Mercurial > repos > bgruening > graphmap_align
comparison graphmap_align.xml @ 1:1c6c961851de draft default tip
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/graphmap commit ba787e88cb93e78516b2fced5b60285d5f033ca3
author | bgruening |
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date | Fri, 15 Mar 2024 13:12:50 +0000 |
parents | 190175f4e143 |
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0:190175f4e143 | 1:1c6c961851de |
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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. |