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comparison graphmap_align.xml @ 0:190175f4e143 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 15:26:47 -0400
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children 1c6c961851de
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-1:000000000000 0:190175f4e143
1 <tool id="graphmap_align" name="Mapper" version="@VERSION@">
2 <description>for long, error-prone reads, like Nanopore ONT and PacBio</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 align
13 -r ref.${r.ext}
14 -d reads.${d.ext}
15 #if $preset:
16 -x $preset
17 #end if
18 -t \${GALAXY_SLOTS:-4} |
19 samtools view -b -u | samtools sort -@ "\${GALAXY_SLOTS:-4}" -T tmp -O bam -o output.bam -
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 to increase sensitivity for different sequencing technologies. (-x)">
25 <option value="illumina">illumina preset</option>
26 <option value="overlap">overlap preset</option>
27 <option value="sensitive">sensitive preset</option>
28 </param>
29 <!--
30 <param type="data" name="reference" format="fasta,fastq" label="Sequences"/>
31 <param type="data" name="reads" format="fasta,fastq" label="Sequences"/>
32 <param type="data" name="overlaps" format="sam,tabular" label="Overlaps"/>
33 <param type="data" name="corrected_reads" format="fasta,fasta.gz,fastq,fastq.gz" label="Target sequences"/> -->
34
35 </inputs>
36 <outputs>
37 <data name="output" format="bam" from_work_dir="output.bam" />
38 </outputs>
39 <tests>
40 <test>
41 <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 <output name="output" ftype="bam" file="result1_map.bam"/>
44 </test>
45 <test>
46 <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="preset" value="illumina"/>
49 <output name="output" ftype="bam" file="result2_map.bam"/>
50 </test>
51 <test>
52 <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="preset" value="sensitive"/>
55 <output name="output" ftype="bam" file="result3_map.bam"/>
56 </test></tests>
57 <help><![CDATA[
58 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 is licensed under The MIT License.
61 ]]></help>
62 <expand macro="citations" />
63 </tool>