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annotate fermi2.xml @ 0:b808c0bc19a9 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fermikit commit 47795b03c956d0f239aede8e27d2aa4e3c4c1d27
author mvdbeek
date Fri, 30 Dec 2016 10:25:59 -0500
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b808c0bc19a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fermikit commit 47795b03c956d0f239aede8e27d2aa4e3c4c1d27
mvdbeek
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1 <tool id="fermi2" name="fermi2" version="0.14.dev1">
b808c0bc19a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fermikit commit 47795b03c956d0f239aede8e27d2aa4e3c4c1d27
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2 <description>assembles Illumina reads into unitigs</description>
b808c0bc19a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fermikit commit 47795b03c956d0f239aede8e27d2aa4e3c4c1d27
mvdbeek
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3 <requirements>
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mvdbeek
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4 <requirement type="package" version="r188">fermi2</requirement>
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mvdbeek
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5 <requirement type="package" version="r181">bfc</requirement>
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6 </requirements>
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mvdbeek
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7 <command detect_errors="aggressive"><![CDATA[
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mvdbeek
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8 fermi2.pl unitig
b808c0bc19a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fermikit commit 47795b03c956d0f239aede8e27d2aa4e3c4c1d27
mvdbeek
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9 -s$genome_size
b808c0bc19a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fermikit commit 47795b03c956d0f239aede8e27d2aa4e3c4c1d27
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10 -t\${GALAXY_SLOTS:-4}
b808c0bc19a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fermikit commit 47795b03c956d0f239aede8e27d2aa4e3c4c1d27
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11 -l$readlength
b808c0bc19a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fermikit commit 47795b03c956d0f239aede8e27d2aa4e3c4c1d27
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12 -p prefix '$input1'
b808c0bc19a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fermikit commit 47795b03c956d0f239aede8e27d2aa4e3c4c1d27
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13 $T
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14 $2
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15 $E
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16 > prefix.mak &&
b808c0bc19a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fermikit commit 47795b03c956d0f239aede8e27d2aa4e3c4c1d27
mvdbeek
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17 make -f prefix.mak
b808c0bc19a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fermikit commit 47795b03c956d0f239aede8e27d2aa4e3c4c1d27
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18 ]]></command>
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mvdbeek
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19 <inputs>
b808c0bc19a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fermikit commit 47795b03c956d0f239aede8e27d2aa4e3c4c1d27
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20 <param type="data" name="input1" format="fastqsanger,fastqsanger.gz"/>
b808c0bc19a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fermikit commit 47795b03c956d0f239aede8e27d2aa4e3c4c1d27
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21 <param argument="-l" name="readlength" type="integer" label="primary read length" value="101" min="70"/>
b808c0bc19a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fermikit commit 47795b03c956d0f239aede8e27d2aa4e3c4c1d27
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22 <param argument="-s" name="genome_size" type="integer" value="180000" min="1" label="approximate genome size in kilobases" help="Enter approximate genome size in kilobases. For a human genome of 3.2 gigabases enter 3200000"/>
b808c0bc19a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fermikit commit 47795b03c956d0f239aede8e27d2aa4e3c4c1d27
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23 <param argument="-T" type="integer" value="61" label="use INT-mer for post-trimming/filtering" min="10"/>
b808c0bc19a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fermikit commit 47795b03c956d0f239aede8e27d2aa4e3c4c1d27
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24 <param argument="-2" type="boolean" checked="false" truevalue="-2" falsevalue="" label="Use 2-pass error correction"/>
b808c0bc19a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fermikit commit 47795b03c956d0f239aede8e27d2aa4e3c4c1d27
mvdbeek
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25 <param argument="-E" type="boolean" checked="false" truevalue="-E" falsevalue="" label="Do not apply error correction"/>
b808c0bc19a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fermikit commit 47795b03c956d0f239aede8e27d2aa4e3c4c1d27
mvdbeek
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26 </inputs>
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mvdbeek
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27 <outputs>
b808c0bc19a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fermikit commit 47795b03c956d0f239aede8e27d2aa4e3c4c1d27
mvdbeek
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28 <data name="unitigs" format="fastqsanger.gz" from_work_dir="prefix.mag.gz"/>
b808c0bc19a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fermikit commit 47795b03c956d0f239aede8e27d2aa4e3c4c1d27
mvdbeek
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29 </outputs>
b808c0bc19a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fermikit commit 47795b03c956d0f239aede8e27d2aa4e3c4c1d27
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30 <tests>
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31 <test>
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32 <param name="input1" value="test.fastq.gz"/>
b808c0bc19a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fermikit commit 47795b03c956d0f239aede8e27d2aa4e3c4c1d27
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33 <param name="readlength" value="150"/>
b808c0bc19a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fermikit commit 47795b03c956d0f239aede8e27d2aa4e3c4c1d27
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34 <param name="genome_size" value="1"/>
b808c0bc19a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fermikit commit 47795b03c956d0f239aede8e27d2aa4e3c4c1d27
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35 <output name="unitigs" file="unitigs.gz" compare="sim_size"/>
b808c0bc19a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fermikit commit 47795b03c956d0f239aede8e27d2aa4e3c4c1d27
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36 </test>
b808c0bc19a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fermikit commit 47795b03c956d0f239aede8e27d2aa4e3c4c1d27
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37 </tests>
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38 <help><![CDATA[
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39 fermi2 can assemble reads into unitigs.
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40 Unitig output can be further analysed by alignment to a reference genome using bwa-mem,
b808c0bc19a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fermikit commit 47795b03c956d0f239aede8e27d2aa4e3c4c1d27
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41 and based on the alignment variants can be called using the fermi-variants tool.
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42
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43 ::
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44
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45 Usage: fermi2.pl unitig [options] <in.fq>
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46
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47 Options: -p STR output prefix [fmdef]
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48 -s STR approximate genome size [100m]
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49 -2 2-pass error correction
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50 -l INT primary read length [101]
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51 -T INT use INT-mer for post-trimming/filtering [61]
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52 -k INT min overlap length during unitig construction [based on -l]
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53 -o INT min overlap length during graph cleaning [based on -l]
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54 -m INT min overlap length for unambiguous merging [based on -l]
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55 -t INT number of threads [4]
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56 -E don't apply error correction
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57
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58 ]]></help>
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59 <citations>
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60 <citation type="doi">10.1093/bioinformatics/btv440</citation>
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61 </citations>
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62 </tool>