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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/megahit_contig2fastg commit 55d148dd4fae2d0156cc0ab680fd4f00efc6f242
author galaxyp
date Thu, 08 Nov 2018 16:06:30 -0500
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f7b0d03c7862 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/megahit_contig2fastg commit 55d148dd4fae2d0156cc0ab680fd4f00efc6f242
galaxyp
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1 <?xml version='1.0' encoding='utf-8'?>
f7b0d03c7862 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/megahit_contig2fastg commit 55d148dd4fae2d0156cc0ab680fd4f00efc6f242
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2 <tool id="megahit_contig2fastg" name="MEGAHIT Contig2fastg" version="@VERSION@">
f7b0d03c7862 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/megahit_contig2fastg commit 55d148dd4fae2d0156cc0ab680fd4f00efc6f242
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3 <description>for converting MEGAHIT's contigs to fastg</description>
f7b0d03c7862 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/megahit_contig2fastg commit 55d148dd4fae2d0156cc0ab680fd4f00efc6f242
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4 <macros>
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5 <token name="@VERSION@">1.1.2</token>
f7b0d03c7862 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/megahit_contig2fastg commit 55d148dd4fae2d0156cc0ab680fd4f00efc6f242
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6 </macros>
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7 <requirements>
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8 <requirement type="package" version="@VERSION@">megahit</requirement>
f7b0d03c7862 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/megahit_contig2fastg commit 55d148dd4fae2d0156cc0ab680fd4f00efc6f242
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9 </requirements>
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10 <version_command>megahit --version</version_command>
f7b0d03c7862 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/megahit_contig2fastg commit 55d148dd4fae2d0156cc0ab680fd4f00efc6f242
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11 <command detect_errors="exit_code"><![CDATA[
f7b0d03c7862 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/megahit_contig2fastg commit 55d148dd4fae2d0156cc0ab680fd4f00efc6f242
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12 megahit_toolkit contig2fastg
f7b0d03c7862 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/megahit_contig2fastg commit 55d148dd4fae2d0156cc0ab680fd4f00efc6f242
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13 '${kmer}'
f7b0d03c7862 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/megahit_contig2fastg commit 55d148dd4fae2d0156cc0ab680fd4f00efc6f242
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14 '${contigs}' > '${fastg}'
f7b0d03c7862 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/megahit_contig2fastg commit 55d148dd4fae2d0156cc0ab680fd4f00efc6f242
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15 ]]></command>
f7b0d03c7862 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/megahit_contig2fastg commit 55d148dd4fae2d0156cc0ab680fd4f00efc6f242
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16 <inputs>
f7b0d03c7862 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/megahit_contig2fastg commit 55d148dd4fae2d0156cc0ab680fd4f00efc6f242
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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" />
f7b0d03c7862 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/megahit_contig2fastg commit 55d148dd4fae2d0156cc0ab680fd4f00efc6f242
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18 <param name="kmer" type="integer" value="99" label="K-mer length" />
f7b0d03c7862 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/megahit_contig2fastg commit 55d148dd4fae2d0156cc0ab680fd4f00efc6f242
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19 </inputs>
f7b0d03c7862 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/megahit_contig2fastg commit 55d148dd4fae2d0156cc0ab680fd4f00efc6f242
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20 <outputs>
f7b0d03c7862 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/megahit_contig2fastg commit 55d148dd4fae2d0156cc0ab680fd4f00efc6f242
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21 <data format="txt" name="fastg" label="Conversion to FASTG with ${tool.name} on ${on_string}" />
f7b0d03c7862 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/megahit_contig2fastg commit 55d148dd4fae2d0156cc0ab680fd4f00efc6f242
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22 </outputs>
f7b0d03c7862 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/megahit_contig2fastg commit 55d148dd4fae2d0156cc0ab680fd4f00efc6f242
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23 <tests>
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24 <test>
f7b0d03c7862 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/megahit_contig2fastg commit 55d148dd4fae2d0156cc0ab680fd4f00efc6f242
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25 <param name="contigs" value="k21.contigs.fa" ftype="fasta" />
f7b0d03c7862 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/megahit_contig2fastg commit 55d148dd4fae2d0156cc0ab680fd4f00efc6f242
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26 <param name="kmer" value="21"/>
f7b0d03c7862 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/megahit_contig2fastg commit 55d148dd4fae2d0156cc0ab680fd4f00efc6f242
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27 <output name="fastg">
f7b0d03c7862 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/megahit_contig2fastg commit 55d148dd4fae2d0156cc0ab680fd4f00efc6f242
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28 <assert_contents>
f7b0d03c7862 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/megahit_contig2fastg commit 55d148dd4fae2d0156cc0ab680fd4f00efc6f242
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29 <has_text text=">NODE_1_length_576" />
f7b0d03c7862 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/megahit_contig2fastg commit 55d148dd4fae2d0156cc0ab680fd4f00efc6f242
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30 </assert_contents>
f7b0d03c7862 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/megahit_contig2fastg commit 55d148dd4fae2d0156cc0ab680fd4f00efc6f242
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31 </output>
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32 </test>
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33 </tests>
f7b0d03c7862 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/megahit_contig2fastg commit 55d148dd4fae2d0156cc0ab680fd4f00efc6f242
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34 <help><![CDATA[
f7b0d03c7862 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/megahit_contig2fastg commit 55d148dd4fae2d0156cc0ab680fd4f00efc6f242
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35
f7b0d03c7862 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/megahit_contig2fastg commit 55d148dd4fae2d0156cc0ab680fd4f00efc6f242
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36 **MEGAHIT_toolkit contig2fastg**
f7b0d03c7862 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/megahit_contig2fastg commit 55d148dd4fae2d0156cc0ab680fd4f00efc6f242
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37
f7b0d03c7862 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/megahit_contig2fastg commit 55d148dd4fae2d0156cc0ab680fd4f00efc6f242
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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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f7b0d03c7862 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/megahit_contig2fastg commit 55d148dd4fae2d0156cc0ab680fd4f00efc6f242
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40 **MEGAHIT**
f7b0d03c7862 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/megahit_contig2fastg commit 55d148dd4fae2d0156cc0ab680fd4f00efc6f242
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f7b0d03c7862 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/megahit_contig2fastg commit 55d148dd4fae2d0156cc0ab680fd4f00efc6f242
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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.
f7b0d03c7862 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/megahit_contig2fastg commit 55d148dd4fae2d0156cc0ab680fd4f00efc6f242
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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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f7b0d03c7862 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/megahit_contig2fastg commit 55d148dd4fae2d0156cc0ab680fd4f00efc6f242
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f7b0d03c7862 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/megahit_contig2fastg commit 55d148dd4fae2d0156cc0ab680fd4f00efc6f242
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52 ]]></help>
f7b0d03c7862 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/megahit_contig2fastg commit 55d148dd4fae2d0156cc0ab680fd4f00efc6f242
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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>