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comparison graphmap_align.xml @ 1:1c6c961851de draft default tip

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/graphmap commit ba787e88cb93e78516b2fced5b60285d5f033ca3
author bgruening
date Fri, 15 Mar 2024 13:12:50 +0000
parents 190175f4e143
children
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0:190175f4e143 1:1c6c961851de
1 <tool id="graphmap_align" name="Mapper" version="@VERSION@"> 1 <tool id="graphmap_align" name="Mapper" version="@VERSION@">
2 <description>for long, error-prone reads, like Nanopore ONT and PacBio</description> 2 <description>for long, error-prone reads, like Nanopore ONT and PacBio</description>
3 <macros> 3 <macros>
4 <import>macros.xml</import> 4 <import>macros.xml</import>
5 </macros> 5 </macros>
6 <expand macro="xrefs" />
6 <expand macro="requirements" /> 7 <expand macro="requirements" />
7 <command detect_errors="exit_code"> 8 <command detect_errors="exit_code">
8 <![CDATA[ 9 <![CDATA[
9 ln -s '$r' ref.${r.ext} && 10 ln -s '$r' ref.${r.ext} &&
10 ln -s '$d' reads.${d.ext} && 11 ln -s '$d' reads.${d.ext} &&
38 </outputs> 39 </outputs>
39 <tests> 40 <tests>
40 <test> 41 <test>
41 <param name="r" value="Loman_E.coli_MAP006-1_2D_50x_first_500_reads.fasta"/> 42 <param name="r" value="Loman_E.coli_MAP006-1_2D_50x_first_500_reads.fasta"/>
42 <param name="d" value="E.coli_contigs.fasta"/> 43 <param name="d" value="E.coli_contigs.fasta"/>
43 <output name="output" ftype="bam" file="result1_map.bam"/> 44 <output name="output" ftype="bam" file="result1_map.bam" lines_diff="2"/>
44 </test> 45 </test>
45 <test> 46 <test>
46 <param name="r" value="Loman_E.coli_MAP006-1_2D_50x_first_500_reads.fasta"/> 47 <param name="r" value="Loman_E.coli_MAP006-1_2D_50x_first_500_reads.fasta"/>
47 <param name="d" value="E.coli_contigs.fasta"/> 48 <param name="d" value="E.coli_contigs.fasta"/>
48 <param name="preset" value="illumina"/> 49 <param name="preset" value="illumina"/>
49 <output name="output" ftype="bam" file="result2_map.bam"/> 50 <output name="output" ftype="bam" file="result2_map.bam" lines_diff="2"/>
50 </test> 51 </test>
51 <test> 52 <test>
52 <param name="r" value="Loman_E.coli_MAP006-1_2D_50x_first_500_reads.fasta"/> 53 <param name="r" value="Loman_E.coli_MAP006-1_2D_50x_first_500_reads.fasta"/>
53 <param name="d" value="E.coli_contigs.fasta"/> 54 <param name="d" value="E.coli_contigs.fasta"/>
54 <param name="preset" value="sensitive"/> 55 <param name="preset" value="sensitive"/>
55 <output name="output" ftype="bam" file="result3_map.bam"/> 56 <output name="output" ftype="bam" file="result3_map.bam" lines_diff="2"/>
56 </test></tests> 57 </test></tests>
57 <help><![CDATA[ 58 <help><![CDATA[
58 GraphMap - A very accurate and sensitive long-read, high error-rate sequence mapper 59 GraphMap - A very accurate and sensitive long-read, high error-rate sequence mapper
59 GraphMap (c) by Ivan Sovic, Mile Sikic and Niranjan Nagarajan 60 GraphMap (c) by Ivan Sovic, Mile Sikic and Niranjan Nagarajan
60 GraphMap is licensed under The MIT License. 61 GraphMap is licensed under The MIT License.