Mercurial > repos > bgruening > graphmap_overlap
comparison graphmap_owler.xml @ 0:d0a712cf0518 draft
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 15:27:40 -0400 |
parents | |
children | 815251b32ccc |
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-1:000000000000 | 0:d0a712cf0518 |
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1 <tool id="graphmap_overlap" name="Owler" version="@VERSION@"> | |
2 <description>fast, trimmed overlap pipeline without aligning</description> | |
3 <macros> | |
4 <import>macros.xml</import> | |
5 </macros> | |
6 <expand macro="requirements" /> | |
7 <command detect_errors="exit_code"> | |
8 <![CDATA[ | |
9 ln -s '$r' ref.${r.ext} && | |
10 ln -s '$d' reads.${d.ext} && | |
11 | |
12 graphmap owler | |
13 -r ref.${r.ext} | |
14 -d reads.${d.ext} | |
15 -o output.mhap | |
16 #if $preset: | |
17 -x $preset | |
18 #end if | |
19 -t \${GALAXY_SLOTS:-4} | |
20 ]]></command> | |
21 <inputs> | |
22 <param argument="-r" type="data" format="fasta,fastq" label="reference sequence" /> | |
23 <param argument="-d" type="data" format="fasta,fastq" label="reads" /> | |
24 <param name="preset" type="select" optional="True" label="Pre-set parameters (-x)"> | |
25 <option value="no-filters">Disable filters</option> | |
26 </param> | |
27 <!-- | |
28 <param type="data" name="reference" format="fasta,fastq" label="Sequences"/> | |
29 <param type="data" name="reads" format="fasta,fastq" label="Sequences"/> | |
30 <param type="data" name="overlaps" format="sam,tabular" label="Overlaps"/> | |
31 <param type="data" name="corrected_reads" format="fasta,fasta.gz,fastq,fastq.gz" label="Target sequences"/> --> | |
32 | |
33 </inputs> | |
34 <outputs> | |
35 <data name="output" format="txt" from_work_dir="output.mhap" /> | |
36 </outputs> | |
37 <tests> | |
38 <test> | |
39 <param name="r" value="Loman_E.coli_MAP006-1_2D_50x_first_500_reads.fasta"/> | |
40 <param name="d" value="E.coli_contigs.fasta"/> | |
41 <output name="output" ftype="txt" file="result1_owler.mhap"/> | |
42 </test> | |
43 <test> | |
44 <param name="r" value="Loman_E.coli_MAP006-1_2D_50x_first_500_reads.fasta"/> | |
45 <param name="d" value="E.coli_contigs.fasta"/> | |
46 <param name="preset" value="no-filters"/> | |
47 <output name="output" ftype="txt" file="result2_owler.mhap"/> | |
48 </test></tests> | |
49 <help><![CDATA[ | |
50 GraphMap - A very accurate and sensitive long-read, high error-rate sequence mapper | |
51 GraphMap (c) by Ivan Sovic, Mile Sikic and Niranjan Nagarajan | |
52 GraphMap is licensed under The MIT License. | |
53 ]]></help> | |
54 <expand macro="citations" /> | |
55 </tool> |