diff parsimony.xml @ 2:4e3816a6462a draft

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

--- a/parsimony.xml	Tue Sep 05 17:16:57 2017 -0400
+++ b/parsimony.xml	Tue Mar 20 22:04:18 2018 -0400
@@ -7,44 +7,45 @@
     <expand macro="stdio"/>
     <expand macro="version_command"/>
     <command><![CDATA[
-        @SHELL_OPTIONS@
+@SHELL_OPTIONS@
 
-        ## create symlinks to input datasets
-        ln -s "$tree" tree.dat &&
-        ln -s "$group" group.dat &&
-        ln -s "$count" count.dat &&
-        ln -s "$name" name.dat &&
+## create symlinks to input datasets
+ln -s '$tree' tree.dat &&
+ln -s '$group' group.dat &&
+ln -s '$count' count.dat &&
+ln -s '$name' name.dat &&
 
-        echo 'parsimony(
-            tree=tree.dat,
-            iters=$iters,
-            group=group.dat,
-            #if $groups:
-                groups=${ str($groups).replace(",","-") },
-            #end if
-            #if $name:
-                name=name.dat,
-            #end if
-            #if $count:
-                count=count.dat,
-            #end if
-            processors='\${GALAXY_SLOTS:-8}'
-        )'
-        | sed 's/ //g'  ## mothur trips over whitespace
-        | mothur
-        | tee mothur.out.log
+echo 'parsimony(
+    tree=tree.dat,
+    iters=$iters,
+    group=group.dat,
+    #if $groups:
+        groups=${ str($groups).replace(",","-") },
+    #end if
+    #if $name:
+        name=name.dat,
+    #end if
+    #if $count:
+        count=count.dat,
+    #end if
+    processors='\${GALAXY_SLOTS:-8}'
+)'
+| sed 's/ //g'  ## mothur trips over whitespace
+| mothur
+| tee mothur.out.log
     ]]></command>
     <inputs>
-        <param name="tree" type="data" format="mothur.tre" label="tree - Phylogenetic Tree"/>
-        <param name="group" type="data" format="mothur.groups" label="group - Group file for the tree"/>
-        <param name="groups" type="select" label="groups - Groups to display" multiple="true" help="By default all are included if no selection is made.">
+        <param argument="tree" type="data" format="mothur.tre" label="tree - Phylogenetic Tree"/>
+        <param argument="group" type="data" format="mothur.groups" label="group - Group file for the tree"/>
+        <param argument="groups" type="select" multiple="true" label="groups - Groups to display" help="By default all are included if no selection is made.">
             <options>
                 <filter type="data_meta" ref="group" key="groups"/>
             </options>
         </param>
-        <param name="name" type="data" format="mothur.names" optional="true" label="name - Sequences Name reference file for the tree"/>
-        <param name="iters" type="integer" min="1" value="1000" label="iters - Number of bootstrap iterations to try (default 1000)"/>
-        <param name="count" type="data" format="mothur.count_table" optional="true" label="count - a count_table" help="generated by count.seqs"/>
+        <param argument="name" type="data" format="mothur.names" optional="true" label="name - Sequences Name reference file for the tree"/>
+        <param argument="iters" type="integer" min="1" value="1000" label="iters - Number of bootstrap iterations to try (default 1000)"/>
+        <param argument="count" type="data" format="mothur.count_table" optional="true" label="count - a count_table" help="generated by count.seqs"/>
+        <expand macro="param-savelog"/>
     </inputs>
     <outputs>
         <expand macro="logfile-output"/>
@@ -58,25 +59,35 @@
             <param name="groups" value="green,orange"/>
             <param name="name" value="treetest.names"/>
             <param name="iters" value="1000"/>
-            <output name="psummary" md5="011c202c5e5e33cb1af7c742aeb06457"/>
-            <output name="parsimony" md5="f49e0d64fd0c5df01abc913f398d428a"/>
+            <output name="psummary" ftype="tabular">
+                <assert_contents>
+                    <has_line_matching expression="^Tree#\tGroups\tParsScore\tParsSig$"/>
+                </assert_contents>
+            </output>
+            <output name="parsimony" ftype="tabular">
+                <assert_contents>
+                    <has_text text="green-orangeScore"/>
+                </assert_contents>
+            </output>
+            <param name="savelog" value="true"/>
             <expand macro="logfile-test"/>
         </test>
     </tests>
-    <help>
-<![CDATA[
+    <help><![CDATA[
 
 @MOTHUR_OVERVIEW@
 
 **Command Documentation**
 
-The parsimony_ command implements the parsimony method (aka P-test), which was previously implemented in TreeClimber and is also available in MacClade and on the UniFrac website. The parsimony method is a generic test that describes whether two or more communities have the same structure. The significance of the test statistic can only indicate the probability that the communities have the same structure by chance. The value does not indicate a level of similarity.
+The parsimony_ command implements the parsimony method (aka P-test), which was previously implemented in TreeClimber
+and is also available in MacClade and on the UniFrac website. The parsimony method is a generic test that describes
+whether two or more communities have the same structure. The significance of the test statistic can only indicate the
+probability that the communities have the same structure by chance. The value does not indicate a level of similarity.
 
 .. _parsimony: https://www.mothur.org/wiki/Parsimony
 
 v.1.20.0: Added count parameter
 
-]]>
-    </help>
+    ]]></help>
     <expand macro="citations"/>
 </tool>