diff canu.xml @ 4:86f150c8019d draft default tip

"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/canu commit 9e1d3a4dcabeec3c52e08372753d32d684dbed59"

--- a/canu.xml	Mon Feb 15 12:31:26 2021 +0000
+++ b/canu.xml	Wed Nov 03 16:10:37 2021 +0000
@@ -4,7 +4,7 @@
         <xref type="bio.tools">canu</xref>
     </xrefs>
     <macros>
-        <token name="@TOOL_VERSION@">2.1.1</token>
+        <token name="@TOOL_VERSION@">2.2</token>
         <token name="@VERSION_SUFFIX@">0</token>
     </macros>
     <requirements>
@@ -42,7 +42,7 @@
         #if $stopOnLowCoverage
             stopOnLowCoverage=$stopOnLowCoverage
         #end if
-        #if $minInputCoverage
+        #if $minInputCoverage ##and $stage in ["all", "trim-assemble", "assemble"]
             minInputCoverage=$minInputCoverage
         #end if
         contigFilter='
@@ -56,21 +56,25 @@
         genomeSize='$genomeSize'
         minThreads=\${GALAXY_SLOTS:-4}
         maxThreads=\${GALAXY_SLOTS:-4}
-        redMemory=\${GALAXY_MEMORY_MB:-4096}M
+        redMemory=\${GALAXY_MEMORY_MB:-6144}M
         redThreads=\${GALAXY_SLOTS:-4}
         obtovlThreads=\${GALAXY_SLOTS:-4}
         utgovlThreads=\${GALAXY_SLOTS:-4}
         batThreads=\${GALAXY_SLOTS:-4}
-        batMemory=\${GALAXY_MEMORY_MB:-4096}M
-        cormhapMemory=\${GALAXY_MEMORY_MB:-4096}M
-        obtovlMemory=\${GALAXY_MEMORY_MB:-4096}M
-        utgovlMemory=\${GALAXY_MEMORY_MB:-4096}M
+        batMemory=\${GALAXY_MEMORY_MB:-6144}M
+        cormhapMemory=\${GALAXY_MEMORY_MB:-6144}M
+        obtovlMemory=\${GALAXY_MEMORY_MB:-6144}M
+        utgovlMemory=\${GALAXY_MEMORY_MB:-6144}M
         corThreads=\${GALAXY_SLOTS:-4}
-        corMemory=\${GALAXY_MEMORY_MB:-4096}M
+        corMemory=\${GALAXY_MEMORY_MB:-6144}M
         cnsThreads=\${GALAXY_SLOTS:-4}
-        cnsMemory=\${GALAXY_MEMORY_MB:-4096}M
-        oeaMemory=\${GALAXY_MEMORY_MB:-4096}M
+        cnsMemory=\${GALAXY_MEMORY_MB:-6144}M
+        oeaMemory=\${GALAXY_MEMORY_MB:-6144}M
         oeaThreads=\${GALAXY_SLOTS:-4}
+        merylThreads=\${GALAXY_SLOTS:-4}
+        merylMemory=\${GALAXY_MEMORY_MB:-6144}M
+        corovlThreads=\${GALAXY_SLOTS:-4}
+        corovlMemory=\${GALAXY_MEMORY_MB:-6144}M
         useGrid=false
 
         #for $haplotype in $haplotypes:
@@ -165,7 +169,7 @@
             <output name="trimmed_reads" ftype="fasta.gz" decompress="True" file="ecoli_canu_trimmed_reads_result1.fa.gz"/>
             <output name="report">
                 <assert_contents>
-                    <has_n_lines n="488"/>
+                    <has_n_lines n="486"/>
                     <has_text_matching expression="[UNITIGGING/CONTIGS]"/>
                     <has_text_matching expression="-- Contig sizes based on genome size 20kbp:"/>
                 </assert_contents>
@@ -188,7 +192,7 @@
             <output name="trimmed_reads" ftype="fasta.gz" decompress="True" file="ecoli_canu_trimmed_reads_result2.fa.gz"/>
             <output name="report">
                 <assert_contents>
-                    <has_n_lines n="464"/>
+                    <has_n_lines n="456"/>
                     <has_text_matching expression="[UNITIGGING/CONTIGS]"/>
                     <has_text_matching expression="-- Contig sizes based on genome size 20kbp:"/>
                 </assert_contents>
@@ -204,9 +208,9 @@
             <output name="corrected_reads" ftype="fasta.gz" decompress="True" file="ecoli_canu_corrected_reads_result3.fa.gz"/>
             <output name="report">
                 <assert_contents>
-                    <has_n_lines n="187"/>
+                    <has_n_lines n="189"/>
                     <has_text_matching expression="[TRIMMING/READS]"/>
-                    <has_text_matching expression="--   Found 89 reads."/>
+                    <has_text_matching expression="--   Found 93 reads."/>
                 </assert_contents>
             </output>
         </test>
@@ -214,14 +218,17 @@
         <test expect_num_outputs="2">
             <param name="inputs" ftype="fasta" value="ecoli-reads.fasta"/>
             <param name="technology" value="-nanopore"/>
-            <param name="genomeSize" value="3.4m"/>
+            <param name="processing" value="-corrected"/>
+            <!-- <param name="minInputCoverage" value="1"/> -->
+            <param name="genomeSize" value="0.01m"/>
             <param name="stage" value="-trim"/>
             <param name="minReadLength" value="500"/>
             <output name="report">
                 <assert_contents>
                     <has_text_matching expression="[TRIMMING/READS]"/>
-                    <has_n_lines n="6"/>
-                    <has_text_matching expression="Found 0 reads."/>
+                    <has_n_lines n="209"/>
+		    <has_text_matching expression="Found 112 reads."/><!-- before trimming -->
+		    <has_text_matching expression="Found 61 reads."/><!-- after trimming -->
                 </assert_contents>
             </output>
         </test>