Mercurial > repos > matthias > dada2_learnerrors
diff macros.xml @ 3:10141f4eaae9 draft
planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit 5b1603bbcd3f139cad5c876be83fcb39697b5613-dirty
| author | matthias |
|---|---|
| date | Mon, 29 Apr 2019 08:56:03 -0400 |
| parents | 57eb7437f646 |
| children | 9aeea74a1fc9 |
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--- a/macros.xml Tue Apr 09 07:00:24 2019 -0400 +++ b/macros.xml Mon Apr 29 08:56:03 2019 -0400 @@ -8,8 +8,8 @@ </xml> <token name="@DADA2_VERSION@">1.10.0</token> - <token name="@WRAPPER_VERSION@">0</token> - + <token name="@WRAPPER_VERSION@">1</token> + <xml name="version_command"> <version_command><![CDATA[ echo $(R --version | grep version | grep -v GNU)", dada2 version" $(R --vanilla --slave -e "library(dada2); cat(sessionInfo()\$otherPkgs\$dada2\$Version)" 2> /dev/null | grep -v -i "WARNING: ") @@ -19,6 +19,7 @@ <xml name="citations"> <citations> <citation type="doi">10.1038/nmeth.3869</citation> + <yield/> </citations> </xml> @@ -27,13 +28,13 @@ <token name="@READ_FOO@"><![CDATA[ #def read_data($dataset) #if $dataset.is_of_type('dada2_derep') - readRDS(file.path('$dataset.extra_files_path', 'Rdata')) + readRDS('$dataset) #else if $dataset.is_of_type('dada2_dada') readRDS('$dataset') #else if $dataset.is_of_type('dada2_sequencetable') as.matrix( read.table('$dataset', header=T, sep="\t", row.names=1) ) #else if $dataset.is_of_type('dada2_mergepairs') - read.table('$dataset', header=T, sep="\t" ) + readRDS('$dataset') #else if $dataset.is_of_type('tabular') read.table('$dataset', header=T, sep="\t", row.names=1 ) #else @@ -41,32 +42,42 @@ #end if #end def ]]></token> - <!-- for filterAndTrim --> - <xml name="trimmers"> + <!-- for filterAndTrim --> + <xml name="trimmers"> <section name="trim" title="Trimming parameters"> - <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"/> - <param name="trimLeft" type="integer" value="0" min="0" label="Trim start of each read" help="The number of nucleotides to remove from the start of each read."/> - <param name="trimRight" type="integer" value="0" min="0" label="Trim end of each read" help="The number of nucleotides to remove from the end of each read"/> - <param name="truncLen" type="integer" value="0" min="0" label="Truncate read length" help="Truncate reads after this amount of bases. Reads shorter than this are discarded."/> - </section> + <param argument="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"/> + <param argument="trimLeft" type="integer" value="0" min="0" label="Trim start of each read" help="The number of nucleotides to remove from the start of each read."/> + <param argument="trimRight" type="integer" value="0" min="0" label="Trim end of each read" help="The number of nucleotides to remove from the end of each read"/> + <param argument="truncLen" type="integer" value="0" min="0" label="Truncate read length" help="Truncate reads after this amount of bases. Reads shorter than this are discarded."/> + </section> </xml> <xml name="filters"> <section name="filter" title="Filtering parameters"> - <param name="maxLen" type="integer" value="" optional="true" min="0" label="Remove long reads" help="Remove reads with length greater than this value. Default: no length threshold"/> - <param name="minLen" type="integer" value="20" min="0" label="Remove short reads" help="Remove reads with length less than this value. Default: 20"/> - <param name="maxN" type="integer" value="0" min="0" label="Remove reads with more Ns" help="Note that some of the subsequent dada pipeline steps do not allow Ns"/> - <param name="minQ" type="integer" value="0" min="0" label="Remove low quality reads" help="Reads contain a quality score less than this value will be discarded"/> - <param name="maxEE" type="integer" value="" optional="true" min="0" label="Remove reads by number expected errors" help="Reads with a higher number of expected errors (EE) will be discarded, where EE = sum(10^(-Q_i/10)), with Q are the nominal quality scores at the read positions"/> + <param argument="maxLen" type="integer" value="" optional="true" min="0" label="Remove long reads" help="Remove reads with length greater than this value. Default: no length threshold"/> + <param argument="minLen" type="integer" value="20" min="0" label="Remove short reads" help="Remove reads with length less than this value. Default: 20"/> + <param argument="maxN" type="integer" value="0" min="0" label="Remove reads with more Ns" help="Note that some of the subsequent dada pipeline steps do not allow Ns"/> + <param argument="minQ" type="integer" value="0" min="0" label="Remove low quality reads" help="Reads contain a quality score less than this value will be discarded"/> + <param argument="maxEE" type="integer" value="" optional="true" min="0" label="Remove reads by number expected errors" help="Reads with a higher number of expected errors (EE) will be discarded, where EE = sum(10^(-Q_i/10)), with Q are the nominal quality scores at the read positions"/> </section> </xml> <xml name="errorEstimationFunction"> - <param name="errfoo" type="select" label="Error function"> + <param name="errfoo" argument="errorEstimationFunction" type="select" label="Error function"> <option value="loessErrfun">loess</option> <option value="noqualErrfun">noqual</option> <option value="PacBioErrfun">PacBio</option> </param> </xml> + <token name="@HELP_OVERVIEW@"><![CDATA[ +Overview +........ +The intended use of the dada2 tools for paired sequencing data is shown in the following image. +.. image:: pairpipe.png + +For single end data you the steps "Unzip collection" and "mergePairs" are not necessary. + +More information may be found on the dada2 homepage:: https://benjjneb.github.io/dada2/index.html (in particular tutorials) or the documentation of dada2's R package https://bioconductor.org/packages/release/bioc/html/dada2.html (in particular the pdf which contains the full documentation of all parameters) + ]]></token> </macros>