diff macros.xml @ 2:ea3c356bff55 draft

planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit 5b1603bbcd3f139cad5c876be83fcb39697b5613-dirty

--- a/macros.xml	Fri Mar 08 08:36:35 2019 -0500
+++ b/macros.xml	Tue Apr 09 07:05:06 2019 -0400
@@ -16,8 +16,6 @@
         ]]></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>
@@ -45,24 +43,23 @@
     ]]></token>
     <!-- for filterAndTrim --> 
 	<xml name="trimmers">
-        <section name="trim" title="trimming parameters">
+        <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=""/>
+            <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>
     </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 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"/>
         </section>
     </xml>
 
-
     <xml name="errorEstimationFunction">
         <param name="errfoo" type="select" label="Error function">
             <option value="loessErrfun">loess</option>