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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 15:25:00 -0400
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808422916b78 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/graphmap commit a1461f1e83079de821b269125c49eca2460e7693
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1 <tool id="graphmap_align" name="Mapper" version="@VERSION@">
808422916b78 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/graphmap commit a1461f1e83079de821b269125c49eca2460e7693
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2 <description>for long, error-prone reads, like Nanopore ONT and PacBio</description>
808422916b78 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/graphmap commit a1461f1e83079de821b269125c49eca2460e7693
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3 <macros>
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4 <import>macros.xml</import>
808422916b78 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/graphmap commit a1461f1e83079de821b269125c49eca2460e7693
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5 </macros>
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6 <expand macro="requirements" />
808422916b78 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/graphmap commit a1461f1e83079de821b269125c49eca2460e7693
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7 <command detect_errors="exit_code">
808422916b78 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/graphmap commit a1461f1e83079de821b269125c49eca2460e7693
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8 <![CDATA[
808422916b78 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/graphmap commit a1461f1e83079de821b269125c49eca2460e7693
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9 ln -s '$r' ref.${r.ext} &&
808422916b78 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/graphmap commit a1461f1e83079de821b269125c49eca2460e7693
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10 ln -s '$d' reads.${d.ext} &&
808422916b78 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/graphmap commit a1461f1e83079de821b269125c49eca2460e7693
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11
808422916b78 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/graphmap commit a1461f1e83079de821b269125c49eca2460e7693
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12 graphmap align
808422916b78 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/graphmap commit a1461f1e83079de821b269125c49eca2460e7693
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13 -r ref.${r.ext}
808422916b78 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/graphmap commit a1461f1e83079de821b269125c49eca2460e7693
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14 -d reads.${d.ext}
808422916b78 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/graphmap commit a1461f1e83079de821b269125c49eca2460e7693
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15 #if $preset:
808422916b78 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/graphmap commit a1461f1e83079de821b269125c49eca2460e7693
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16 -x $preset
808422916b78 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/graphmap commit a1461f1e83079de821b269125c49eca2460e7693
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17 #end if
808422916b78 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/graphmap commit a1461f1e83079de821b269125c49eca2460e7693
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18 -t \${GALAXY_SLOTS:-4} |
808422916b78 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/graphmap commit a1461f1e83079de821b269125c49eca2460e7693
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19 samtools view -b -u | samtools sort -@ "\${GALAXY_SLOTS:-4}" -T tmp -O bam -o output.bam -
808422916b78 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/graphmap commit a1461f1e83079de821b269125c49eca2460e7693
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20 ]]></command>
808422916b78 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/graphmap commit a1461f1e83079de821b269125c49eca2460e7693
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21 <inputs>
808422916b78 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/graphmap commit a1461f1e83079de821b269125c49eca2460e7693
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22 <param argument="-r" type="data" format="fasta,fastq" label="reference sequence" />
808422916b78 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/graphmap commit a1461f1e83079de821b269125c49eca2460e7693
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23 <param argument="-d" type="data" format="fasta,fastq" label="reads" />
808422916b78 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/graphmap commit a1461f1e83079de821b269125c49eca2460e7693
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24 <param name="preset" type="select" optional="True" label="Pre-set parameters to increase sensitivity for different sequencing technologies. (-x)">
808422916b78 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/graphmap commit a1461f1e83079de821b269125c49eca2460e7693
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25 <option value="illumina">illumina preset</option>
808422916b78 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/graphmap commit a1461f1e83079de821b269125c49eca2460e7693
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26 <option value="overlap">overlap preset</option>
808422916b78 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/graphmap commit a1461f1e83079de821b269125c49eca2460e7693
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27 <option value="sensitive">sensitive preset</option>
808422916b78 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/graphmap commit a1461f1e83079de821b269125c49eca2460e7693
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28 </param>
808422916b78 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/graphmap commit a1461f1e83079de821b269125c49eca2460e7693
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29 <!--
808422916b78 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/graphmap commit a1461f1e83079de821b269125c49eca2460e7693
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30 <param type="data" name="reference" format="fasta,fastq" label="Sequences"/>
808422916b78 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/graphmap commit a1461f1e83079de821b269125c49eca2460e7693
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31 <param type="data" name="reads" format="fasta,fastq" label="Sequences"/>
808422916b78 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/graphmap commit a1461f1e83079de821b269125c49eca2460e7693
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32 <param type="data" name="overlaps" format="sam,tabular" label="Overlaps"/>
808422916b78 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/graphmap commit a1461f1e83079de821b269125c49eca2460e7693
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33 <param type="data" name="corrected_reads" format="fasta,fasta.gz,fastq,fastq.gz" label="Target sequences"/> -->
808422916b78 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/graphmap commit a1461f1e83079de821b269125c49eca2460e7693
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34
808422916b78 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/graphmap commit a1461f1e83079de821b269125c49eca2460e7693
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35 </inputs>
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36 <outputs>
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37 <data name="output" format="bam" from_work_dir="output.bam" />
808422916b78 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/graphmap commit a1461f1e83079de821b269125c49eca2460e7693
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38 </outputs>
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39 <tests>
808422916b78 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/graphmap commit a1461f1e83079de821b269125c49eca2460e7693
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40 <test>
808422916b78 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/graphmap commit a1461f1e83079de821b269125c49eca2460e7693
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41 <param name="r" value="Loman_E.coli_MAP006-1_2D_50x_first_500_reads.fasta"/>
808422916b78 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/graphmap commit a1461f1e83079de821b269125c49eca2460e7693
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42 <param name="d" value="E.coli_contigs.fasta"/>
808422916b78 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/graphmap commit a1461f1e83079de821b269125c49eca2460e7693
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43 <output name="output" ftype="bam" file="result1_map.bam"/>
808422916b78 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/graphmap commit a1461f1e83079de821b269125c49eca2460e7693
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44 </test>
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45 <test>
808422916b78 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/graphmap commit a1461f1e83079de821b269125c49eca2460e7693
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46 <param name="r" value="Loman_E.coli_MAP006-1_2D_50x_first_500_reads.fasta"/>
808422916b78 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/graphmap commit a1461f1e83079de821b269125c49eca2460e7693
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47 <param name="d" value="E.coli_contigs.fasta"/>
808422916b78 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/graphmap commit a1461f1e83079de821b269125c49eca2460e7693
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48 <param name="preset" value="illumina"/>
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49 <output name="output" ftype="bam" file="result2_map.bam"/>
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50 </test>
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51 <test>
808422916b78 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/graphmap commit a1461f1e83079de821b269125c49eca2460e7693
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52 <param name="r" value="Loman_E.coli_MAP006-1_2D_50x_first_500_reads.fasta"/>
808422916b78 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/graphmap commit a1461f1e83079de821b269125c49eca2460e7693
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53 <param name="d" value="E.coli_contigs.fasta"/>
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54 <param name="preset" value="sensitive"/>
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55 <output name="output" ftype="bam" file="result3_map.bam"/>
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56 </test></tests>
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57 <help><![CDATA[
808422916b78 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/graphmap commit a1461f1e83079de821b269125c49eca2460e7693
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58 GraphMap - A very accurate and sensitive long-read, high error-rate sequence mapper
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59 GraphMap (c) by Ivan Sovic, Mile Sikic and Niranjan Nagarajan
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60 GraphMap is licensed under The MIT License.
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61 ]]></help>
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62 <expand macro="citations" />
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63 </tool>