diff dada2_mergePairs.xml @ 2:5ccfc129619c draft

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

--- a/dada2_mergePairs.xml	Fri Mar 08 08:40:08 2019 -0500
+++ b/dada2_mergePairs.xml	Tue Apr 09 07:07:52 2019 -0400
@@ -1,4 +1,4 @@
-<tool id="dada2_mergePairs" name="dada2: mergePairs" version="@DADA2_VERSION@">
+<tool id="dada2_mergePairs" name="dada2: mergePairs" version="@DADA2_VERSION@+galaxy@WRAPPER_VERSION@">
     <description>Merge denoised forward and reverse reads</description>
     <macros>
         <import>macros.xml</import>
@@ -27,21 +27,24 @@
     ]]></configfile>
     </configfiles>
     <inputs>
-        <param name="dadaf" type="data" format="dada2_dada" label="dada results for forward reads"/>
-        <param name="derepf" type="data" format="dada2_derep" label="dereplicated forward reads"/>
-        <param name="dadar" type="data" format="dada2_dada" label="dada results for reverse reads"/>
-        <param name="derepr" type="data" format="dada2_derep" label="dereplicated reverse reads"/>
-        <param name="minoverlap" type="integer" value="12" min="0" label="minimum length of the overlap"/>
-        <param name="maxmismatch" type="integer" value="0" min="0" label="maximum number of mismatches"/>
-        <param name="justconcatenate" type="boolean" checked="false" truevalue="FALSE" falsevalue="FALSE" label="concatenated rather than merge"/>
-        <param name="trimoverhang" type="boolean" checked="false" truevalue="FALSE" falsevalue="FALSE" label="trim overhangs"/>
+        <param name="dadaf" type="data" format="dada2_dada" label="Dada results for forward reads"/>
+        <param name="derepf" type="data" format="dada2_derep" label="Dereplicated forward reads"/>
+        <param name="dadar" type="data" format="dada2_dada" label="Dada results for reverse reads"/>
+        <param name="derepr" type="data" format="dada2_derep" label="Dereplicated reverse reads"/>
+        <param name="minoverlap" type="integer" value="12" min="0" label="Minimum length of the overlap"/>
+        <param name="maxmismatch" type="integer" value="0" min="0" label="Maximum number of mismatches"/>
+        <param name="justconcatenate" type="boolean" checked="false" truevalue="FALSE" falsevalue="FALSE" label="Concatenated rather than merge" help="The forward and reverse-complemented reverse read are concatenated rather than merged, with a 10 Ns spacer inserted between them"/>
+        <param name="trimoverhang" type="boolean" checked="false" truevalue="FALSE" falsevalue="FALSE" label="Trim overhangs" help="Overhangs are when the reverse read extends past the start of the forward read, and vice-versa, as can happen when reads are longer than the amplicon and read into the other-direction primer region"/>
     </inputs>
     <outputs>
         <data name="merged" format="dada2_mergepairs" label="${tool.name} on ${on_string}"/>
     </outputs>
 
     <help><![CDATA[
-        TODO: Fill in help.
+Description
+...........
+
+This function attempts to merge each denoised pair of forward and reverse reads, rejecting any pairs which do not sufficiently overlap or which contain too many (>0 by default) mismatches in the overlap region.
     ]]></help>
     <expand macro="citations"/>
 </tool>