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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/megahit_contig2fastg commit 2614718d10b8e8b4bb7722d310c845e30fb267ac
author galaxyp
date Fri, 09 Nov 2018 12:49:48 -0500
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a4739171f886 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/megahit_contig2fastg commit 2614718d10b8e8b4bb7722d310c845e30fb267ac
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1 <?xml version='1.0' encoding='utf-8'?>
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2 <tool id="megahit_contig2fastg" name="MEGAHIT Contig2fastg" version="@VERSION@">
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3 <description>for converting MEGAHIT's contigs to fastg</description>
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4 <macros>
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5 <token name="@VERSION@">1.1.2</token>
a4739171f886 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/megahit_contig2fastg commit 2614718d10b8e8b4bb7722d310c845e30fb267ac
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6 </macros>
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7 <requirements>
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8 <requirement type="package" version="@VERSION@">megahit</requirement>
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9 </requirements>
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10 <version_command>megahit --version</version_command>
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11 <command detect_errors="exit_code"><![CDATA[
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12 megahit_toolkit contig2fastg
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13 '${kmer}'
a4739171f886 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/megahit_contig2fastg commit 2614718d10b8e8b4bb7722d310c845e30fb267ac
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14 '${contigs}' > '${fastg}'
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15 ]]></command>
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16 <inputs>
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17 <param name="contigs" type="data" format="fastq,fastqsanger,fasta,fastq.gz,fastqsanger.gz" multiple="true" label="Single-end file(s)" help="FASTQ/FASTA/FASTQ.GZ files accepted" />
a4739171f886 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/megahit_contig2fastg commit 2614718d10b8e8b4bb7722d310c845e30fb267ac
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18 <param name="kmer" type="integer" value="99" label="K-mer length" />
a4739171f886 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/megahit_contig2fastg commit 2614718d10b8e8b4bb7722d310c845e30fb267ac
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19 </inputs>
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20 <outputs>
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21 <data format="txt" name="fastg" label="Conversion to FASTG with ${tool.name} on ${on_string}" />
a4739171f886 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/megahit_contig2fastg commit 2614718d10b8e8b4bb7722d310c845e30fb267ac
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22 </outputs>
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23 <tests>
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24 <test>
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25 <param name="contigs" value="k21.contigs.fa" ftype="fasta" />
a4739171f886 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/megahit_contig2fastg commit 2614718d10b8e8b4bb7722d310c845e30fb267ac
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26 <param name="kmer" value="21"/>
a4739171f886 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/megahit_contig2fastg commit 2614718d10b8e8b4bb7722d310c845e30fb267ac
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27 <output name="fastg">
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28 <assert_contents>
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29 <has_text text=">NODE_1_length_576" />
a4739171f886 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/megahit_contig2fastg commit 2614718d10b8e8b4bb7722d310c845e30fb267ac
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30 </assert_contents>
a4739171f886 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/megahit_contig2fastg commit 2614718d10b8e8b4bb7722d310c845e30fb267ac
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31 </output>
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32 </test>
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33 </tests>
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34 <help><![CDATA[
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35
a4739171f886 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/megahit_contig2fastg commit 2614718d10b8e8b4bb7722d310c845e30fb267ac
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36 **MEGAHIT_toolkit contig2fastg**
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a4739171f886 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/megahit_contig2fastg commit 2614718d10b8e8b4bb7722d310c845e30fb267ac
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38 Contig2fastg is a subprogram within the MEGAHIT toolkit. It converts MEGAHIT's k*.contigs.fa to fastg format that can be viewed by Bandage.
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40 **MEGAHIT**
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42 MEGAHIT is a single node assembler for large and complex metagenomics NGS reads, such as soil. It makes use of succinct de Bruijn graph (SdBG) to achieve low memory assembly. MEGAHIT can optionally utilize a CUDA-enabled GPU to accelerate its SdBG contstruction. The GPU-accelerated version of MEGAHIT has been tested on NVIDIA GTX680 (4G memory) and Tesla K40c (12G memory) with CUDA 5.5, 6.0 and 6.5.
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44 --------
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46 **Project links:**
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48 https://github.com/voutcn/megahit
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49 https://github.com/voutcn/megahit/blob/master/tools/toolkit.cpp
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52 ]]></help>
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53 <citations>
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54 <citation type="doi">10.1093/bioinformatics/btv033</citation>
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55 </citations>
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56 </tool>