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annotate 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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d0a712cf0518 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/graphmap commit a1461f1e83079de821b269125c49eca2460e7693
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1 <tool id="graphmap_overlap" name="Owler" version="@VERSION@">
d0a712cf0518 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/graphmap commit a1461f1e83079de821b269125c49eca2460e7693
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2 <description>fast, trimmed overlap pipeline without aligning</description>
d0a712cf0518 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/graphmap commit a1461f1e83079de821b269125c49eca2460e7693
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3 <macros>
d0a712cf0518 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/graphmap commit a1461f1e83079de821b269125c49eca2460e7693
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4 <import>macros.xml</import>
d0a712cf0518 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/graphmap commit a1461f1e83079de821b269125c49eca2460e7693
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5 </macros>
d0a712cf0518 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/graphmap commit a1461f1e83079de821b269125c49eca2460e7693
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6 <expand macro="requirements" />
d0a712cf0518 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">
d0a712cf0518 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/graphmap commit a1461f1e83079de821b269125c49eca2460e7693
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8 <![CDATA[
d0a712cf0518 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} &&
d0a712cf0518 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} &&
d0a712cf0518 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/graphmap commit a1461f1e83079de821b269125c49eca2460e7693
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11
d0a712cf0518 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/graphmap commit a1461f1e83079de821b269125c49eca2460e7693
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12 graphmap owler
d0a712cf0518 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/graphmap commit a1461f1e83079de821b269125c49eca2460e7693
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13 -r ref.${r.ext}
d0a712cf0518 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/graphmap commit a1461f1e83079de821b269125c49eca2460e7693
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14 -d reads.${d.ext}
d0a712cf0518 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/graphmap commit a1461f1e83079de821b269125c49eca2460e7693
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15 -o output.mhap
d0a712cf0518 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/graphmap commit a1461f1e83079de821b269125c49eca2460e7693
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16 #if $preset:
d0a712cf0518 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/graphmap commit a1461f1e83079de821b269125c49eca2460e7693
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17 -x $preset
d0a712cf0518 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/graphmap commit a1461f1e83079de821b269125c49eca2460e7693
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18 #end if
d0a712cf0518 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/graphmap commit a1461f1e83079de821b269125c49eca2460e7693
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19 -t \${GALAXY_SLOTS:-4}
d0a712cf0518 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/graphmap commit a1461f1e83079de821b269125c49eca2460e7693
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20 ]]></command>
d0a712cf0518 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/graphmap commit a1461f1e83079de821b269125c49eca2460e7693
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21 <inputs>
d0a712cf0518 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" />
d0a712cf0518 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" />
d0a712cf0518 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 (-x)">
d0a712cf0518 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/graphmap commit a1461f1e83079de821b269125c49eca2460e7693
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25 <option value="no-filters">Disable filters</option>
d0a712cf0518 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/graphmap commit a1461f1e83079de821b269125c49eca2460e7693
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26 </param>
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27 <!--
d0a712cf0518 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/graphmap commit a1461f1e83079de821b269125c49eca2460e7693
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28 <param type="data" name="reference" format="fasta,fastq" label="Sequences"/>
d0a712cf0518 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/graphmap commit a1461f1e83079de821b269125c49eca2460e7693
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29 <param type="data" name="reads" format="fasta,fastq" label="Sequences"/>
d0a712cf0518 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/graphmap commit a1461f1e83079de821b269125c49eca2460e7693
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30 <param type="data" name="overlaps" format="sam,tabular" label="Overlaps"/>
d0a712cf0518 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/graphmap commit a1461f1e83079de821b269125c49eca2460e7693
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31 <param type="data" name="corrected_reads" format="fasta,fasta.gz,fastq,fastq.gz" label="Target sequences"/> -->
d0a712cf0518 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/graphmap commit a1461f1e83079de821b269125c49eca2460e7693
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32
d0a712cf0518 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/graphmap commit a1461f1e83079de821b269125c49eca2460e7693
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33 </inputs>
d0a712cf0518 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/graphmap commit a1461f1e83079de821b269125c49eca2460e7693
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34 <outputs>
d0a712cf0518 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/graphmap commit a1461f1e83079de821b269125c49eca2460e7693
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35 <data name="output" format="txt" from_work_dir="output.mhap" />
d0a712cf0518 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/graphmap commit a1461f1e83079de821b269125c49eca2460e7693
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36 </outputs>
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37 <tests>
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38 <test>
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39 <param name="r" value="Loman_E.coli_MAP006-1_2D_50x_first_500_reads.fasta"/>
d0a712cf0518 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/graphmap commit a1461f1e83079de821b269125c49eca2460e7693
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40 <param name="d" value="E.coli_contigs.fasta"/>
d0a712cf0518 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/graphmap commit a1461f1e83079de821b269125c49eca2460e7693
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41 <output name="output" ftype="txt" file="result1_owler.mhap"/>
d0a712cf0518 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/graphmap commit a1461f1e83079de821b269125c49eca2460e7693
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42 </test>
d0a712cf0518 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/graphmap commit a1461f1e83079de821b269125c49eca2460e7693
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43 <test>
d0a712cf0518 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/graphmap commit a1461f1e83079de821b269125c49eca2460e7693
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44 <param name="r" value="Loman_E.coli_MAP006-1_2D_50x_first_500_reads.fasta"/>
d0a712cf0518 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/graphmap commit a1461f1e83079de821b269125c49eca2460e7693
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45 <param name="d" value="E.coli_contigs.fasta"/>
d0a712cf0518 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/graphmap commit a1461f1e83079de821b269125c49eca2460e7693
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46 <param name="preset" value="no-filters"/>
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47 <output name="output" ftype="txt" file="result2_owler.mhap"/>
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48 </test></tests>
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49 <help><![CDATA[
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50 GraphMap - A very accurate and sensitive long-read, high error-rate sequence mapper
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51 GraphMap (c) by Ivan Sovic, Mile Sikic and Niranjan Nagarajan
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52 GraphMap is licensed under The MIT License.
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53 ]]></help>
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54 <expand macro="citations" />
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55 </tool>