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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/graphmap commit a1461f1e83079de821b269125c49eca2460e7693
author | bgruening |
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date | Thu, 27 Sep 2018 15:25:28 -0400 |
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<tool id="graphmap_overlap" name="Owler" version="@VERSION@"> <description>fast, trimmed overlap pipeline without aligning</description> <macros> <import>macros.xml</import> </macros> <expand macro="requirements" /> <command detect_errors="exit_code"> <![CDATA[ ln -s '$r' ref.${r.ext} && ln -s '$d' reads.${d.ext} && graphmap owler -r ref.${r.ext} -d reads.${d.ext} -o output.mhap #if $preset: -x $preset #end if -t \${GALAXY_SLOTS:-4} ]]></command> <inputs> <param argument="-r" type="data" format="fasta,fastq" label="reference sequence" /> <param argument="-d" type="data" format="fasta,fastq" label="reads" /> <param name="preset" type="select" optional="True" label="Pre-set parameters (-x)"> <option value="no-filters">Disable filters</option> </param> <!-- <param type="data" name="reference" format="fasta,fastq" label="Sequences"/> <param type="data" name="reads" format="fasta,fastq" label="Sequences"/> <param type="data" name="overlaps" format="sam,tabular" label="Overlaps"/> <param type="data" name="corrected_reads" format="fasta,fasta.gz,fastq,fastq.gz" label="Target sequences"/> --> </inputs> <outputs> <data name="output" format="txt" from_work_dir="output.mhap" /> </outputs> <tests> <test> <param name="r" value="Loman_E.coli_MAP006-1_2D_50x_first_500_reads.fasta"/> <param name="d" value="E.coli_contigs.fasta"/> <output name="output" ftype="txt" file="result1_owler.mhap"/> </test> <test> <param name="r" value="Loman_E.coli_MAP006-1_2D_50x_first_500_reads.fasta"/> <param name="d" value="E.coli_contigs.fasta"/> <param name="preset" value="no-filters"/> <output name="output" ftype="txt" file="result2_owler.mhap"/> </test></tests> <help><![CDATA[ GraphMap - A very accurate and sensitive long-read, high error-rate sequence mapper GraphMap (c) by Ivan Sovic, Mile Sikic and Niranjan Nagarajan GraphMap is licensed under The MIT License. ]]></help> <expand macro="citations" /> </tool>