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annotate fermi2.xml @ 1:06d22a2d3c64 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fermikit commit ab4afb50e6c991cc2e784a93a0c7a75329eac88c
author iuc
date Mon, 27 Jun 2022 11:22:11 +0000
parents b59546214e63
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06d22a2d3c64 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fermikit commit ab4afb50e6c991cc2e784a93a0c7a75329eac88c
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1 <tool id="fermi2" name="fermi2" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
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2 <description>assembles Illumina reads into unitigs</description>
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3 <macros>
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4 <token name="@TOOL_VERSION@">r193</token>
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5 <token name="@VERSION_SUFFIX@">0</token>
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6 </macros>
0
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7 <requirements>
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8 <requirement type="package" version="@TOOL_VERSION@">fermi2</requirement>
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9 </requirements>
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10 <command detect_errors="aggressive"><![CDATA[
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11 fermi2.pl unitig
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12 -s$genome_size
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13 -t\${GALAXY_SLOTS:-4}
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14 -l$readlength
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15 -p prefix "cat
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16 #for fastq in $input1:
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17 '$fastq'
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18 #end for
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19 "
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20 -T $T
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21 $two_pass_error
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22 $E
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23 > prefix.mak &&
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24 make -f prefix.mak
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25 ]]></command>
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26 <inputs>
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27 <param type="data" multiple="true" name="input1" format="fastqsanger,fastqsanger.gz"/>
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28 <param argument="-l" name="readlength" type="integer" label="primary read length" value="101" min="70"/>
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29 <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"/>
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30 <param argument="-T" type="integer" value="61" label="use INT-mer for post-trimming/filtering" min="10"/>
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31 <param argument="-2" name="two_pass_error" type="boolean" checked="false" truevalue="-2" falsevalue="" label="Use 2-pass error correction"/>
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32 <param argument="-E" type="boolean" checked="false" truevalue="-E" falsevalue="" label="Do not apply error correction"/>
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33 </inputs>
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34 <outputs>
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35 <data name="unitigs" format="fastqsanger.gz" from_work_dir="prefix.mag.gz"/>
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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="input1" value="test.fastq.gz,test.fastq.gz"/>
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40 <param name="readlength" value="150"/>
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41 <param name="genome_size" value="1"/>
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42 <output name="unitigs" file="unitigs.gz" compare="sim_size"/>
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43 </test>
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44 </tests>
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45 <help><![CDATA[
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46 fermi2 can assemble reads into unitigs.
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47 Unitig output can be further analysed by alignment to a reference genome using bwa-mem,
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48 and based on the alignment variants can be called using the fermi-variants tool.
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49
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50 ::
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51
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52 Usage: fermi2.pl unitig [options] <in.fq>
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53
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54 Options: -p STR output prefix [fmdef]
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55 -s STR approximate genome size [100m]
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56 -2 2-pass error correction
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57 -l INT primary read length [101]
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58 -T INT use INT-mer for post-trimming/filtering [61]
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59 -k INT min overlap length during unitig construction [based on -l]
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60 -o INT min overlap length during graph cleaning [based on -l]
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61 -m INT min overlap length for unambiguous merging [based on -l]
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62 -t INT number of threads [4]
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63 -E don't apply error correction
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64
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65 ]]></help>
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66 <citations>
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67 <citation type="doi">10.1093/bioinformatics/btv440</citation>
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68 </citations>
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69 </tool>