diff count.seqs.xml @ 2:0cd054e2876d draft

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

--- a/count.seqs.xml	Tue Sep 05 16:55:24 2017 -0400
+++ b/count.seqs.xml	Tue Mar 20 22:17:19 2018 -0400
@@ -7,27 +7,26 @@
     <expand macro="stdio"/>
     <expand macro="version_command"/>
     <command><![CDATA[
-        @SHELL_OPTIONS@
+@SHELL_OPTIONS@
 
-        ## create symlinks to input datasets
-        ln -s "$name" name.dat &&
-        #if $grouping.use == "yes":
-            ln -s "$grouping.group" grouping.group.dat &&
-        #end if
+## create symlinks to input datasets
+ln -s '$name' name.dat &&
+#if $grouping.use == "yes":
+    ln -s '$grouping.group' grouping.group.dat &&
+#end if
 
-        echo 'count.seqs(
-            name=name.dat,
-            #if $grouping.use == "yes":
-                group=grouping.group.dat,
-                #if $grouping.groups:
-                    groups=${ str($grouping.groups).replace(",","-") },
-                #end if
-            #end if
-            large=$large
-        )'
-        | sed 's/ //g'  ## mothur trips over whitespace
-        | mothur
-        | tee mothur.out.log
+echo 'count.seqs(
+    #if $grouping.use == "yes":
+        group=grouping.group.dat,
+        #if $grouping.groups:
+            groups=${ str($grouping.groups).replace(",","-") },
+        #end if
+    #end if
+    name=name.dat
+)'
+| sed 's/ //g'  ## mothur trips over whitespace
+| mothur
+| tee mothur.out.log
     ]]></command>
     <inputs>
         <param name="name" type="data" format="mothur.names" label="name - Sequences Name reference"/>
@@ -47,7 +46,7 @@
             </when>
             <when value="no"/>
         </conditional>
-        <param name="large" type="boolean" checked="false" truevalue="true" falsevalue="false" label="large - Datasets are large and may not fit in RAM"/>
+        <expand macro="param-savelog"/>
     </inputs>
     <outputs>
         <expand macro="logfile-output"/>
@@ -57,6 +56,7 @@
         <test><!-- test default params -->
             <param name="name" value="amazon.names"/>
             <output name="seq_count" file="amazon.count_table" ftype="mothur.count_table"/>
+            <param name="savelog" value="true"/>
             <expand macro="logfile-test"/>
         </test>
         <test><!-- test with group file -->
@@ -64,6 +64,7 @@
             <param name="use" value="yes"/>
             <param name="group" value="amazon.groups"/>
             <output name="seq_count" file="amazon_withgroups.count_table" ftype="mothur.count_table"/>
+            <param name="savelog" value="true"/>
             <expand macro="logfile-test"/>
         </test>
         <test> <!-- test with group file and subset of groups -->
@@ -72,6 +73,7 @@
             <param name="group" value="amazon.groups" ftype="mothur.groups"/>
             <param name="groups" value="pasture"/>
             <output name="seq_count" file="amazon_withgroups_pasture.count_table" ftype="mothur.count_table"/>
+            <param name="savelog" value="true"/>
             <expand macro="logfile-test"/>
         </test>
         <test> <!-- test with group file and multiple groups -->
@@ -80,11 +82,11 @@
             <param name="group" value="amazon.groups" ftype="mothur.groups"/>
             <param name="groups" value="pasture,forest"/>
             <output name="seq_count" md5="b18c03aee561cd24a36b00ad9b22255a" ftype="mothur.count_table"/>
+            <param name="savelog" value="true"/>
             <expand macro="logfile-test"/>
         </test>
     </tests>
-    <help>
-<![CDATA[
+    <help><![CDATA[
 
 @MOTHUR_OVERVIEW@
 
@@ -98,7 +100,7 @@
 .. _count_table: https://www.mothur.org/wiki/Count_File
 
 v.1.21.0: Updated to Mothur 1.33
-]]>
-    </help>
+
+    ]]></help>
     <expand macro="citations"/>
 </tool>