="-S" falsevalue="" label="Enable read selection" help="If enabled, hifiasm_meta will estimate the total number of read overlaps." />
-            <param argument='--lowq-10' type="integer" value='50' label="lower 10% runtime kmer frequency threshold." />
-            <param argument='--lowq-5' type="integer" value='50' label="lower 5% runtime kmer frequency threshold." />
-            <param argument='--lowq-3' type="integer" value='10' label="lower 3% runtime kmer frequency threshold." />
+            <conditional name="forced_read_selection">
+                <param argument="--force-rs" type="select" label="Force read selection" help="Drop reads according to configurable runtime kmer frequency thresholds">
+                    <option value="no" selected="true">No</option>
+                    <option value="yes">Yes</option>                    
+                </param>
+                <when value="yes">
+                    <param argument='--lowq-10' type="integer" value='50' label="Lower 10% runtime kmer frequency threshold" />
+                    <param argument='--lowq-5' type="integer" value='50' label="Lower 5% runtime kmer frequency threshold" />
+                    <param argument='--lowq-3' type="integer" value='10' label="Lower 3% runtime kmer frequency threshold" />
+                </when>
+                <when value="no">
+                    <param argument='-S' type="boolean" checked="false" truevalue="-S" falsevalue="" label="Enable read selection" help="If enabled, hifiasm_meta will estimate the total number of read overlaps. If the estimation seems acceptable, no read will be dropped; otherwise, reads will be dropped from the most redundant ones until the criteria are satisfied. This can only be enabled if forced read selection is disabled." />
+                </when>
+            </conditional>
         </section>
         <section name="overlap_correction" title="Overlap/Error correction" expanded="false">
             <param argument='-k' type="integer" value='51' min="1" max="63" label="k-mer length" />
@@ -77,6 +96,30 @@
                 <element name="Alternate contigs" file="asm.a_ctg.gfa"/>
             </output_collection>
         </test>
+        <!-- 02: forced read selection -->
+        <test>
+            <param name="reads" value="tiny.fa.gz" />
+            <param name='f' value="0" />
+            <param name='force_rs' value='yes' />
+            <output_collection name="contig_graphs" type="list">
+                <element name="Primary contigs">
+                    <assert_contents>
+                        <has_size value="93053" delta="30000" />
+                    </assert_contents>
+                </element>
+            </output_collection>
+        </test>
+        <!-- 03: read selection -->
+        <test>
+            <param name="reads" value="zymoD6331std-ecoli-ten-percent.42.1.fq.gz" />
+            <param name='f' value="0" />
+            <param name='force_rs' value='no' />
+            <param name='S' value='true' />
+            <output_collection name="contig_graphs" type="list">
+                <element name="Primary contigs" file="S.p_ctg.gfa"/>
+                <element name="Alternate contigs" file="S.a_ctg.gfa"/>
+            </output_collection>
+        </test>
     </tests>
         <help><![CDATA[
 hifiasm_meta