changeset 5:41006d6914cd draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"

--- a/dada2_seqCounts.xml	Fri Jul 02 20:04:08 2021 +0000
+++ b/dada2_seqCounts.xml	Tue Aug 31 07:54:08 2021 +0000
@@ -1,5 +1,6 @@
 <tool id="dada2_seqCounts" name="dada2: sequence counts" version="@DADA2_VERSION@+galaxy@WRAPPER_VERSION@" profile="19.09">
     <description></description>
+    <expand macro="bio_tools"/>
     <macros>
         <import>macros.xml</import>
     </macros>

--- a/macros.xml	Fri Jul 02 20:04:08 2021 +0000
+++ b/macros.xml	Tue Aug 31 07:54:08 2021 +0000
@@ -6,7 +6,11 @@
             <yield/>
         </requirements>
     </xml>
-
+    <xml name="bio_tools">
+        <xrefs>
+            <xref type="bio.tools">dada2</xref>
+        </xrefs>
+    </xml>
     <token name="@DADA2_VERSION@">1.20</token>
     <token name="@WRAPPER_VERSION@">0</token>
 

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/macros.xml.orig	Tue Aug 31 07:54:08 2021 +0000
@@ -0,0 +1,143 @@
+<?xml version="1.0"?>
+<macros>
+    <xml name="requirements">
+        <requirements>
+            <requirement type="package" version="@DADA2_VERSION@">bioconductor-dada2</requirement>
+            <yield/>
+        </requirements>
+    </xml>
+<<<<<<< HEAD
+
+    <token name="@DADA2_VERSION@">1.20</token>
+=======
+    <xml name="bio_tools">
+        <xrefs>
+            <xref type='bio.tools'>dada2</xref>
+        </xrefs>
+    </xml>
+    <token name="@DADA2_VERSION@">1.16</token>
+>>>>>>> 449abf790 (add bio.tools ID)
+    <token name="@WRAPPER_VERSION@">0</token>
+
+    <xml name="version_command">
+        <version_command><![CDATA[
+echo $(R --version | grep version | grep -v GNU)", dada2 version" $(R --vanilla --slave -e "library(dada2); cat(sessionInfo()\$otherPkgs\$dada2\$Version)" 2> /dev/null | grep -v -i "WARNING: ")
+        ]]></version_command>
+    </xml>
+
+    <xml name="stdio">
+        <stdio>
+            <regex match="Error: cannot allocate" source="stderr" level="fatal_oom" description="Out of memory error occurred" />
+            <regex match="'Calloc' could not allocate memory" source="stderr" level="fatal_oom" description="Out of memory error occurred" />
+        </stdio>
+    </xml>
+
+    <xml name="citations">
+        <citations>
+            <citation type="doi">10.1038/nmeth.3869</citation>
+            <yield/>
+        </citations>
+    </xml>
+
+    <token name="@DADA_UNIQUES@">dada2_dada,dada2_mergepairs</token>
+
+    <!-- function to read dada2 data types
+         - dada, and mergepairs are simply read as RDS
+         - sequence_table is a named integer matrix (rows=samples, columns=ASVs)
+         - uniques is a named integer vector (columns=ASVs, only one rows)-->
+    <token name="@READ_FOO@"><![CDATA[
+    read.uniques <- function ( fname ) {
+         p <- read.table(fname, header=F, sep="\t")
+         n <-x[,2]
+         names(n)<-x[,1]
+    }
+    #def read_data($dataset)
+        #if $dataset.is_of_type('dada2_sequencetable')
+            t(as.matrix( read.table('$dataset', header=T, sep="\t", row.names=1) ))
+        #else if $dataset.is_of_type('dada2_uniques')
+            read.uniques('$dataset')
+        #else if $dataset.is_of_type('tabular')
+            read.table('$dataset', header=T, sep="\t", row.names=1)
+        #else
+            readRDS('$dataset')
+        #end if
+    #end def
+    ]]></token>
+    <!-- function to write dada2 data types (the content or the R variable 'out' is written)
+         - dada, and mergepairs are written as RDS
+         - sequence_table is a named integer matrix (rows=samples, columns=ASVs)
+         - uniques is a named integer vector (columns=ASVs, only one rows)-->
+    <token name="@WRITE_FOO@"><![CDATA[
+write.data <- function( data, fname, type ){
+    if( type == 'dada2_uniques'){
+        write.table(data, file = fname, quote = F, sep = "\t", row.names = T, col.names = F)
+    }else if( type== 'dada2_sequencetable'){
+        write.table(t(data), file=fname, quote=F, sep="\t", row.names = T, col.names = NA)
+    }else{
+        saveRDS(data, file=fname)
+    }
+}
+    ]]></token>
+
+    <xml name="fastq_input" token_multiple="" token_collection_type="" token_argument_fwd="" token_argument_rev="">
+        <conditional name="paired_cond">
+            <param name="paired_select" type="select" label="Paired reads">
+                <option value="paired">paired - in a data set pair</option>
+                <option value="separate">paired - in two separate data sets</option>
+                <option value="single">single</option>
+            </param>
+            <when value="paired">
+                <param name="reads" argument="@ARGUMENT_FWD@/@ARGUMENT_REV@" type="data_collection" collection_type="@COLLECTION_TYPE@" format="fastq,fastq.gz" label="Paired short read data"/>
+            </when>
+            <when value="separate">
+                <param name="reads" argument="@ARGUMENT_FWD@" type="data" format="fastq,fastq.gz" multiple="@MULTIPLE@" label="Forward read data"/>
+                <param name="sdaer" argument="@ARGUMENT_REV@" type="data" format="fastq,fastq.gz" multiple="@MULTIPLE@" label="Reverse read data"/>
+            </when>
+            <when value="single">
+                <param name="reads" argument="@ARGUMENT_FWD@" type="data" format="fastq,fastq.gz" multiple="@MULTIPLE@" label="Short read data"/>
+            </when>
+        </conditional>
+    </xml>
+
+    <!-- for filterAndTrim -->
+    <xml name="trimmers">
+        <section name="trim" title="Trimming parameters">
+            <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. (default 0: no truncation)"/>
+        </section>
+    </xml>
+    <xml name="filters">
+        <section name="filter" title="Filtering parameters">
+            <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" argument="errorEstimationFunction" type="select" label="Error function">
+            <option value="loessErrfun">loess: Use a loess fit to estimate error rates from transition counts</option>
+            <option value="noqualErrfun">noqual: Estimate error rates for each type of transition while ignoring quality scores.</option>
+            <option value="PacBioErrfun">PacBio: Estimate error rates from transition counts in PacBio CCS data.</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
+
+Note: In particular for the analysis of paired collections the collections should be sorted lexicographical
+before the analysis.
+
+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>