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comparison graphmap_owler.xml @ 0:d0a712cf0518 draft

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/graphmap commit a1461f1e83079de821b269125c49eca2460e7693
author bgruening
date Thu, 27 Sep 2018 15:27:40 -0400
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children 815251b32ccc
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-1:000000000000 0:d0a712cf0518
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>