# HG changeset patch
# User iuc
# Date 1723556708 0
# Node ID b1f16ffc171f228691a8bc8bf4eacfee33e46ba1

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pacu commit 4290547cefb0459595f28fbba063f2cf58b35086

diff -r 000000000000 -r b1f16ffc171f macros.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/macros.xml	Tue Aug 13 13:45:08 2024 +0000
@@ -0,0 +1,28 @@
+<macros>
+    <xml name="requirements">
+        <requirements>
+            <requirement type="package" version="@VERSION@">pacu_snp</requirement>
+            <yield/>
+        </requirements>
+    </xml>
+
+    <xml name="version_command">
+        <version_command><![CDATA[PACU --version]]></version_command>
+    </xml>
+
+    <token name="@VERSION@">0.0.5</token>
+    <token name="@VERSION_SUFFIX@">0</token>
+    <token name="@PROFILE@">21.01</token>
+
+    <xml name="xrefs">
+        <xrefs>
+            <xref type='bio.tools'>pacu</xref>
+        </xrefs>
+    </xml>
+
+    <xml name="citations">
+        <citations>
+            <citation type="doi">10.1128/jcm.01576-23</citation>
+        </citations>
+    </xml>
+</macros>
diff -r 000000000000 -r b1f16ffc171f pacu_map.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/pacu_map.xml	Tue Aug 13 13:45:08 2024 +0000
@@ -0,0 +1,106 @@
+<tool id="pacu_map" name="PACU - mapping" version="@VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
+    <description>Map ONT / Illumina reads to a reference genome for PACU</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro='xrefs'/>
+    <expand macro="requirements" />
+    <expand macro="version_command"/>
+    <command detect_errors="exit_code">
+        <![CDATA[
+        PACU_map
+
+        ## FASTA input
+        --ref-fasta '$ref_fasta'
+        --ref-fasta-name '$ref_fasta.element_identifier'
+
+        ## FASTQ input
+        --read-type $fastq_tech.read_type
+        #if str($fastq_tech.read_type) == 'illumina':
+            --fastq-illumina $fastq_tech.fastq_illumina_1 $fastq_tech.fastq_illumina_2
+            --fastq-illumina-names '$fastq_tech.fastq_illumina_1.element_identifier' '$fastq_tech.fastq_illumina_2.element_identifier'
+        #elif str($fastq_tech.read_type) == 'ont':
+            --fastq-ont $fastq_tech.fastq_ont
+            --fastq-ont-name '$fastq_tech.fastq_ont.element_identifier'
+        #end if
+
+        ## Output
+        --output '$bam'
+
+        ## Other options
+        $trim
+        --dir-working \$PWD
+        --threads \${GALAXY_SLOTS}
+        ]]>
+    </command>
+    <inputs>
+        <param argument="--ref-fasta" type="data" format="fasta" label="Reference genome"/>
+        <conditional name="fastq_tech">
+            <param argument="--read-type" type="select" label="FASTQ type">
+                <option value="illumina">Illumina paired-end reads</option>
+                <option value="ont">ONT single-end reads</option>
+            </param>
+            <when value="illumina">
+                <param name="fastq_illumina_1" type="data" format="fastq,fastqsanger.gz" label="Forward reads"/>
+                <param name="fastq_illumina_2" type="data" format="fastq,fastqsanger.gz" label="Reverse reads"/>
+            </when>
+            <when value="ont">
+                <param name="fastq_ont" type="data" format="fastq,fastqsanger.gz" label="ONT reads"/>
+            </when>
+        </conditional>
+        <param argument="--trim" type="boolean" label="Trim reads" checked="true" truevalue="--trim" falsevalue=""/>
+    </inputs>
+    <outputs>
+        <data name="bam" format="bam" label="Mapping on ${on_string}"/>
+    </outputs>
+    <tests>
+        <test>
+            <!-- The line differences correspond to the three commands in the SAM header -->
+            <param name="ref_fasta" value="NC_002695.2-subset.fasta"/>
+            <conditional name="fastq_tech">
+                <param name="read_type" value="ont"/>
+                <param name="fastq_ont" value="TIAC1151-ont.gz"/>
+            </conditional>
+            <param name="trim" value="false" />
+            <output name="bam" ftype="bam" file="mapped_reads-ont.bam" lines_diff="6"/>
+        </test>
+        <test>
+            <!-- The line differences correspond to the three commands in the SAM header -->
+            <param name="ref_fasta" value="NC_002695.2-subset.fasta"/>
+            <conditional name="fastq_tech">
+                <param name="read_type" value="illumina"/>
+                <param name="fastq_illumina_1" value="TIAC1151_1P.fastq.gz"/>
+                <param name="fastq_illumina_2" value="TIAC1151_2P.fastq.gz"/>
+            </conditional>
+            <param name="trim" value="false" />
+            <output name="bam" ftype="bam" file="mapped_reads-ilmn.bam" lines_diff="6"/>
+        </test>
+                <test>
+            <!-- The line differences correspond to the three commands in the SAM header -->
+            <param name="ref_fasta" value="NC_002695.2-subset.fasta"/>
+            <conditional name="fastq_tech">
+                <param name="read_type" value="ont"/>
+                <param name="fastq_ont" value="TIAC1151-ont.gz"/>
+            </conditional>
+            <param name="trim" value="true" />
+            <output name="bam" ftype="bam" file="mapped_reads_trimmed-ont.bam" lines_diff="6"/>
+        </test>
+        <test>
+            <!-- The line differences correspond to the three commands in the SAM header -->
+            <param name="ref_fasta" value="NC_002695.2-subset.fasta"/>
+            <conditional name="fastq_tech">
+                <param name="read_type" value="illumina"/>
+                <param name="fastq_illumina_1" value="TIAC1151_1P.fastq.gz"/>
+                <param name="fastq_illumina_2" value="TIAC1151_2P.fastq.gz"/>
+            </conditional>
+            <param name="trim" value="true" />
+            <output name="bam" ftype="bam" file="mapped_reads_trimmed-ilmn.bam" lines_diff="6"/>
+        </test>
+    </tests>
+    <help>
+        This script maps Illumina or ONT reads to an input reference genome in FASTA format.
+        It also writes a custom tag to the BAM file to propagate the sample name to PACU within Galaxy.
+        The sample name is derived from the name of the input FASTQ files.
+    </help>
+    <expand macro="citations"/>
+</tool>
diff -r 000000000000 -r b1f16ffc171f test-data/NC_002695.2-sample.bed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/NC_002695.2-sample.bed	Tue Aug 13 13:45:08 2024 +0000
@@ -0,0 +1,1 @@
+NC_002695.2	0	1000
diff -r 000000000000 -r b1f16ffc171f test-data/NC_002695.2-subset.fasta
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/NC_002695.2-subset.fasta	Tue Aug 13 13:45:08 2024 +0000
@@ -0,0 +1,154 @@
+>NC_002695.2 Escherichia coli O157:H7 str. Sakai DNA, complete genome
+AAGTCATGATACCGCCGTAATAGGTCGGGATCGCCGCCTGATAAAAGCCAACGTCGCTGAAGTAATGGCT
+GAGTTTGCGATGGCTGTCGATGGCTTCTTCCTGCTGTAAAAAGCAGACGCCGTTTTGTGCGACGAAGATA
+CCGCCAGGATTCAGGCAACGTTTGCAGCCTTCATAAAATGCCGAAGTGAAAAGGCTTTCGCCGGGACCGA
+TAGGATCGGTGCAGTCGGAGATAATGACATCAAAGGTCTGGCTGGTTTGATTAACGAAATTGACGCCATC
+GTCGATCACCAGCTTAAAGCGCGGATCGTCGTAGCTACCGGCGTTATGGTTGGGTAGATACTGACGGCAG
+AACGACACGACACCCGCATCGATTTCCACCATCGTGATTGACTCAACGTTTTTATGTCGGGTTACTTCAC
+GCAGCATGGCACCGTCGCCGCCGCCGATAATCAGCACATGTTTCGCGTGACCGTGGGCCAGTAGCGGAAC
+ATGGGTCATCATCTCATGATAGATAAACTCGTCGCGCTCGGTGGTTTGTACTACGCCATCCAGCGCCATT
+ACGCGACCAAATGCAGCGTTCTCAAAAATGATCAGATCCTGGTGATCGGTCTTTTCATGATACAGAACGT
+TATCTACCGCAAAGTACTGCCCAAACTGGTCGTGTAGCGTTTCATGCCACTGTTTTTTTTCGGCCATGGG
+TTGATACCTCCTTTGTTAACACCCGTAAAAAAAGGGCGCAACATAATAGCTAACATTGACCGCGGATGCA
+CGGTCAATATTTCTACAAAAAGGTATCAGGGATTATTTGACGTAGGCAAGCAGGCTTAAGGAATCGCGAG
+CCAGGGCCTTGCACTTTTTAGCGACGGGAATGCCAATGCCGCTGAGATCGCGGTAGCTGTCTTCACCGAG
+AGCTTTCATGTCGAAGGTGTCGTAATTACTGAGATCCCACTGGTTTTGCTGGGCGAAAAAGACCAGTGCG
+CGACGAATTTGCCCGTTAGGTAAGTTCTGGTAACCACAATCGTTCTTCAGAAAGACAAAAACTGCCGTTA
+AATCGGCCATATCTTCGGCTTCAGACTCACTGAGCGCGTAACTGTTTGCGCAAACGGCCATCAGGCTGCC
+GAATAACACTGTTCTGAAAAACGTCTTCATTGCTTCTACCAGGGGCTTAAAGAAGATAAACGTTAGCACA
+CTGCGAGCGAGGCGACGACCATTATTGTCGATTAAATTGTGTCTGCGGCTTGACCTTCCCGTAAGGGGAA
+GGACTATGCTCAACGTTTGATTTTGTTTCGCCTGCTTAAGAATAAGGAAATAACTATGCAACGTCGTGAT
+TTCTTGAAATATTCCGTCGCACTGGGTGTGGCTTCAGCCTTGCCACTGTGGAGCCGTGCAGTCTTTGCGG
+CGGAACGCCCAACGTTACCGATCCCTGATTTGCTCACGACCGATGCCCGTAATCGCATTCAGTTAACTAT
+TGGCGCAGGTCAGTCTACCTTTGGCGAGAAAACTGCAACTACCTGGGGCTATAACGGCAATCTGCTGGGG
+CCGGCGGTGAAATTACAGCGCGGCAAAGCGGTAACGGTTGATATCTATAACCAACTGACGGAAGAGACGA
+CGTTGCACTGGCACGGGCTGGAAGTACCGGGTGAAGTCGACGGCGGCCCACAGGGAATTATTCCGCCAGG
+TGGCAAGCGCTCGGTGACGTTGAACGTTGATCAACCTGCCGCTACCTGCTGGTTCCATCCACATCAACAT
+GGCAAGACCGGGCGACAGGTGGCGATGGGGCTGGCTGGTCTGGTGGTGATTGAAGATGACGAGATCCTGA
+AATTAATGCTGCCAAAACAGTGGGGTATCGATGATGTTCCGGTGATCGTTCAGGATAAGAAATTTAGCGC
+CGACGGGCAGATTGATTATCAACTGGATGTGATGACCGCCGCCGTGGGCTGGTTTGGCGATACGTTGCTG
+ACCAACGGTGCAATCTACCCGCAACACGCTGCCCCGCGTGGTTGGCTGCGCCTGCGTTTGCTCAATGGCT
+GTAATGCCCGCTCGCTCAATTTCGCCACCAGCGACAATCGCCCGCTTTATGTGATTGCCAGCGACGGTGG
+TCTGCTACCTGAACCGGTGAAGGTGAACGAGCTGCCGGTGCTGATGGGCGAGCGTTTTGAAGTGCTGGTG
+GAGGTTAACGACAACAAACCCTTTGACCTGGTGACGCTGCCGGTCAGCCAGATGGGGATGGCGATTGCGC
+CGTTTGATAAGCCTCATCCGGTAATGCGGATTCAGCCGATTGCTATTAGTGCTTCCGGTGCTTTGCCAGA
+CACATTAAGTAGCCTGCCTGCGTTACCTTCGCTGGAAGGGCTGACGGTACGCAAGCTGCAACTTTCTATG
+GACCCGATGCTCGATATGATGGGGATGCAGATGCTAATGGAGAAATATGGCGATCAGGCGATGGTCGGAA
+TGGATCACAGCCAGATGATGGGCCATATGGGGCACGGCAATATGAATCATATGAACCACGGCGGGAAGTT
+CGATTTCCACCATGCCAATAAAATCAACGGTCAGGCGTTTGATATGAATAAGCCGATGTTTGCGGCGGCG
+AAAGGGCAGTACGAACGTTGGGTTATCTCTGGCGTGGGCGACATGATGCTGCATCCGTTCCATATTCACG
+GCACGCAGTTCCGTATCTTGTCAGAAAATGGCAAACCGCCAGCGGCTCATCGCGCGGGCTGGAAAGATAC
+CGTTAAGGTCGAAGGCAATGTCAGTGAAGTGCTGGTGAAGTTTAATCACGACGCACCGAAAGAACGTGCT
+TATATGGCGCACTGCCATCTGCTGGAGCATGAAGATACGGGGATGATGTTAGGGTTTACGGTATAAAAAG
+ACCGTATTCGGGAATATGCCCGGATCTCTCCGGGCATTAAACTGATGACAAACGCAAATCTGCCTGATGC
+GCTACGCTTATCAGGCCTACGTTACCTGTGCAATCCATTGATTTTGCACAATTTTGTAGGCTGGATAAGG
+CGTTCACGCCGCATCCGGCATGAACAACGCGCACGTTGTCAGCAATCTGAGCAAGTCTTACTTCACATCA
+TCCGGCAGCGCATAAGCCACAATATAGTCACCCATCTTCGTACCAAATGAACCGTGACCGCCTGCGGAGA
+TCACCACATACTGCTTACCATTCACTTCATAGGTCATTGGCGTCGCCTGACCACCCGCTGGTAAACGACC
+CTGCCACAGTTTTTCACCGTTGCTCATGTTGTAAGCGCGCAGGTAGTTATCTGCCGTAGCGGCGATAAAC
+AGCACGTTACCCGCCGTGGAGATTGGCCCGCCCAGCATCGGCATACCCATATTGAACGGCACCGGTACAG
+GCATCGGGAACGGCATACTGTCCTGCGGCGTACCAATACGTTTCTTCCACACCACTTCATTAGTTTTCAG
+ATCCAGCGCCGAGATATAACCCCATGCTGGCTGTTTACATGGCAGACCAAATGGTGAGAGGAACGGGTTG
+AGCGTGACACCATACGGTACACCGTACTGTGGCTGAATGCCGGATTCCGTACCCGTGCCTTTGGCATCTT
+TCGGCTGCTCCATCGGGTTACCCGGACCGCGTGGGATCAGTTTCGAAACAAACGGCAGTGCCATTGGGTT
+GGCAATTGCCACTTCACGATTTGGATCAACGGAAATCCCGCCCCATTCAAACATTCCCAGGTTACCCGGG
+AAGACCAGCGTGCCCTGTTCAGATGGCGGCGTGAAAATGCCTTCATAGCGCATCTGGTGGAACATCACGC
+GGCACACCAGTTGGTCAAACATGGTGGCTCCCCACATATCCGCACCGCTCAAATCTTTCGTCGGACGGAA
+GCTCAGTTCCGAGAATGGTTGAGTAGGGGTAACGTAATCGCCTTTGGCAGCACCTTGGGGAACCGGTTTT
+TCCGGTGCCGGAACCACCAGTTCGCCATTACGACGATCGAGCACAAAAATGTTGCCGGTTTTCGCCGGAG
+CGTAAATAACTGGCACTTTCTGACCATTAACGGTGATGTCCGCCAGCGTCGGCTGTGCCGGAAGATCCAT
+ATCCCACAGGTCGTGGTGAACGGTCTGGTAGCTCCACGCCAATTTCCCGGTTGTGGCATTCAGCGCCAGA
+ATCGAGCTGGCATAACGTTCCTGTTCCGGTGTGCGGTTACCGCCCCAGATATCCGGCGTGGTCACGCCCA
+TCGGCAGATACACCAGATCCAGCTTCGCGTCATAGGCCGCTGGTGCCCACGAGTTTGGCGAGTTAAAGGT
+AAAGGTGTGTTCGTCAGACGGGATTGCGTTCGGATCTTTCGCGCCCGGATCAAAAGCCCACAGCAGCTCC
+CCGGTGTTGACATCAAAACCACGGATCACGCCAGACGTTTCGCGGGTTGAGAAGTTATCGGTAACTGAAC
+CTGCCATCACGATGGTTTTATCGGTGATAATCGGTGGCGAAGTCGGTTCATACAGACCCGGTTTGGTGTC
+TGGCATATTGCTTTGCAGATTGAGCACGCCTTTATTGGCGAAGGTTTCGCACAGCTTGCCGTTTTCAGCG
+TTAATCGCAATCAGGCGACCATCATTGACCGGAAGAATGATACGACGCGGGCAATCCGCCATCACTTCCG
+GCGAAGCCGTTTCTGCTTTGGCTTCATGATAAGAGACGCCACGGCAGGTTACGTGCTGGAAAGACTCGTT
+AGTTTTCAGCTCAGGATCGTAATGCCATTTCTCTTTGCCGCTGGCGGCATCGAGCGCAAACAGGCGCTGG
+TGAGCGGTACACAGGTAAAGGGTGTCGCCCACTTTAATCGGCGTCACTTCATTGGTGATTTCGCCCGGAT
+CGTTCGGCTGCTTCACATCGCCAGTACGGAACACCCAGGCTTCTTTCAGATTATGGACGTTATCGGCGTT
+AATTTGTTTCAGAGGTGAAAAGCGTTGACCTTCCTGATTGCGACCATAGGCAGGCCAGTCCTGATCGGCA
+ACGGGTGAGATAGCTTCCGCAGGTGTGGCATCGGCGCTTAAGGTGCCGTTGATTTCCTGCGGATCGTTAA
+ATCCGGCCCAGGTCAGGATACTACCGCTAATCAGCAGTGCCACCACCAGTGCGGCAACTGCGCCGCTGGC
+AGGAATGACCAGGCGACGCCAGACAAACGGCAGGATCAGCCAGATGCCGAAGAAGACCAGAATATCGCTG
+CGCGGAGTCAGCGCCCAGAAGTCGAAACCAACTTCCCAGACGCCCCAAATCATGGTGCCGAGCAGCAGGG
+CGGCGTATAGCCAAAGCGCGGCACGTTTACTGCGCCACAGCATCCAGGCGACGCCGAGCATCACAAGGCC
+AGCGATAGGGTAGTACCAGGAGCCGCCAATCGCGACCAGCCAGCCTCCGCCAATGAGTAGATACAGCCCG
+CAAAGCGCTGCAAAAAGGGCTGTTAGCGTGACGAGTAATCGTCGCGAGCCTGTATTGTTAATTGCCATAA
+AGAGACACCATTTCAATTCATTAATATTTTAGTAGCAATTAATTATAGGTTTTAACATGTGTGATCGTCA
+TCACAATTTGAGCTTTATTAACAGATTCCGCGAATGAATCGTTTTGCTGGTATACTGCGTGTCTTGCGCT
+TTGTTGCGGTGCCAAAACCTGCCCGTGCGAAGTGATTTGTTTTTAAATCATATGGTTAGAGATATGAAAC
+ATACTGTAGAAGTAATGATCCCCGAAGCGGAGATTAAAGCGCGTATCGCCGAACTGGGTCGTCAGATTAC
+TGAGCGTTACAAAGACAGCGGCAGCGATATGGTGCTGGTGGGTCTGCTGCGTGGCTCATTTATGTTTATG
+GCGGACCTGTGCCGTGAAGTTCAGGTATCTCATGAAGTCGACTTTATGACCGCCTCCAGCTACGGTAGCG
+GCATGTCCACCACCCGTGATGTGAAAATCCTCAAAGATCTGGATGAAGATATCCGTGGCAAGGATGTGCT
+GATTGTTGAAGATATCATCGACTCGGGGAATACACTGTCGAAAGTGCGTGAGATCTTAAGCCTGCGCGAA
+CCGAAGTCGTTGGCGATTTGTACGCTGCTGGATAAACCGTCCCGTCGTGAAGTGAACGTCCCGGTAGAAT
+TTATCGGTTTCTCGATCCCGGATGAGTTTGTGGTGGGTTACGGCATTGATTACGCACAGCGTTACCGTCA
+TCTGCCGTATATCGGCAAAGTGATTCTGCTGGACGAGTAAGTGTGAAGTTGCCGGATGTGTTGCATCCGG
+CATGGCATTTTTATTTGTGGTTGGCGTGTTTCAGCTTGAGGTTGGAAATCCCGTGACGGTAACGTTGCTC
+AAGGGTTTCGCGGTTGGTGGCAGTAACATCCAGATCACGCAGCAAGCCGTCGTGAATGCCATAAGCCCAG
+CCGTGAATGGTAACTTTCTGCCCGCGTTTCCACGCTGATTGCATAATGGTGGAGTGGCCCAGGTTATACA
+CCTGTTCCATGACGTTCAGTTCACACAAGGTATCCAGACGGCGCTCTTGCGGCATTTCGTCGAGCAATGA
+GCTATGTTTGAACCAGATATCGCGGATATGCAGCAGCCAGTTGTTGATAAGCCCCAGTTCCGGGTTTTCA
+ACTGCGGCTTGTACGCCGCCGCAACCGTAGTGGCCACAGATAATAATGTGTTCAACTTCGAGTACATCCA
+CTGCATACTGAACCACGGAAAGGCAGTTCAGGTCGGTGTGAATGACCAGGTTAGCAACATTACGGTGAAC
+AAAGAGTTCGCCCGGCTCAAGACCGGTTAAACGTTCTGCAGGAACGCGACTGTCGGAACATCCAATCCAT
+AGAAAGCGCGGTTTTTGCGCTTGTGCCAGTTTCTCAAAAAACCCGGGATCCTCTTCCACCAGCATTTTTG
+ACCATAGTGCATTGTTGCTGATGAGTGTATCTATGTCTTTCATGGAGGTTAACGACCTGTAACCAAATAA
+TTACGTTTGGCTAATATAGGGCAACTCCGGGACGATTTAAACCACAGATAAAGTGTAAGAACGTAAGGTA
+AGTAAAAATTTATGACCATTGCACTGGAACTTCAACAGCTTAAAAAAAACTATCCAGGCGGCGTTCAGGC
+GCTTCGTGGAATAGATTTGCAGGTCGAAGCGGGTGATTTTTATGCGCTTCTCGGGCCGAACGGGGCCGGG
+AAATCGACCACTATCGGTATTATCAGCTCTCTGGTAAATAAAACCTCCGGGCGGGTCAGCGTATTTGGTT
+ACGATCTCGAGAAAGATGTCGTGAACGCTAAACGTCAGTTGGGACTGGTGCCGCAGGAATTTAACTTCAA
+CCCGTTTGAAACCGTGCAGCAAATTGTGGTGAATCAGGCAGGGTACTACGGTGTGGAGCGCAAAGAGGCG
+TACATCCGCAGCGAAAAATATCTTAAGCAGCTCGATTTATGGGGAAAACGCAACGAACGTGCGCGCATGT
+TATCTGGCGGGATGAAGCGCCGTTTAATGATTGCCCGTGCGTTAATGCATGAACCTAAACTACTGATTCT
+CGACGAGCCGACTGCAGGCGTGGATATTGAACTTCGCCGCTCAATGTGGGGCTTTTTGAAGGATTTAAAC
+GACAAAGGCACCACCATCATTCTCACCACACACTACCTGGAAGAAGCAGAAATGCTGTGCCGCAATATCG
+GCATTATTCAACACGGTGAGCTGGTGGAAAATACCTCGATGAAGGCGCTGCTGGCGAAGCTGAAATCGGA
+AACCTTTATTCTCGATCTCGCACCGAAAAGTCCGTTACCGAAGCTCGATGGCTATCAGTATCGACTGGTC
+GATACCGCGACGCTGGAAGTTGAAGTGCTGCGTGAGCAGGGGATCAACAGCGTATTTACGCAGTTAAGTG
+AGCAGGGCATTCAGGTATTAAGTATGCGTAACAAAGCTAACCGTCTGGAAGAGCTGTTTGTTTCACTGGT
+TAATGAAAAACAAGGAGATCGCGCATGATGCATCTTTACTGGGTGGCGCTAAAAAGCATCTGGGCGAAAG
+AGATCCATCGCTTTATGCGTATCTGGGTGCAGACGCTGGTGCCGCCAGTCATCACCATGACCCTTTACTT
+TATTATTTTCGGTAACCTGATTGGTTCGCGTATTGGCGATATGCATGGCTTCAGCTACATGCAGTTCATC
+GTACCGGGGCTGATCATGATGTCGGTGATCACCAACGCCTACGCCAACGTCGCGTCATCATTTTTTGGTG
+CCAAGTTCCAGCGTAATATTGAAGAGCTGCTGGTAGCGCCGGTTCCGACTCACGTCATTATTGCCGGATA
+TGTCGGCGGTGGCGTGGCGCGTGGTCTGTTTGTTGGCATTCTGGTGACGGCAATTTCACTGTTTTTTGTG
+CCGTTTCAGGTGCATTCGTGGGTATTCGTTGCCTTAACCCTGGTGCTCACGGCGGTGTTGTTCTCCCTTG
+CGGGTTTGCTGAACGGTGTGTTTGCCAAAACGTTCGATGACATCAGCCTGGTGCCAACCTTTGTGTTAAC
+GCCACTCACGTATTTGGGTGGGGTCTTTTACTCACTGACTTTGTTGCCGCCGTTCTGGCAAGGGCTGTCG
+CACCTGAACCCAATCGTTTATATGATCAGTGGTTTCCGCTACGGCTTCCTCGGTATCAATGATGTTCCGC
+TGGTCACTACCTTTGGCGTACTGGTGGTCTTTATTGTGGCGTTTTATTTGATCTGTTGGTCGCTGATCCA
+ACGTGGACGTGGTTTGCGTAGCTAAGGCTATTTCCTCTCCTCTGGATTTGGGGGAGAGGAGTTTTGACGG
+CTATCACCCTTTATCAACAATGGTCAGGGTAGACTGATTTTCGGCTAAGGAGGAAGGCGATGTTAGGTTG
+GGTAATTACCTGTCACGATGACCGGGCGCAAGAGATACTGGATGTGCTGGAGAAAAAACATGGGGCGCTT
+CTTCAGTGCCGGGCCGTGAATTTCTGGCGCGGATTAAGTTCTAATATGCTCAGCCGCATGATGTGCGATG
+CTCTGCATGAAGCGGACTCTGGTGAGGGTGTCATCTTCTTAACCGATATAGCCGGAGCGCCACCGTACCG
+CGTGGCTTCATTATTAAGCCACAAACACTCCCGTTGCGAAGTGATTTCTGGTGTCACGTTACCGTTAATT
+GAACAGATGATGGCTTGCCGTGAAACCATGACCAGTTCAGAGTTTCGCGAGCGTATTGTCGAACTGGGTG
+CGCCGGAGGTGAGTAGTATTTGGCACCAGCAACAAAAAAATCCGCCTTTCGTCCTCAAACATAATTTGTA
+TGAGTATTAACCCGCGATTCTGATGGCGCTTTTGCTACAATAAAAGCGTTGTTTCACCCTCGGTGATTTT
+TTCATGTACAAACAAGCTGTTATTCTCCTGCTGATGCTGTTTACCGCAAGTGTCAGTGCCGCGTTACCTG
+CCCGTTATATGCAAACCATCGAAAATGCTGCGGTCTGGGCGCAAATTGGTGACAAGATGGTGACCGTGGG
+GAATATTCGGGCCGGACAAATCATTGCCGTGGAGCCCACTGCCGCAAGTTATTACGCATTTAATTTTGGC
+TTTGATAAAGGGTTTATCGATAAAGGTCATCTTGAGCCGGTTCAGGGGCGACAAAAAGTTGAAGACGGTT
+TGGGTGACCTCAACAAGCCGCTGAGTAATCAGAACTTAGTTACCTGGAAAGATACGCCGGTCTATAACGC
+GCCGAGTGTGGGCAGTGCGCCATTTGGGGTACTGGCGGACAATTTGCGCTACCCGATTTTGCATAAACTG
+AAAGACAGGTTAAATCAAACCTGGTATCAGATCCGTATTGGCGATCGACTGGCCTATATCAGCGCGCTGG
+ATGCCCAACCCGATAATGGCCTTCCGGTGCTAACCTATCACCATATTCTGCGCGACGAAGAAAACACCCG
+TTTTCGCCATACTTCGACGACCACCTCGGTACGCGCTTTCAATAACCAGATGGCCTGGCTGCGCGACAGG
+GGATACGCGACACTGAGCATGGTGCAGCTGGAAGGTTACGTGAAGAATAAGATCAATCTTCCTGCGCGAG
+CGGTGGTGATTACCTTTGATGATGGCCTCAAGTCAGTGAGCCGCTATGCGTATCCTGTGTTGAAACAATA
+TGGCATGAAGGCGACGGCGTTTATTGTTACCTCGCGCATCAAACGTCACCCGCAGAAGTGGGAACCAAAA
+TCGCTGCAATTTATGAGCGTTTCTGAGCTTAACGAAATTCGCGATGTATTTGATTTCCAGTCACATACCC
+ATTTTTTGCATCGGGTAGATGGTTATCGCCGACCCATATTACTGAGCCGTAGTGAGCACAATATTCTGTT
+TGATTTTGCACGTTCACGTCGCGCTCTGGCGCAATTTAATCCGCATGTCTGGTATCTTTCGTATCCGTTT
+GGCGGCTTTAATGACAAAGCCGTGAAGGCAGCAAACGATGCCGGATTTCACCTGGCGGTGACAACCATGA
+AAGGCAAAGTAAAACCGGGGGATAATCCGTTGTTACTAAAACGACTTTATATCTTAAGAACGGATTCGCT
+GGAGACGATGTCGCGGCTGGTGAGTAACCAGCCGCAGGGATAACAATCAAGCAACCTGTACCGGAATCGC
+TTTCGCGGTACGTTTCATTTCATTGTCGCCTTCAAAATAGGCGACGTTGGGTCGCCAGGTGCGAGCTTCT
+TCATCTGGCATGGTAACGAAGCTGGCGATGATGACAATATCGCCGACACTGGCGCAGTGGGCCGCCGC
diff -r 000000000000 -r b1f16ffc171f test-data/TIAC1151-R10-ds.bam
Binary file test-data/TIAC1151-R10-ds.bam has changed
diff -r 000000000000 -r b1f16ffc171f test-data/TIAC1151-R10-ds.bam.bai
Binary file test-data/TIAC1151-R10-ds.bam.bai has changed
diff -r 000000000000 -r b1f16ffc171f test-data/TIAC1151-ont.gz
Binary file test-data/TIAC1151-ont.gz has changed
diff -r 000000000000 -r b1f16ffc171f test-data/TIAC1151.bam
Binary file test-data/TIAC1151.bam has changed
diff -r 000000000000 -r b1f16ffc171f test-data/TIAC1151.bam.bai
Binary file test-data/TIAC1151.bam.bai has changed
diff -r 000000000000 -r b1f16ffc171f test-data/TIAC1151_1P.fastq.gz
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