Mercurial > repos > matthias > dada2_filterandtrim

annotate macros.xml @ 0:1d6e206b8291 draft

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planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty
author matthias
date Fri, 08 Mar 2019 06:36:53 -0500
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children ea3c356bff55
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1 <?xml version="1.0"?>
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2 <macros>
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3 <xml name="requirements">
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4 <requirements>
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5 <requirement type="package" version="@DADA2_VERSION@">bioconductor-dada2</requirement>
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6 <yield/>
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7 </requirements>
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8 </xml>
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9
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10 <token name="@DADA2_VERSION@">1.10.0</token>
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11 <token name="@WRAPPER_VERSION@">0</token>
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13 <xml name="version_command">
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14 <version_command><![CDATA[
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15 echo $(R --version | grep version | grep -v GNU)", dada2 version" $(R --vanilla --slave -e "library(dada2); cat(sessionInfo()\$otherPkgs\$dada2\$Version)" 2> /dev/null | grep -v -i "WARNING: ")
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16 ]]></version_command>
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17 </xml>
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19 echo $(R --version | grep version | grep -v GNU)", DESeq2 version" $(R --vanilla --slave -e "library(dada2); cat(sessionInfo()\$otherPkgs\$dada2\$Version)" 2> /dev/null | grep -v -i "WARNING: ")
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20
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21 <xml name="citations">
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22 <citations>
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23 <citation type="doi">10.1038/nmeth.3869</citation>
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24 </citations>
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25 </xml>
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26
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27 <token name="@DADA_UNIQUES@">dada2_derep,dada2_dada,dada2_mergepairs</token>
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28
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29 <token name="@READ_FOO@"><![CDATA[
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30 #def read_data($dataset)
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31 #if $dataset.is_of_type('dada2_derep')
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32 readRDS(file.path('$dataset.extra_files_path', 'Rdata'))
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33 #else if $dataset.is_of_type('dada2_dada')
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34 readRDS('$dataset')
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35 #else if $dataset.is_of_type('dada2_sequencetable')
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36 as.matrix( read.table('$dataset', header=T, sep="\t", row.names=1) )
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37 #else if $dataset.is_of_type('dada2_mergepairs')
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38 read.table('$dataset', header=T, sep="\t" )
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39 #else if $dataset.is_of_type('tabular')
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40 read.table('$dataset', header=T, sep="\t", row.names=1 )
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41 #else
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42 #raise Exception("error: unknown input type")
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43 #end if
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44 #end def
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45 ]]></token>
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46 <!-- for filterAndTrim -->
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47 <xml name="trimmers">
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48 <section name="trim" title="trimming parameters">
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49 <param name="truncQ" type="integer" value="2" min="0" label="Truncate reads at quality threshold" help="Truncate reads at the first instance of a quality score less than or equal to this threshold"/>
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50 <param name="truncLen" type="integer" value="0" min="0" label="Truncate read length" help=""/>
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51 <param name="trimLeft" type="integer" value="0" min="0" label="Remove nucleotides from start" help=""/>
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52 <param name="trimRight" type="integer" value="0" min="0" label="Remove nucleotides from end" help=""/>
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53 </section>
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54 </xml>
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55 <xml name="filters">
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56 <section name="filter" title="filtering parameters">
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57 <param name="maxLen" type="integer" value="" optional="true" min="0" label="Remove reads longer than" help=""/>
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58 <param name="minLen" type="integer" value="20" min="0" label="Remove reads shorter than" help=""/>
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59 <param name="maxN" type="integer" value="0" min="0" label="Remove reads with more Ns" help=""/>
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60 <param name="minQ" type="integer" value="0" min="0" label="Remove reads containing quality" help=""/>
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61 <param name="maxEE" type="integer" value="" optional="true" min="0" label="Remove reads by expected errors" help=""/>
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62 </section>
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63 </xml>
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64
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65
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66 <xml name="errorEstimationFunction">
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67 <param name="errfoo" type="select" label="Error function">
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68 <option value="loessErrfun">loess</option>
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69 <option value="noqualErrfun">noqual</option>
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70 <option value="PacBioErrfun">PacBio</option>
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71 </param>
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72 </xml>
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73
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74
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75 </macros>