# HG changeset patch
# User iuc
# Date 1731405400 0
# Node ID 915637bd1d1aa77f5cd2545bc3ff578b011ff46b
# Parent  f355085dd2aa12ab6ada3567fb3ba93b9a70bab9
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit f3b5a8f978923c5bbf663b0a99025245458e6ee0

diff -r f355085dd2aa -r 915637bd1d1a macro.xml
--- a/macro.xml	Thu Jan 11 16:44:56 2024 +0000
+++ b/macro.xml	Tue Nov 12 09:56:40 2024 +0000
@@ -1,48 +1,43 @@
-
 <macros>
-  <token name="@TOOL_VERSION@">0.5.0</token>
-  <token name="@VERSION_SUFFIX@">2</token>
-  <token name="@PROFILE@">21.05</token>
-
-  <token name="@THREADS@"><![CDATA[
+    <token name="@TOOL_VERSION@">0.6.0</token>
+    <token name="@VERSION_SUFFIX@">0</token>
+    <token name="@PROFILE@">23.02</token>
+    <token name="@THREADS@"><![CDATA[
       ##compute the number of ADDITIONAL threads to be used by samtools (-@)
       addthreads=\${GALAXY_SLOTS:-1} && (( addthreads-- )) &&
   ]]></token>
-
-  <xml name="version_command">
-     <version_command><![CDATA[polypolish -V]]></version_command>
-  </xml>
-  <xml name="xrefs">
-    <xrefs>
-      <xref type='bio.tools'>Polypolish</xref>
-    </xrefs>
-  </xml>
-  <xml name="requirements">
-    <requirements>
-      <requirement type="package" version="@TOOL_VERSION@">polypolish</requirement>
-      <requirement type="package" version="1.19">samtools</requirement>
-    </requirements>
-  </xml>
-  <xml name="citations">
-      <citations>
-          <citation type="doi">10.1371/journal.pcbi.1009802</citation>
-      </citations>
-  </xml>
-  <!-- Filter option of polypolish -->
-  <xml name="filter_option">
-      <conditional name="insert_filter">
-          <param name="filter_select" type="select" label="Filter by insert size ? [recommanded]"
-                 help="Exclude some alignments based on their insert size. It reduce the number of excessive alignments,
-                 particularly near the edges of repeat sequences">
-              <option value="filter" selected="true">Filter by insert size</option>
-              <option value="non_filter"> No filtering step</option>
-          </param>
-          <when value="filter">
-              <param argument="--low" type="float" min="0" value="0.1" label="Low percentile threshold" help="Select the lower value to remove [default: 0.1]"/>
-              <param argument="--high" type="float" min="0" value="99.9" label="High percentile threshold" help="Select the lower value to remove [default: 99.9]"/>
+    <xml name="version_command">
+        <version_command><![CDATA[polypolish -V]]></version_command>
+    </xml>
+    <xml name="xrefs">
+        <xrefs>
+            <xref type="bio.tools">Polypolish</xref>
+        </xrefs>
+    </xml>
+    <xml name="requirements">
+        <requirements>
+            <requirement type="package" version="@TOOL_VERSION@">polypolish</requirement>
+            <requirement type="package" version="1.19.2">samtools</requirement>
+        </requirements>
+    </xml>
+    <xml name="citations">
+        <citations>
+            <citation type="doi">10.1371/journal.pcbi.1009802</citation>
+        </citations>
+    </xml>
+    <!-- Filter option of polypolish -->
+    <xml name="filter_option">
+        <conditional name="insert_filter">
+            <param name="filter_select" type="select" label="Filter by insert size ? [recommanded]" help="Exclude some alignments based on their insert size. It reduce the number of excessive alignments,                  particularly near the edges of repeat sequences">
+                <option value="filter" selected="true">Filter by insert size</option>
+                <option value="non_filter"> No filtering step</option>
+            </param>
+            <when value="filter">
+                <param argument="--low" type="float" min="0" value="0.1" label="Low percentile threshold" help="Select the lower value to remove [default: 0.1]"/>
+                <param argument="--high" type="float" min="0" value="99.9" label="High percentile threshold" help="Select the lower value to remove [default: 99.9]"/>
+            </when>
+            <when value="non_filter">
           </when>
-          <when value="non_filter">
-          </when>
-      </conditional>
-  </xml>
+        </conditional>
+    </xml>
 </macros>
diff -r f355085dd2aa -r 915637bd1d1a polypolish.xml
--- a/polypolish.xml	Thu Jan 11 16:44:56 2024 +0000
+++ b/polypolish.xml	Tue Nov 12 09:56:40 2024 +0000
@@ -5,9 +5,9 @@
     <macros>
         <import>macro.xml</import>
     </macros>
-    <expand macro='xrefs'/>
-    <expand macro="requirements" />
-    <expand macro="version_command" />
+    <expand macro="xrefs"/>
+    <expand macro="requirements"/>
+    <expand macro="version_command"/>
     <command detect_errors="aggressive"><![CDATA[
         ln -s '$input.fasta_file' input_data &&
         #*======================================
@@ -21,7 +21,7 @@
             #else
                 echo "${input.sam_data_type.single_sam} not a sam/bam file"
             #end if
-            polypolish input_data input_sam > '$polished_fasta'
+            polypolish polish input_data input_sam > '$polished_fasta'
         #*======================================
                     For paired SAM
         ======================================*#
@@ -41,15 +41,15 @@
                 echo "${input.sam_data_type.single_sam} not a sam/bam file"
             #end if
             #if $input.sam_data_type.insert_filter.filter_select == 'filter'
-                polypolish_insert_filter.py --low '$input.sam_data_type.insert_filter.low'
+                polypolish filter --low '$input.sam_data_type.insert_filter.low'
                                             --high '$input.sam_data_type.insert_filter.high'
                                             --in1 sample_R1.sam
                                             --in2 sample_R2.sam
                                             --out1 'filtered_1.sam'
                                             --out2 'filtered_2.sam' &&
-                polypolish input_data 'filtered_1.sam' 'filtered_2.sam' >  $polished_fasta
+                polypolish polish input_data 'filtered_1.sam' 'filtered_2.sam' >  $polished_fasta
             #else
-                polypolish input_data sample_R1.sam sample_R2.sam  >  $polished_fasta
+                polypolish polish input_data sample_R1.sam sample_R2.sam  >  $polished_fasta
             #end if
         #*======================================
             For multiple single-end SAM
@@ -65,7 +65,7 @@
                     echo "${single_sam} is not a sam/bam file"
                 #end if
             #end for
-            polypolish input_data single_collection/*.sam > '$polished_fasta'
+            polypolish polish input_data single_collection/*.sam > '$polished_fasta'
         #*======================================
             For multiple paired-end SAM
         ======================================*#
@@ -83,7 +83,7 @@
                     ln -s '$paired_sam.reverse' 'paired_collection/reverse_input$(value)$(paired_sam.reverse.element_identifier).sam' &&
                 #end if
                 #if $input.sam_data_type.insert_filter.filter_select == 'filter'
-                    polypolish_insert_filter.py --low '$input.sam_data_type.insert_filter.low'
+                    polypolish filter --low '$input.sam_data_type.insert_filter.low'
                                                 --high '$input.sam_data_type.insert_filter.high'
                                                 --in1 'paired_collection/forward_input$(value)$(paired_sam.forward.element_identifier).sam'
                                                 --in2 'paired_collection/reverse_input$(value)$(paired_sam.reverse.element_identifier).sam'
@@ -95,9 +95,9 @@
                     Filtering option
         ======================================*#
             #if $input.sam_data_type.insert_filter.filter_select == 'filter'
-                polypolish input_data paired_collection/*_filtered.sam > '$polished_fasta'
+                polypolish polish input_data paired_collection/*_filtered.sam > '$polished_fasta'
             #else
-                polypolish input_data paired_collection/*.sam > '$polished_fasta'
+                polypolish polish input_data paired_collection/*.sam > '$polished_fasta'
             #end if
         #end if
         #*======================================
@@ -116,8 +116,7 @@
     </command>
     <inputs>
         <section name="input" title="Input sequences" expanded="True">
-            <param name="fasta_file" type="data" format="fasta" label="Select a draft genome for polishing"
-                   help="Fasta sequence to be cleaned using short-reads data"/>
+            <param name="fasta_file" type="data" format="fasta" label="Select a draft genome for polishing" help="Fasta sequence to be cleaned using short-reads data"/>
             <conditional name="sam_data_type">
                 <param name="sam_selector" type="select" label="Select aligned data to polish" help="Choose number of aligned sam/bam files. Need aligned file with all possible locations in aligner option">
                     <option value="single">Single SAM/BAM file</option>
@@ -143,14 +142,10 @@
             </conditional>
         </section>
         <section name="options" title="Options" expanded="False">
-            <param argument="--min_depth" type="integer" min="0" value="5" label="Minimal depth"
-                   help="A base must occur at least this many times in the pileup to be considered valid [default: 5]"/>
-            <param argument="--fraction_invalid" type="float" min="0" value="0.2" max="1" label="Minimal invalid fraction"
-                   help="A base must make up less than this fraction of the read depth to be considered invalid [default: 0.2]"/>
-            <param argument="--max_errors" type="integer" min="0" value="10" label="Number of mismatch/indels to ignore alignments"
-                   help="Ignore alignments with more than this many mismatches and indels [default: 10]"/>
-            <param argument="--fraction_valid" type="float" min="0" value="0.5" max="1" label="Minimal valid fraction"
-                   help="A base must make up at least this fraction of the read depth to be considered valid [default: 0.5"/>
+            <param argument="--min_depth" type="integer" min="0" value="5" label="Minimal depth" help="A base must occur at least this many times in the pileup to be considered valid [default: 5]"/>
+            <param argument="--fraction_invalid" type="float" min="0" value="0.2" max="1" label="Minimal invalid fraction" help="A base must make up less than this fraction of the read depth to be considered invalid [default: 0.2]"/>
+            <param argument="--max_errors" type="integer" min="0" value="10" label="Number of mismatch/indels to ignore alignments" help="Ignore alignments with more than this many mismatches and indels [default: 10]"/>
+            <param argument="--fraction_valid" type="float" min="0" value="0.5" max="1" label="Minimal valid fraction" help="A base must make up at least this fraction of the read depth to be considered valid [default: 0.5"/>
             <param name="keep_logfile" type="boolean" truevalue="true" falsevalue="false" label="Keep log file"/>
             <param argument="--debug" type="boolean" truevalue="true" falsevalue="false" label="Keep per base information file"/>
         </section>
@@ -369,29 +364,29 @@
             <section name="input">
                 <param name="fasta_file" value="contigs.fa"/>
                 <conditional name="sam_data_type">
-                  <param name="sam_selector" value="multiple_paired"/>
-                  <param name="paired_collection">
-                      <collection type="list:paired">
-                          <element name="paired_1">
-                              <collection type="paired">
-                                  <element name="forward" value="aligned_test_file/alignement_R1.bam" ftype="unsorted.bam"/>
-                                  <element name="reverse" value="aligned_test_file/alignement_R2.bam" ftype="unsorted.bam"/>
-                              </collection>
-                          </element>
-                          <element name="paired_2">
-                              <collection type="paired">
-                                  <element name="forward" value="aligned_test_file/alignement_R1_bis.bam" ftype="unsorted.bam"/>
-                                  <element name="reverse" value="aligned_test_file/alignement_R2_bis.bam" ftype="unsorted.bam"/>
-                              </collection>
-                          </element>
-                          <element name="paired_3">
-                              <collection type="paired">
-                                  <element name="forward" value="aligned_test_file/alignement_R1_ter.bam" ftype="unsorted.bam"/>
-                                  <element name="reverse" value="aligned_test_file/alignement_R2_ter.bam" ftype="unsorted.bam"/>
-                              </collection>
-                          </element>
-                      </collection>
-                  </param>
+                    <param name="sam_selector" value="multiple_paired"/>
+                    <param name="paired_collection">
+                        <collection type="list:paired">
+                            <element name="paired_1">
+                                <collection type="paired">
+                                    <element name="forward" value="aligned_test_file/alignement_R1.bam" ftype="unsorted.bam"/>
+                                    <element name="reverse" value="aligned_test_file/alignement_R2.bam" ftype="unsorted.bam"/>
+                                </collection>
+                            </element>
+                            <element name="paired_2">
+                                <collection type="paired">
+                                    <element name="forward" value="aligned_test_file/alignement_R1_bis.bam" ftype="unsorted.bam"/>
+                                    <element name="reverse" value="aligned_test_file/alignement_R2_bis.bam" ftype="unsorted.bam"/>
+                                </collection>
+                            </element>
+                            <element name="paired_3">
+                                <collection type="paired">
+                                    <element name="forward" value="aligned_test_file/alignement_R1_ter.bam" ftype="unsorted.bam"/>
+                                    <element name="reverse" value="aligned_test_file/alignement_R2_ter.bam" ftype="unsorted.bam"/>
+                                </collection>
+                            </element>
+                        </collection>
+                    </param>
                 </conditional>
             </section>
             <section name="options">
@@ -429,7 +424,7 @@
             <output name="debug_file" value="debug_file_test_2.tsv"/>
         </test>
     </tests>
-  <help><![CDATA[
+    <help><![CDATA[
     **What it does**
     Polypolish is a tool for polishing genome assemblies with short reads.
     Polypolish uses SAM/BAM files where each read has been aligned to all possible locations (not just a single best location).
diff -r f355085dd2aa -r 915637bd1d1a test-data/polished.fasta
--- a/test-data/polished.fasta	Thu Jan 11 16:44:56 2024 +0000
+++ b/test-data/polished.fasta	Tue Nov 12 09:56:40 2024 +0000
@@ -1,8 +1,8 @@
->contig00001_polypolish
+>contig00001 len=5513 cov=11.7 corr=0 origname=NODE_1_length_5513_cov_11.741181_pilon sw=shovill-spades/1.1.0 date=20220302 polypolish
 CAGCATCGGACTCAGATAGTAATCCACGCTCTTTTAAAATGTCAACAAGAGAATCTCTACCATGAACAAAATGTGACTCATATCTAAACCAGTCCTTGACGAACGTGCCAAGCATATTAAGCCACTTCTCCTCATCCAACGCGTCAGTTTTTGACAGAATCGTTAGTTGATGGCGAAAGGTCGCAAAGTAAGAGCTTCTCGAGCTGCGCAAGGATAGGTCGAATTTTCTCATTTTCCGCCAGCAGTCCACTTCGATTTAATTCGTAAACAAGCAGTAGTAATTCCTGCTTTATCAAGATAATTTTTCGACTCATCAGAAATATCCGAAAGTGTTAACTTCTGCGTCATGGAAGCGATAAAACTCTGCAGGTTGGATACGCCAATCATTTTTATCGAAGCGCGCATAAATTTGAGCAGATTTGTCGTCACAGGTTGCGCCGCCAAAACGTCGGCTACAGTAACTTTTCCCAGCCTCAATCTCATCTCTCTTTTTGCGTTCTGCTTCAATATCTGGTTGAACGGCGTCGCGTCGTAACCCAGCTTGGTAAGTTGGATTAAGCACTCCGTGGACAGATTTGTCATTGTGAGCATTTTCATCCCGAAGTTGCGGCTCATTCTGATTCTGAACAGCTTCTTGGGAAGTAGCGACAGCTTGGTTTTTAGTGAGTTGTTCCATTCTTTAGCTCCTAGACCTTTAGCAGCAAGGTCCATATCTGACTTTTTGTTAACGTATTTAGCCACATAGAAACCAACAGCCATATAACTGGTAGCTTTAAGCGGCTCACCTTTAGCATCAACAGGCCACAACCAACCAGAACGTGAAAAAGCGTCCTGCGTGTAGCGAACTGCGATGGGCATACTGTAACCATAAGGCCACGTATTTTGCAAGCTATTTAACTGGCGGCGATTGCGTACCCGACGACCAAAATTAGGGTCAACGCTACCTGTAGGAAGTGTCCGCATAAAGTGCACCGCATGGAAATGAAGACGGCCATTAGCTGTACCATACTCAGGCACACAAAAATACTGATAGCAGTCGGCGTGTGAATCATTAGCCTTGCGACCCTCGGCAGCAAGAACCATACGACCAATATCACGAAAATAGTCACGCAAAGCATTGGGATTATCATAAAACGCCTCTAATCGGTCGTCAGCCAACGTGAGAGTGTCAAAAACGATAAACCAACCATCAGCATGAGCCTGTCGCATTGCATTCATCAAACGCTGAATAGCAAAGCCTCTACGCGATTTCATAGTGGAGGCCTCCAGCAATCTTGAACACTCATCCTTAATACCTTTCTTTTTGGGGTAATTATACTCATCGCGAATATCCTTAAGAGGGCGTTCAGCAGCCAGCTTGCGGCAAAACTGCGTAACCGTCTTCTCGTTCTCTAAAAACCATTTTTCGTCCCCTTCGGGGCGGTGGTCTATAGTGTTATTAATATCAAGTTGGGGGAGCACATTGTAGCATTGTGCCAATTCATCCATTAACTTCTCAGTAACAGATACAAACTCATCACGAACGTCAGAAGCAGCCTTATGGCCGTCAACATACATATCACCATTATCGAACTCAACGCCCTGCATACGAAAAGACAGAATCTCTTCCAAGAGCTTGATGCGGTTATCCATCTGCTTATGGAAGCCAAGCATTGGGGATTGAGAAAGAGTAGAAATGCCACAAGCCTCAATAGCAGGTTTAAGAGCCTCGATACGCTCAAAGTCAAAATAATCAGCGTGACATTCAGAAGGGTAATAAGAACGAACCATAAAAAAGCCTCCAAGATTTGGAGGCATGAAAACATACAATTGGGAGGGTGTCAATCCTGACGGTTATTTCCTAGACAAATTAGAGCCAATACCATCAGCTTTACCGTCTTTCCAGAAATTGTTCCAAGTATCGGCAACAGCTTTATCAATACCATGAAAAATATCAACCACACCAGAAGCAGCATCAGTGACGACATTAGAAATATCCTTTGCAGTAGCGCCAATATGAGAAGAGCCATACCGCTGATTCTGCGTTTGCTGATGAACTAAGTCAACCTCAGCACTAACCTTGCGAGTCATTTCTTTGATTTGGTCATTGGTAAAATACTGACCAGCCGTTTGAGCTTGAGTAAGCATTTGGCGCATAATCTCGGAAACCTGCTGTTGCTTGGAAAGATTGGTGTTTTCCATAATAGACGCAACGCGAGCAGTAGACTCCTTCTGTTGATAAGCAAGCATCTCATTTTGTGCATATACCTGGTCTTTCGTATTCTGGCGTGAAGTCGCCGACTGAATGCCAGCAATCTCTTTTTGAGTCTCATTTTGCATCTCGGCAATCTCTTTCTGATTGTCCAGTTGCATTTTAGTAAGCTCTTTTTGATTCTCAAATCCGGCGTCAACCATACCAGCAGAGGAAGCATCAGCACCAGCACGCTCCCAAGCATTAAGCTCAGGAAATGCAGCAGCAAGATAATCACGAGTATCCTTTCCTTTATCAGCGGCAGACTTGCCACCAAGTCCAACCAAATCAAGCAACTTATCAGAAACGGCAGAAGTGCCAGCCTGCAACGTACCTTCAAGAAGTCCTTTACCAGCTTTAGCCATAGCACCAGAAACAAAACTAGGGACGGCCTCATCAGGGTTAGGAACATTAGAGCCTTGAATGGCAGATTTAATACCAGCATCACCCATGCCTACAGTATTGTTATCGGTAGCAAGCACATCACCTTGAATGCCACCGGAGGCGGCTTTTTGACCGCCTCCAAACAATTTAGACATGGCGCCACCAGCAAGAGCAGAAGCAATACCGCCAGCAATAGCACCAAACATAAATCACCTCACTTAAGTGGCTGGAGACAAATAATCTCTTTAATAACCTGATTCAGCGAAACCAATCCGCGGCATTTAGTAGCGGTAAAGTTAGACCAAACCATGAAACCAACATAAACATTATTGCCCGGCGTACGGGGAAGGACGTCAATAGTCACACAGTCCTTGACGGTATAATAACCACCATCATGGCGACCATCCAAAGGATAAACATCATAGGCAGTCGGGAGGGTAGTCGGAACCGAAGAAGACTCAAAGCGAACCAAACAGGCAAAAAATTTAGGGTCGGCATCAAAAGCAATATCAGCACCAACAGAAACAACCTGATTAGCGGCGTTGACAGATGTATCCATCTGAATGCAATGAAGAAAACCACCATTACCAGCATTAACCGTCAAACTATCAAAATATAACGTTGACGATGTAGCTTTAGGTGTCTGTAAAACAGGTGCCGAAGAAGCTGGAGTAACAGAAGTGAGAACCAGCTTATCAGAAAAAAAGTTTGAATTATGGCGAGAAATAAAAGTCTGAAACATGATTAAACTCCTAAGCAGAAAACCTACCGCGCTTCGCTTGGTCAACCCCTCAGCGGCAAAAATTAAAATTTTTACCGCTTCGGCGTTATAACCTCACACTCAATCTTTTATCACGAAGTCATGATTGAATCGCGAGTGGTCGGCAGATTGCGATAAACGGTCACATTAAATTTAACCTGACTATTCCACTGCAACAACTGAACGGACTGGAAACACTGGTCATAATCATGGTGGCGAATAAGTACGCGTTCTTGCAAATCACCAGAAGGCGGTTCCTGAATGAATGGGAAGCCTTCAAGAAGGTGATAAGCAGGAGAAACATACGAAGGCGCATAACGATACCACTGACCCTCAGCAATCTTAAACTTCTTAGACGAATCACCAGAACGGAAAACATCCTTCATAGAAATTTCACGCGGCGGCAAGTTGCCATACAAAACAGGGTCGCCAGCAATATCGGTATAAGTCAAAGCACCTTTAGCGTTAAGGTACTGAATCTCTTTAGTCGCAGTAGGCGGAAAACGAACAAGCGCAAGAGTAAACATAGTGCCATGCTCAGGAACAAAGAAACGCGGCACAGAATGTTTATAGGTCTGTTGAACACGACCAGAAAACTGGCCTAACGACGTTTGGTCAGTTCCATCAACATCATAGCCAGATGCCCAGAGATTAGAGCGCATGACAAGTAAAGGACGGTTGTCAGCGTCATAAGAGGTTTTACCTCCAAATGAAGAAATAACATCATGGTAACGCTGCATGAAGTAATCACGTTCTTGGTCAGTATGCAAATTAGCATAAGCAGCTTGCAGACCCATAATGTCAATAGATGTGGTAGAAGTCGTCATTTGGCGAGAAAGCTCAGTCTCAGGAGGAAGCGGAGCAGTCCAAATGTTTTTGAGATGGCAGCAACGGAAACCATAACGAGCATCATCTTGATTAAGCTCATTAGGGTTAGCCTCGGTACGGTCAGGCATCCACGGCGCTTTAAAATAGTTGTTATAGATATTCAAATAACCCTGAAACAAATGCTTAGGGATTTTATTGGTATCAGGGTTAATCGTGCCAAGAAAAGCGGCATGGTCAATATAACCAGTAGTGTTAACAGTCGGGAGAGGAGTGGCATTAACACCATCCTTCATGAACTTAATCCACTGTTCACCATAAACGTGACGATGAGGGACATAAAAAGTAAAAATGTCTACAGTAGAGTCAATAGCAAGGCCACGACGCAATGGAGAAAGACGGAGAGCGCCAACGGCGTCCATCTCGAAGGAGTCGCCAGCGATAACCGGAGTAGTTGAAATGGTAATAAGACGACCAATCTGACCAGCAAGGAAGCCAAGATGGGAAAGGTCATGCGGCATACGCTCGGCGCCAGTTTGAATATTAGACATAATTTATCCTCAAGTAAGGGGCCGAAGCCCCTGCAATTAAAATTGTTGACCACCTACATACCAAAGACGAGCGCCTTTACGCTTGCCTTTAGTACCTCGCAACGGCTGCGGACGACCAGGGCGAGCGCCAGAACGTTTTTTACCTTTAGACATTACATCACTCCTTCTGCACGTAATTTTTGACGCACGTTTTCTTCTGCGTCAGTAAGAACGTCAGTGTTTCCTGCGCGTACACGCAAGGTAAACGCGAACAATTCAGCGGCTTTAACCGGACGCTCGACGCCATTAATAATGTTTTCCGTAAATTCAGCGCCTTCCATGATGAGACAGGCCGTTTGAATGTTGACGGGATGAACATAATAAGCAATGACGGCAGCAATAAACTCAACAGGAGCAGGAAAGCGAGGGTATCCTACAAAGTCCAGCGTACCATAAACGCAAGCCTCAACGCAGCGACGAGCACGAGAGCGGTCAGTAGCAATCCAAACTTTGTTACTCGTCAGAAAATCGAAATCATCTTCGGTTAAATCCAAAACGGCAGAAGCCTGAATGAGCTTAATAGAGGCCAAAGCGGTCTGGAAACGTACGGATTGTTCAGTAACTTGACTCATGATTTCTTACCTATTAGTGGTTGAACAGCATCGGACTCAGATAGTAATCCACGCTCTTTTAAAATGTCAACAAGAGAATCTCTACCATGAACAAAATGTGACTCATATCTAAACCAGTCCTTGACGAACGTGCCAAGCATATTAAGCCACTT
->contig00002_polypolish
+>contig00002 len=3532 cov=5.1 corr=0 origname=NODE_2_length_3532_cov_5.072834_pilon sw=shovill-spades/1.1.0 date=20220302 polypolish
 CGGACTACCGTCCCGAAATACTCATATAAATGCCAAAAACCATTTGCTGTCAAAACGGCGTAACAATTTCCTACTGTCAGTTTCTTTTTAATTTCTGCTTTACTGGAACCATATTTATGTTGAGCATATTGGTCCCACTCTGCAAACTCATTTCCCTTGATCATCTGATTGAATGTATTGTCAGAAACAAAATAATAATCCTCTTGATCTTTTTCCCCAGGTCTTGGTGATCGATTCGTGTAAGTAATGATCTTTTGTTCCGGCTGAAAAATAGCTTCTGCGAGTGAAGTTTTTCCAGAACCAGAAGGACCGATAAATACATAGCAATAATTCATTGTCATTTCTCCTTTGATGATTGAACAAGTGAAAAAGCTTTGGAAAATATTTCCAAAGCTTTTAAAAGTAACTTTGCTTTTTTGTATATTATACCAGCAAGCCAGTCACAATAGCACTTAAAAAGCTGACTAAAGTCGCTGTTAGCAAAATTTTCAATCCGTGTTTTGCGACAAGATTTCCTTTTTCTTCATTTAATCCCTTCATCGCACCAGAAATGATCCCGATAGAAGAGAAGTTGGCAAATGAAACGAGGAAGACAGATATAATTGCTGTTGTACGCTCAGTAAAATGGAAAGATTTTCTGTAGTTGCTTCTTTCCGTTTCTTTGTGAATTTTTACCAGTCATTTTTTACTGGATTGTTATTTTTTATAAAATATGATAAAATTTTGGTAGCGCTTTATAAGCGCGTTGCTTTTTCAAGAATAAACTCTCATTATTTTTTTAACTGGCTGCTCGAAAGAGCAGTCTTTTTTATTATTTATCCGTCTCTTTTACAAACAATTCTTCGTTAGGACTGTTGTAATAATTTGAATTTAATTTAAGTTCTCCGTTGGAATTGTTTTTTCCAATTACGGATAATAGCATGGGGCTAAAACCTAATATTCCTAGAGAAATAGAACCCAGTACCAACACAGTTTTTTTTAACATAGGTTATACCTCCACTTTTTTTAACGCTACCACTTGTATACACATTTTAAATACTAGCCTTCAGTTTATCAAATGTTTAAATTGAACGGATATAAATCAAAATTAAATTTTCAAAAGTTGTTCTAAAAAATTTTTCTTTTTTGGAAGTTACTCTAACTTTTTTTGCTTGTGGTGCTTGGTATGTTTTCTTCGCCGACCGTTTAGGTTCTTGACCATTTTCTCTTATAAGTGGGATTTTTACCACGTTGAGAGAAAATGGTCAAGAACCTGGGAGGCGGAGAATGCCCTTAATACCAAGCACCGCAAGCCTTTCCCATACTTTATTCGATGATCCCACGATGATCTCATAATGATTCTACAATGACCCTACGATGATCAAAATTCTCAAAAAAAATAAACGAAATTTCAAACGATTTTTTTGAAATTTTGTTAAAATCACATTTGTTTTTTTATGACTTTTTCAACAAAATCGATTAGAATTTATTTTGTTTTTCCACCAAAAATTGAGTGAGATTTCAACCTATTTTAAGCAATAAGTCACCATATAGTTTGATAGTTTACAACTATAAACATTGATTGTTTACAGTTGTAAACTATTTTTTCTTTCTCATAAAAATTTGAGTGATCTCCCCATCAGGTAGTACAACTTTTTCCTCTACTATCCGAACTAACTTCTAGAAAATTTTAGAGATTGGTTCTATTAGATTTCCAAATTTGCCACCACTTTTTTTCAATAAGTGGTTGTGTATTGTCTGCTTTTTTTTCAGAAAAGGCAGTTGATTCGGTTGTTGGAGTTTCTTCTGTATAAGTTAAATGGAGCTGTTCTTGTAGGTTCTCAATTTGTTGGTTCGCTTGTAGAGTGAGTTGTTGTTGCTGGTCGAGTAATTTTTGCATTTGTTTTATTTGATTATCTTTTTCTTGTAGCTGTATATCTTTTCGATTTAACTGTTTTTCTAGGAAAGAAAGGAGTTTTAATTCGGAAACTTGGTTGGTGTTTTTATGGTTTTTGGTTTTTGATTTTTCGCCAACTAGTTTTCGATTTAAGTTTGCGTTATCGACTAAAAACATTGATTTTATAGCTTTTTGACCGGTTTCGTTAATCACAAACTTGTTTCCGTTTTTTGCAAACCAAAGTTTTCGATTTTTGTCAGAAACTTTTTTGTTAATTGCTGTTTTACTAACTCCTAATTCTTCCGCAAGTTCTTTGATTGTTTTATCTGCCATAAATACTCCTTAAGCTTAATCGAATAAGTTTTGTAAATTTCCTAGTAAATCTTGTTTGAGTTTGTTTGAAAGTTCTCGTTTTTCTGCCTGTTTTTCTTCAGTTTGTTGTTGTTGTTTAAAATCAGCTTCATGAGTGCCTAAGGGAAGATTTAGTATTCGATCTTTAGCGCGCCATTTTTCTTCTCGTGTTAATTCTCCATTGTGATCAATATTAAATAATTTGGTTCTGTTGCAAAGTTTTAAATAAAGAATAAAATCCCTTACGGTATCTATGATTTAAGCTGGGATTCCCAATAATACCTTGATTTCAGTACAGACCGAAAACCCGAAGAGAGTGCCTTCTTTTCGGGTTTTCTTATATAATCCTCGAATGGCTTCCATGCCTTTAATCGTGGTAGAGGCAGTGCGTAAACTTCGATAGAATTTATTGCGTCTCTTTACTGGACGATGGTCTTGTTCAATCAAATTATTCAGGTATTTAATGGTACGATGTTCTGTCCCTTGATAAAAGCCGTATTCTTTTAGTTTCTTAAAGGCACTTGTAATAGAGGGGGCTTTATCTGTGACTACAACCTTCGGTTCATCAAACTGCTTCACTAACCGCTTAAGAAAAGCATAGGCTGCTTGTGTGTCCCGTTTTTTACGTAACCAAATATCCAAGGTTAAACCATCTGCATCGATGGCTCGATACAAATAATGCCATTTTCCTTTAATTTTGATGTACGTTTCATCCATTTTCCATGAATAAAAGGATTTTTTATTTTTCTTTTTCCAAATTTGATAGAGTAGTTTGCCATATTCTTGCACCCAACGATAAATCGTCGTATGAGAAACGTTAATGCCACGATCATATAAGATTTCTTGAACTTCACGATAGCTAAGGTTATAACGAAGATAGTAGCCCACGGCTACAATAATCACATCCTGCTGAAATTGCTTTCCTTTAAAATGATTCATCGTCATTCCTCCTGCTATCTTTTTCTATTATTCTACCTTATTTGATAGTAGATTTAAAACTTTGCAACAGAACCGATAATCTTATACGTGGGGAATTTCATTTCCTTTCTGAAAAAGATATGAACATAATCCCCTCGTTTAAAGATTCAGGTTATATTCCTGATACGAAGGCTATGCTTATTTACGATGAAACAGGGCAATTAGAAAATTATTTATCAGAGATAAGTGGTGCAAGACCAAATAGACTTACTGAAGAAAATGCTAATTTTTTGTTGTGTAATTTCTCTAATCTATGGTTGATGGGAATCAACGTTCTAAAAAGAGGAGAATATGCTCGTTCATTAGAACTCTTATCACAACTTCAAA
->contig00003_polypolish
+>contig00003 len=3227 cov=2.2 corr=0 origname=NODE_3_length_3227_cov_2.232903_pilon sw=shovill-spades/1.1.0 date=20220302 polypolish
 GATGGGCGACTTCTGCCTAATTCTGTTAAAGAAAAAAGAAGTGGTTTTTAGGCGGGAAAATTAGCCCCCCTCTTTTTATATCTCTTTTTAAACCTCTTTTTAAACCTCTTTACCGTAAGCTGTGTCCTTACTCTACCAATGGATACAGAATGTTATGAAGGACATTTTGTCTGTTTATGAAGGACATTTTGTCTGTTTATGAAGGACATTTTGTCTGTTTATGAAGGACATTTTGTCTGTTTGAACGTCAAATATGAATGTCTTGACATTTAAAAAATGTCATTCATAATTGGATTGAGGTGATTATATGGCTAATGAGATTGTAAAATACCACCATGAGTTAAATACAATTCCTTTAAGAAAATTTACACCGGTTGAAATGAATTTGTTTTTTTCCATCGTGTCTAGAATGCGTGAAAAAGGGGATAAGACAGTTCGTTTTACGTTTGACCAACTAAAAGATTTAAGTAACTACAAAGCAACTGCAAATGTACGATTTGTAGAAGATTTAAAAGCAACTTATGAAAAAATCTTATCTTTACGCTTTGGTCGTAGAAGTGAGTCTGGGCTTTCTTACGATATGTTTGTAATGTTTACAGAATTTAAAATCAACGGGGACGTAGAAAATCCTTACGTAGATATACGAATTTACGAAAAAGCACTGCCTTTGTTAAATAATTTAGACGAGTGGGTACGCTATTCTTTACAACAATTCAACGAGCTACAAAGTGGCTATGCAAAGACTATGTTTCGTCTGTTAAAGCAATACAGAACCAAAGGTTTCGCATATTTCTCCAAAGAAGACTTTCTTGAATTATTAGATATTCCTAAAAGTTATAAGCAACCTGATATAGATAAACGAGTTATAAAACCTATACGTCAAGAACTAACTGCAATCTTCAAAGGACTAACAATCAAAAAGAAATACGGAAAAGGACGGGGAAAACCTGTTATTGGCTATCAATTTACGTTCAAACCTGAGATCAAAAAAGCAGACGACTTTAACAAACATGCACCAACCAAAGAAGACCAAAATAAAGCATTGGCTTTAGCTGATAAACAAAAAGAATACGAAGAACCCGCTACAACAATTAACGAAAAAATCAAACAGAAGAAACGAGAACTTGAACTCCTCCAACAAATCAAACAACTAGAAAAAGAGAAAAAAGCTCTTGAAAAACAAACAGAGTCCGCACTTTCGGAAAAAGAGAAAAAAAGTTTATTATCTGATTTAGATAATTTATTCCAGTAGCAACCTAGGAGGCAACCAGTATGCAACCACAAGAAACCTTTACAATAAAGGAATTGTCAGATCTTTTTAAGATGAGTAGGCAAGCAATATCGAAACATATCCAAAAATTAGATTCTTCCATGATAGCTAAAAATGAGCGTGGTTATAAGGTTGTATTGCGTTCTGGAGTATTGCAACTTGCTCGCAACTTAGACAATCAAAGGTTGCTAGATAAGTTGCATAAACATGAACAAAACAACGATAAAAATGCTTATATACCAAACAAAAACGTGGTTGCAAACAAGTTGCTAGATCAGTTGCGTGAAGAAAATGAATTTTTACGAGAACAACTTGCCCTCAAAGAGCAAAATAATTCTCATATACAAAAACTACTCGACCAGCAACAACAACTCACCCTGCAAGCCAACCAACAAATCGAAAAACTTCAGGAGCAACTGCAGTTGACTTATACGGAAGAGTCTTCAGAGAATAGTTCAACGACTCTTTCTGAAGCAACAGAAACAATGGACGAACAAACAAAGAATTGGAAAAAATGGTGGCAGCTATGGAAATGAAGAAGGAAATACTTATGACAAAAAAACACTTGCTATTCGGTTCTATCCTACTAGGAATATTAAGCTTTAGCCCAATGTTATTATCAGTGGCCAACAAAGGAAATAAAAAAGGGGAACTAAAACTCAATCCTAATTACTACAACAGTCAAAATGAGGAAGTATTTGTAGAAAAACTTGATAAATAAGAAAAGACTGCTCGTACGAGCAGTCTTTCTGAAAGAGATTATCCTATTATTAACCTTAGAAAAGAATAATAAATGAATATGAGATATGTAAAAAGCATAACAAACACAAACAAAAATAACAAGTATTTAAAAAATGACCGATCAATATTCACAAAGAATTAGAAAGAAACAACCGCAGAAAACCAAGCCTTAAAAAGAGCTTTTAACCTAGACCAATAAAAATTCACAAAATCAGCGCCTGGATCCCTTGGTACAGGCGTTACTTGGTAGTATACACATTATGTCTACTAGCTGTTTAAATAACTGATCTTATAATTTTATTTAAACGATTATGAATTCAAAACTACTTTTTATGACGTTAATCATTGTTATATAATAAAATGTTATATAATAAAATTACTAAGATTATTTAATATAACAAGCAATTTTAAAAAAACGAAAAGGAAAAACAATCATGAAAAAGAAAGTATTAAAACATTGTGTTATTCTAGGAATATTAGGAACTTGTCTAGCTGGCATCGGTACAGGAATAAAAGTTGATGCAGCTACTTACTATGGAAATGGTCTTTATTGTAACAAAGAAAAATGTTGGGTAGATTGGAATCAAGCTAAAGGAGAAATTGGAAAAATTATTGTTAATGGTTGGGTTAATCATGGTCCATGGGCACCTAGAAGGTAGTGGTAGGGAGGTTATTATAATGGATTTTACTAAAGAAGAAAAACTTTTAAATGCAATTAGTAAAGTATACAATGAAGCAACTATAGATGACTATCCTGACTTAAAAGAAAAGCTCTTTCTTTATTCTAAAGAAATCAGTGAGGGAAAAAGTGTTGGTGAAGTTAGTATGAAATTAAGTAGTTTTCTTGGAAGATATATTTTAAAACATAAATTTGGATTACCTAAATCTTTAATAGAATTACAAGAAATTGTTAGTAAGGAATCTCAAGTATATAGAGGATGGGCTTCTATTGGTATTTGGAGTTAATTCTTTGGAATAAAATGAAAATGGGACTGAAGAATCAATTCTGATTCATCAGTCCCATAAATTATAGAGCCGAAAAATTATCATATTTATAGATTTATTAATAGTAAATGGCATAAGAATCTTTGAACAACGAAAAAAATGTAGCTCTACCTAATTATTGATTTGCAACAATTTCACCGAAGGTGAAACAAGCGAAACTTTACAAAAAGTGGCTAGCATTTGCTAGTCTTTTTTGTATTGTGGAGAGTGG
->contig00004_polypolish
+>contig00004 len=3138 cov=2.3 corr=1 origname=NODE_4_length_3138_cov_2.261375_pilon sw=shovill-spades/1.1.0 date=20220302 polypolish
 TTTTTTTCCGATATAATTTGCTGGTAAATCTATCACAGCCAATGAGAGTCCGGGATTGCTTTCTTCCTGATAATCTTTCCGTTGGTATAAAATCTTTTCGCCTAGATATACAGTAATCCATTGATGGTTTCCTTTGATTAGTAAATTTGCTTCGTCCAACGGTTTTTCAAGTGTCGTTTCCATAATGAATGTTTCGTCTTTATCCACGGTAGGAATCGTACGAGTGTACTTGCTGTCAAACTTAAAATCAGGATCATCTTTTGTATAGAAAACCCACGAATCTTTTATTTCTTTCATTTGATTGCTGTCCGCAGGAGAAAAAATAAAATAAAAGAAATAAGCAATTCCTGTTAAAAATAACAATGATAATATAATGATTATGCTCCACTTTATACGTAAATAAAAAGATTCTTTTTTATTATATATGTTATTAAAAAAAGACATAAAGGTATTCCTTTGAGAGTATAAAATATTTTGTGTAAATGAAAAAATCCATACAAAAAAGGAAGTCCCTTCTGTAGAATAAAGTTAACGACAACCAATTCACAGAAAAGAGGACTTCCCTATGAATGATTTTACTACAGAAATTGTGCAAACTCTAGTCACTAAAGGCGATTTAAATGAATTATTCCGTTCGCACTTAGAAAAAGCGATAAACACACTCCTACGGACTGAATTAACGGCTTTTTTAGATTACGAAAAATATGATCGCACTGGTTTTAATTCAGGTAATTCGAGAAACGGTTCTTACTTTCGATCAATCAAAACCGAATATGGTGAATTAACATTGGAAATACCTAGAGATCGTAATGGTGAGTTTAAACAACAAACTTTACCAGCCTACAAAAGAACAAACGATACATTGGAAACCACTATTATCCATTTATTCGAAAAAGGTGTTACGATGTCTGAAATTGCTGATTTGATCGAAAAAATGTACGGTCATCACTATACTCCACAAACCATGTCCAACATGACTAAAGTTCTGACTGAAGAAGTAAATGCCTTTAAATCCAGAGCCTTAAATGATAAGTATGTCGCTATTTTTATGGACGTTACTTACATTCCACTAAAACGTCAAACTGTATCCAAAGAAGCGATTTATATTGCCATTGGTATACGAGAAGACGGCACTAAAGAAGTACTGAGTTATGCGATTGCTCCAACTGAATCAACATACGTTTGGAATGAGCTGCTACAGGATATTAACTCCAGAGGAGTTCAAGAAGTCTTGCTTTTTATTACGGACGGCTTAAAAGGCATGAAAGATACTATCCATCAAATTTATCCTAAAGCAAAATATCAGCATTGTTGTATCCATGTATCTCGTAACATCGCTCATAAAGTACGTGTCAAAGACCGAAAAGAAATCTGTGATGACTTTAAGGCTGTTTATCAAGCTAACTCAAAAGAAGAAGCGAATACCTTCTTATCCGGCATGATTGAGAAATGGAAGAAAAACTATCCTAAAGTGACGCAGTCACTCATAGAAAACCAAGACTTATTAACTTTTTATGATTTTCCACCTAGCATTCGTAGAACCATTTACTCAACCAATCTAATCGAGTCTTTCAATAAGCAAATTAAAAGATACAGCCGTAGAAAAGAGCAGTTTCAAAATGAAGAATCACTAGAACGCTTTCTAGTCAGCATTTTTGATACATACAATCAAAAATTTCTAAACAGAAGCCATAAAGGTTTTCAACAGGTAACCGATACATTAGTTTCAATGTTTACTGAGTAACTAATTATTTTGCAGGAGGACAATTTATTTACACAAAATTATTGACGCTCCCTAACAAAATCCCACCTACTTTATCTTATAACTTGTTTTTTTGCATAAAAACTAAATAAAGAGTGCGGCATTTCGCACTTTTTTATTATATATTATTTGTCAAATTAAGCGAGACAAAACTTTCCATTTACGTAACTCAAAAAAACTTCTAATGGTGTTTGGTAATTTAGTGATTTTCTAGGGATATGGTTTCTTTTGGACGCAACGGATGAGATGAATCCTTGATTGACTTGGTGGAAGTCCATTTCTTTTGGTAGTCCATCTTTTCGGAGGAGTCCGTTTGAATGTTCATTTAATCCCCGTTGGGAAGGCGTTCCTGGGTCTGCGAAATAAATATCAATATCATTCGTATTACTAATACTTTTCCAATTAGAGAATTCTTTTCCACAATCAAAGGTAATTGATTTGAAAAGATTTTTGGGTACGGATTGAAGCCATTCATTAATCGAATTTTCAATATCAACTGCCTTACGGCCTTCTGGTTTCAAGGCGATAATGGCTTTTGAAAGTCGCTCAACGAGTGTGATGACGGCACTTTTATGGTGGATGCCGACAATCGTATCACCCTCTAAATGTCCAAATTCTTCTTCGAAAACGACATAATCTTTTTTACGTTCAGAAATATTTCTTTTGAATGCCTGTTTTCCACGTTTTTCCTTATAACCATTTGGTTTTCGTTTTCCTTGCATCGGTAAATGTAAAACATTGAATTCTCCCGTCTTAAACCGGCGATAGAGGGTACTTACTGAACAAGAGAAGGTTCGCTCTGCACGGCCAATAATGACGTCTGGGGTCCAACCTTCAGTTGATCTTTTTGCAATGTATTCTTTTTCCTCAGCAGGAAAAATGATTTCGGTTCTCCCACAACGTCGCTTATTTTCTTTGTATTGTTCAAAGTATTCAAGTGCTGTTCCACCACATTTGAGAAAGTTATAGACATTGTAAATTGTTTGGCGTCCACGTTTAAGCTGCTTCGCAACGATAGCAACCGGAGTTTCTTGATGAAAATATGCTTCTATCATTACAAGCTCGTTTGGTGTAAGATGGGTATAAGTCATTTATGTTCACTCTCCTTGTATGCTTTAGCGGGTATTACAATTGGAGTGTAACATAAATGGCTTTTTTATTTGTCTCGCTTAATTATACAAACGGCGTTGTTAAATAAATAGGAACAAAAAAATTAAATTATTTAATACACACATTAGGGATCATTCATTGAAGGATTAGAAGACAACGAGGATGGCGAAAAATATGATTACAATAGAAAAGTCGTTCTAAACCAATCAGTTCCTAGTATCACACAACGCAAGCCAGTCGATTTGGTGAGATTAGAGGAGTGAAAG