diff macros.xml @ 0:38959bdb0956 draft

planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/macros.xml	Fri Mar 08 06:45:59 2019 -0500
@@ -0,0 +1,75 @@
+<?xml version="1.0"?>
+<macros>
+    <xml name="requirements">
+        <requirements>
+            <requirement type="package" version="@DADA2_VERSION@">bioconductor-dada2</requirement>
+            <yield/>
+        </requirements>
+    </xml>
+
+    <token name="@DADA2_VERSION@">1.10.0</token>
+    <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>
+
+    echo $(R --version | grep version | grep -v GNU)", DESeq2 version" $(R --vanilla --slave -e "library(dada2); cat(sessionInfo()\$otherPkgs\$dada2\$Version)" 2> /dev/null | grep -v -i "WARNING: ")
+
+    <xml name="citations">
+        <citations>
+            <citation type="doi">10.1038/nmeth.3869</citation>
+        </citations>
+    </xml>
+
+    <token name="@DADA_UNIQUES@">dada2_derep,dada2_dada,dada2_mergepairs</token>
+
+    <token name="@READ_FOO@"><![CDATA[
+    #def read_data($dataset)
+        #if $dataset.is_of_type('dada2_derep')
+            readRDS(file.path('$dataset.extra_files_path', 'Rdata'))
+        #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" )
+        #else if $dataset.is_of_type('tabular')
+              read.table('$dataset', header=T, sep="\t", row.names=1 )
+        #else
+            #raise Exception("error: unknown input type")
+        #end if
+    #end def
+    ]]></token>
+    <!-- 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="truncLen" type="integer" value="0" min="0" label="Truncate read length" help=""/>
+            <param name="trimLeft" type="integer" value="0" min="0" label="Remove nucleotides from start" help=""/>
+    		<param name="trimRight" type="integer" value="0" min="0" label="Remove nucleotides from end" help=""/>
+		</section>
+    </xml>
+    <xml name="filters">
+        <section name="filter" title="filtering parameters">
+            <param name="maxLen" type="integer" value="" optional="true" min="0" label="Remove reads longer than" help=""/>
+            <param name="minLen" type="integer" value="20" min="0" label="Remove reads shorter than" help=""/>
+            <param name="maxN" type="integer" value="0" min="0" label="Remove reads with more Ns" help=""/>
+            <param name="minQ" type="integer" value="0" min="0" label="Remove reads containing quality" help=""/>
+            <param name="maxEE" type="integer" value="" optional="true" min="0" label="Remove reads by expected errors" help=""/>
+        </section>
+    </xml>
+
+
+    <xml name="errorEstimationFunction">
+        <param name="errfoo" type="select" label="Error function">
+            <option value="loessErrfun">loess</option>
+            <option value="noqualErrfun">noqual</option>
+            <option value="PacBioErrfun">PacBio</option>
+        </param>
+    </xml>
+
+
+</macros>