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Merge pull request #2960 from nsoranzo/minia
Add minimal wrapper for minia
2 parents 6de23fe + 5110437 commit cd3b054

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‎tools/minia/.shed.yml‎

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categories:
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- Assembly
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description: Short-read assembler based on a de Bruijn graph
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long_description: |
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Minia is capable of assembling a human genome on a desktop computer in a day.
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The output of Minia is a set of contigs.
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name: minia
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owner: iuc
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remote_repository_url: https://github.com/galaxyproject/tools-iuc/tree/master/tools/minia
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homepage_url: https://gatb.inria.fr/software/minia/
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type: unrestricted

‎tools/minia/minia.xml‎

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<tool id="minia" name="Minia" version="@TOOL_VERSION@">
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<description>Short-read assembler based on a de Bruijn graph</description>
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<macros>
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<token name="@TOOL_VERSION@">3.2.1</token>
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</macros>
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<requirements>
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<requirement type="package" version="@TOOL_VERSION@">minia</requirement>
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</requirements>
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<command detect_errors="exit_code"><![CDATA[
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#set input = 'infile.' + $in.ext
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ln -s '$in' '$input' &&
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minia
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-in '$input'
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-kmer-size $kmer_size
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#if str($abundance_min):
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-abundance-min $abundance_min
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#end if
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#if str($abundance_max):
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-abundance-min $abundance_max
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#end if
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-nb-cores \${GALAXY_SLOTS:-1}
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-out output
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]]></command>
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<inputs>
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<param argument="-in" type="data" format="fasta,fastqsanger,fastqsanger.gz,fasta.gz" label="Reads in FASTA or FASTQ format" />
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<param argument="-kmer-size" type="integer" value="31" min="1" label="Size of a kmer" />
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<param argument="-abundance-min" type="integer" value="" optional="true" min="0" label="Min abundance threshold for solid kmers (default: 2)" />
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<param argument="-abundance-max" type="integer" value="" optional="true" label="Max abundance threshold for solid kmers" />
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</inputs>
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<outputs>
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<data name="output" format="fasta" label="${tool.name} on ${on_string}" from_work_dir="output.contigs.fa" />
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</outputs>
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<tests>
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<test>
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<param name="in" value="ec.fa" />
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<param name="kmer_size" value="21" />
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<param name="abundance_min" value="1" />
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<output name="output" ftype="fasta">
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<assert_contents>
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<has_text text="LN:i:460 KC:i:2200 km:f:5.000"/>
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<has_text text="LN:i:637 KC:i:3085 km:f:5.000"/>
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<has_n_lines n="4"/>
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</assert_contents>
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</output>
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</test>
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</tests>
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<help><![CDATA[
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Minia is a short-read assembler based on a de Bruijn graph, capable of assembling a human genome on a desktop computer in a day.
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The output of Minia is a set of contigs.
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]]></help>
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<citations>
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<citation type="doi">10.1186/1748-7188-8-22</citation>
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</citations>
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</tool>

‎tools/minia/test-data/ec.fa‎

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>works well for k=21; part of genome10K.fasta
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CATCGATGCGAGACGCCTGTCGCGGGGAATTGTGGGGCGGACCACGCTCTGGCTAACGAGCTACCGTTTCCTTTAACCTGCCAGACGGTGACCAGGGCCGTTCGGCGTTGCATCGAGCGGTGTCGCTAGCGCAATGCGCAAGATTTTGACATTTACAAGGCAACATTGCAGCGTCCGATGGTCCGGTGGCCTCCAGATAGTGTCCAGTCGCTCTAACTGTATGGAGACCATAGGCATTTACCTTATTCTCATCGCCACGCCCCAAGATCTTTAGGACCCAGCATTCCTTTAACCACTAACATAACGCGTGTCATCTAGTTCAACAACC
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>remaining part
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TGTCATCTAGTTCAACAACCGTTATGCCGTCCGACTCTTGCGCTCGGATGTCCGCAATGGGTTATCCCTATGTTCCGGTAATCTCTCATCTACTAAGCGCCCTAAAGGTCGTATGGTTGGAGGGCGGTTACACACCCTTAAGTACCGAACGATAGAGCACCCGTCTAGGAGGGCGTGCAGGGTCTCCCGCTAGCTAATGGTCACGGCCTCTCTGGGAAAGCTGAACAACGGATGATACCCATACTGCCACTCCAGTACCTGGGCCGCGTGTTGTACGCTGTGTATCTTGAGAGCGTTTCCAGCAGATAGAACAGGATCACATGTACATG
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>that's the EC
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TGTCATCTAGTTCAACAACCAAAAAAA
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>contig that is split in two by the EC, containing the last kmer of the ec (CTAGTTCAACAACCAAAAAAA)
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GGTGAACAGCACATCTTTTCGTCCTGAGGCCATATTAATTCTACTCAGATTGTCTGTAACCGGAGCTTCGGGCGTATTTTTGCGTAAGACACTGCCTAAAGGGAACATATGTGTCCAGAATAGGGTTCAACGGTGTATGAGCAAA
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CTAGTTCAACAACCAAAAAAA
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TTGTGTGCAAGCTACTTCTAGACCTTATTAAGTGCCCAGGAATTCCTAGGAAGGCGCGCAGCTCAAGCAATCATACATGGCGGAATGCCTGTCCACCGGGGGTTCTACTGTACCACAGTGGCCTGGATAGCTAAGCAGGTCCTGGATTGGCATGTCATCCGGAGTGATAGGCACTGCTCACGACCAGCTTGCGGACAAACGGGGTGCCCGCGCCTGCGTCCGGTAGACGAGCGATGGATTTAGACCGTTCACTGAACCCTCTAATAGGACCTCTTGCCCATCCGAGGCTTAAGC
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>the rest below is just repeated for coverage reasons
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A
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>the rest below is just repeated for coverage reasons
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A
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>the rest below is just repeated for coverage reasons
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A
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>contig that is split in two by the EC, containing the last kmer of the ec (CTAGTTCAACAACCAAAAAAA)
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GGTGAACAGCACATCTTTTCGTCCTGAGGCCATATTAATTCTACTCAGATTGTCTGTAACCGGAGCTTCGGGCGTATTTTTGCGTAAGACACTGCCTAAAGGGAACATATGTGTCCAGAATAGGGTTCAACGGTGTATGAGCAAA
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CTAGTTCAACAACCAAAAAAA
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TTGTGTGCAAGCTACTTCTAGACCTTATTAAGTGCCCAGGAATTCCTAGGAAGGCGCGCAGCTCAAGCAATCATACATGGCGGAATGCCTGTCCACCGGGGGTTCTACTGTACCACAGTGGCCTGGATAGCTAAGCAGGTCCTGGATTGGCATGTCATCCGGAGTGATAGGCACTGCTCACGACCAGCTTGCGGACAAACGGGGTGCCCGCGCCTGCGTCCGGTAGACGAGCGATGGATTTAGACCGTTCACTGAACCCTCTAATAGGACCTCTTGCCCATCCGAGGCTTAAGC
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>contig that is split in two by the EC, containing the last kmer of the ec (CTAGTTCAACAACCAAAAAAA)
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GGTGAACAGCACATCTTTTCGTCCTGAGGCCATATTAATTCTACTCAGATTGTCTGTAACCGGAGCTTCGGGCGTATTTTTGCGTAAGACACTGCCTAAAGGGAACATATGTGTCCAGAATAGGGTTCAACGGTGTATGAGCAAA
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CTAGTTCAACAACCAAAAAAA
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TTGTGTGCAAGCTACTTCTAGACCTTATTAAGTGCCCAGGAATTCCTAGGAAGGCGCGCAGCTCAAGCAATCATACATGGCGGAATGCCTGTCCACCGGGGGTTCTACTGTACCACAGTGGCCTGGATAGCTAAGCAGGTCCTGGATTGGCATGTCATCCGGAGTGATAGGCACTGCTCACGACCAGCTTGCGGACAAACGGGGTGCCCGCGCCTGCGTCCGGTAGACGAGCGATGGATTTAGACCGTTCACTGAACCCTCTAATAGGACCTCTTGCCCATCCGAGGCTTAAGC
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>works well for k=21; part of genome10K.fasta
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CATCGATGCGAGACGCCTGTCGCGGGGAATTGTGGGGCGGACCACGCTCTGGCTAACGAGCTACCGTTTCCTTTAACCTGCCAGACGGTGACCAGGGCCGTTCGGCGTTGCATCGAGCGGTGTCGCTAGCGCAATGCGCAAGATTTTGACATTTACAAGGCAACATTGCAGCGTCCGATGGTCCGGTGGCCTCCAGATAGTGTCCAGTCGCTCTAACTGTATGGAGACCATAGGCATTTACCTTATTCTCATCGCCACGCCCCAAGATCTTTAGGACCCAGCATTCCTTTAACCACTAACATAACGCGTGTCATCTAGTTCAACAACC
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>remaining part
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TGTCATCTAGTTCAACAACCGTTATGCCGTCCGACTCTTGCGCTCGGATGTCCGCAATGGGTTATCCCTATGTTCCGGTAATCTCTCATCTACTAAGCGCCCTAAAGGTCGTATGGTTGGAGGGCGGTTACACACCCTTAAGTACCGAACGATAGAGCACCCGTCTAGGAGGGCGTGCAGGGTCTCCCGCTAGCTAATGGTCACGGCCTCTCTGGGAAAGCTGAACAACGGATGATACCCATACTGCCACTCCAGTACCTGGGCCGCGTGTTGTACGCTGTGTATCTTGAGAGCGTTTCCAGCAGATAGAACAGGATCACATGTACATG
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>works well for k=21; part of genome10K.fasta
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CATCGATGCGAGACGCCTGTCGCGGGGAATTGTGGGGCGGACCACGCTCTGGCTAACGAGCTACCGTTTCCTTTAACCTGCCAGACGGTGACCAGGGCCGTTCGGCGTTGCATCGAGCGGTGTCGCTAGCGCAATGCGCAAGATTTTGACATTTACAAGGCAACATTGCAGCGTCCGATGGTCCGGTGGCCTCCAGATAGTGTCCAGTCGCTCTAACTGTATGGAGACCATAGGCATTTACCTTATTCTCATCGCCACGCCCCAAGATCTTTAGGACCCAGCATTCCTTTAACCACTAACATAACGCGTGTCATCTAGTTCAACAACC
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>remaining part
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TGTCATCTAGTTCAACAACCGTTATGCCGTCCGACTCTTGCGCTCGGATGTCCGCAATGGGTTATCCCTATGTTCCGGTAATCTCTCATCTACTAAGCGCCCTAAAGGTCGTATGGTTGGAGGGCGGTTACACACCCTTAAGTACCGAACGATAGAGCACCCGTCTAGGAGGGCGTGCAGGGTCTCCCGCTAGCTAATGGTCACGGCCTCTCTGGGAAAGCTGAACAACGGATGATACCCATACTGCCACTCCAGTACCTGGGCCGCGTGTTGTACGCTGTGTATCTTGAGAGCGTTTCCAGCAGATAGAACAGGATCACATGTACATG
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>contig that is split in two by the EC, containing the last kmer of the ec (CTAGTTCAACAACCAAAAAAA)
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GGTGAACAGCACATCTTTTCGTCCTGAGGCCATATTAATTCTACTCAGATTGTCTGTAACCGGAGCTTCGGGCGTATTTTTGCGTAAGACACTGCCTAAAGGGAACATATGTGTCCAGAATAGGGTTCAACGGTGTATGAGCAAA
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CTAGTTCAACAACCAAAAAAA
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TTGTGTGCAAGCTACTTCTAGACCTTATTAAGTGCCCAGGAATTCCTAGGAAGGCGCGCAGCTCAAGCAATCATACATGGCGGAATGCCTGTCCACCGGGGGTTCTACTGTACCACAGTGGCCTGGATAGCTAAGCAGGTCCTGGATTGGCATGTCATCCGGAGTGATAGGCACTGCTCACGACCAGCTTGCGGACAAACGGGGTGCCCGCGCCTGCGTCCGGTAGACGAGCGATGGATTTAGACCGTTCACTGAACCCTCTAATAGGACCTCTTGCCCATCCGAGGCTTAAGC
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>contig that is split in two by the EC, containing the last kmer of the ec (CTAGTTCAACAACCAAAAAAA)
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GGTGAACAGCACATCTTTTCGTCCTGAGGCCATATTAATTCTACTCAGATTGTCTGTAACCGGAGCTTCGGGCGTATTTTTGCGTAAGACACTGCCTAAAGGGAACATATGTGTCCAGAATAGGGTTCAACGGTGTATGAGCAAA
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CTAGTTCAACAACCAAAAAAA
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TTGTGTGCAAGCTACTTCTAGACCTTATTAAGTGCCCAGGAATTCCTAGGAAGGCGCGCAGCTCAAGCAATCATACATGGCGGAATGCCTGTCCACCGGGGGTTCTACTGTACCACAGTGGCCTGGATAGCTAAGCAGGTCCTGGATTGGCATGTCATCCGGAGTGATAGGCACTGCTCACGACCAGCTTGCGGACAAACGGGGTGCCCGCGCCTGCGTCCGGTAGACGAGCGATGGATTTAGACCGTTCACTGAACCCTCTAATAGGACCTCTTGCCCATCCGAGGCTTAAGC
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>works well for k=21; part of genome10K.fasta
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CATCGATGCGAGACGCCTGTCGCGGGGAATTGTGGGGCGGACCACGCTCTGGCTAACGAGCTACCGTTTCCTTTAACCTGCCAGACGGTGACCAGGGCCGTTCGGCGTTGCATCGAGCGGTGTCGCTAGCGCAATGCGCAAGATTTTGACATTTACAAGGCAACATTGCAGCGTCCGATGGTCCGGTGGCCTCCAGATAGTGTCCAGTCGCTCTAACTGTATGGAGACCATAGGCATTTACCTTATTCTCATCGCCACGCCCCAAGATCTTTAGGACCCAGCATTCCTTTAACCACTAACATAACGCGTGTCATCTAGTTCAACAACC
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>remaining part
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TGTCATCTAGTTCAACAACCGTTATGCCGTCCGACTCTTGCGCTCGGATGTCCGCAATGGGTTATCCCTATGTTCCGGTAATCTCTCATCTACTAAGCGCCCTAAAGGTCGTATGGTTGGAGGGCGGTTACACACCCTTAAGTACCGAACGATAGAGCACCCGTCTAGGAGGGCGTGCAGGGTCTCCCGCTAGCTAATGGTCACGGCCTCTCTGGGAAAGCTGAACAACGGATGATACCCATACTGCCACTCCAGTACCTGGGCCGCGTGTTGTACGCTGTGTATCTTGAGAGCGTTTCCAGCAGATAGAACAGGATCACATGTACATG
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>works well for k=21; part of genome10K.fasta
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CATCGATGCGAGACGCCTGTCGCGGGGAATTGTGGGGCGGACCACGCTCTGGCTAACGAGCTACCGTTTCCTTTAACCTGCCAGACGGTGACCAGGGCCGTTCGGCGTTGCATCGAGCGGTGTCGCTAGCGCAATGCGCAAGATTTTGACATTTACAAGGCAACATTGCAGCGTCCGATGGTCCGGTGGCCTCCAGATAGTGTCCAGTCGCTCTAACTGTATGGAGACCATAGGCATTTACCTTATTCTCATCGCCACGCCCCAAGATCTTTAGGACCCAGCATTCCTTTAACCACTAACATAACGCGTGTCATCTAGTTCAACAACC
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>remaining part
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TGTCATCTAGTTCAACAACCGTTATGCCGTCCGACTCTTGCGCTCGGATGTCCGCAATGGGTTATCCCTATGTTCCGGTAATCTCTCATCTACTAAGCGCCCTAAAGGTCGTATGGTTGGAGGGCGGTTACACACCCTTAAGTACCGAACGATAGAGCACCCGTCTAGGAGGGCGTGCAGGGTCTCCCGCTAGCTAATGGTCACGGCCTCTCTGGGAAAGCTGAACAACGGATGATACCCATACTGCCACTCCAGTACCTGGGCCGCGTGTTGTACGCTGTGTATCTTGAGAGCGTTTCCAGCAGATAGAACAGGATCACATGTACATG
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‎tools/odgi/build.xml‎

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help="" />
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</inputs>
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<outputs>
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<data name="odgi_output" format="odgi" />
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<data name="gfa_output" format="gfa1">
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<data name="odgi_output" format="odgi" label="${tool.name} on ${on_string}: odgi" />
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<data name="gfa_output" format="gfa1" label="${tool.name} on ${on_string}: GFA">
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<filter>to_gfa</filter>
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</data>
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</outputs>

‎tools/odgi/vis.xml‎

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label="Show thin links of this relative width to connect path pieces" />
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</inputs>
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<outputs>
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<data name="output" format="png" />
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<data name="output" format="png" label="${tool.name} on ${on_string}" />
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</outputs>
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<tests>
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<test>

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