diff cluster.classic.xml @ 2:085625ddf82c draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3

--- a/cluster.classic.xml	Tue Sep 05 17:02:53 2017 -0400
+++ b/cluster.classic.xml	Tue Mar 20 22:15:53 2018 -0400
@@ -7,46 +7,47 @@
     <expand macro="stdio"/>
     <expand macro="version_command"/>
     <command><![CDATA[
-        @SHELL_OPTIONS@
+@SHELL_OPTIONS@
 
-        ## create symlinks to input datasets
-        ln -s "$dist" dist.dat &&
-        ln -s "$name" name.dat &&
-        ln -s "$count" count.dat &&
+## create symlinks to input datasets
+ln -s '$dist' dist.dat &&
+ln -s '$name' name.dat &&
+ln -s '$count' count.dat &&
 
-        echo 'cluster.classic(
-            phylip=dist.dat,
-            #if $name:
-                name=name.dat,
-            #end if
-            #if $count:
-                count=count.dat,
-            #end if
-            method=$method,
-            #if $cutoff:
-                cutoff=$cutoff,
-            #end if
-            hard=$hard,
-            precision=$precision,
-            sim=$sim
-        )'
-        | sed 's/ //g'  ## mothur trips over whitespace
-        | mothur
-        | tee mothur.out.log
+echo 'cluster.classic(
+    phylip=dist.dat,
+    #if $name:
+        name=name.dat,
+    #end if
+    #if $count:
+        count=count.dat,
+    #end if
+    method=$method,
+    #if $cutoff:
+        cutoff=$cutoff,
+    #end if
+    precision=$precision,
+    sim=$sim
+)'
+| sed 's/ //g'  ## mothur trips over whitespace
+| mothur
+| tee mothur.out.log
     ]]></command>
     <inputs>
-        <param name="dist" type="data" format="mothur.dist,mothur.lower.dist,mothur.square.dist" label="phylip - Distance Matrix" help="format must be mothur.lower.dist or mothur.square.dist"/>
-        <param name="name" type="data" format="mothur.names" optional="true" label="name - Sequences Name reference"/>
-        <param name="count" type="data" format="mothur.count_table" optional="true" label="count - a count_table" help="generated by count.seqs"/>
-        <param name="method" type="select" label="method - Select a Clustering Method" help="">
+        <param argument="dist" type="data" format="mothur.dist,mothur.lower.dist,mothur.square.dist" label="phylip - Distance Matrix"
+            help="format must be mothur.lower.dist or mothur.square.dist"/>
+        <param argument="name" type="data" format="mothur.names" optional="true" label="name - Sequences Name reference"/>
+        <param argument="count" type="data" format="mothur.count_table" optional="true" label="count - a count_table" help="generated by count.seqs"/>
+        <param argument="method" type="select" label="method - Select a Clustering Method" help="">
             <option value="furthest">Furthest neighbor</option>
             <option value="nearest">Nearest neighbor</option>
             <option value="average" selected="true">Average neighbor</option>
             <option value="weighted">Weighted</option>
         </param>
-        <param name="cutoff" type="float" value="" min="0" optional="true" label="cutoff - Distance Cutoff threshold" help="Ignore pairwise distances larger than this, a common value would be 0.10"/>
-        <param name="hard" type="boolean" checked="true" truevalue="true" falsevalue="false" label="hard - Use hard cutoff instead of rounding"/>
-        <param name="precision" type="select" optional="true" label="precision - Precision for rounding distance values" help="Set higher precision for longer genome scale sequence lengths">
+        <param argument="cutoff" type="float" value="" min="0" optional="true" label="cutoff - Distance Cutoff threshold"
+            help="Ignore pairwise distances larger than this. Default for methods opti,agc,dgc is 0.03, default for the other methods is 0.15"/>
+        <param argument="precision" type="select" optional="true" label="precision - Precision for rounding distance values"
+            help="Set higher precision for longer genome scale sequence lengths">
             <option value="10">.1</option>
             <option value="100" selected="true">.01</option>
             <option value="1000">.001</option>
@@ -54,7 +55,8 @@
             <option value="100000">.00001</option>
             <option value="1000000">.000001</option>
         </param>
-        <param name="sim" type="boolean" checked="false" truevalue="true" falsevalue="false" label="sim - Matrix values are Similary instead of Distance"/>
+        <param argument="sim" type="boolean" checked="false" truevalue="true" falsevalue="false" label="sim - Matrix values are Similary instead of Distance"/>
+        <expand macro="param-savelog"/>
     </inputs>
     <outputs>
         <expand macro="logfile-output"/>
@@ -74,11 +76,11 @@
                     <has_line_matching expression="^label\tnumOtus\tOtu01\tOtu02\tOtu03\tOtu04\tOtu05\tOtu06\tOtu07\tOtu08\tOtu09\tOtu10\tOtu11\tOtu12\tOtu13\tOtu14\tOtu15\tOtu16\tOtu17\tOtu18\tOtu19\tOtu20\tOtu21\tOtu22\tOtu23\tOtu24$"/>
                 </assert_contents>
             </output>
+            <param name="savelog" value="true"/>
             <expand macro="logfile-test"/>
         </test>
     </tests>
-    <help>
-<![CDATA[
+    <help><![CDATA[
 
 @MOTHUR_OVERVIEW@
 
@@ -88,7 +90,6 @@
 
 .. _cluster.classic: https://www.mothur.org/wiki/Cluster.classic
 
-]]>
-    </help>
+    ]]></help>
     <expand macro="citations"/>
 </tool>