diff dist.shared.xml @ 2:b7da1494afa1 draft

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

--- a/dist.shared.xml	Tue Sep 05 16:56:03 2017 -0400
+++ b/dist.shared.xml	Tue Mar 20 22:11:03 2018 -0400
@@ -7,34 +7,36 @@
     <expand macro="stdio"/>
     <expand macro="version_command"/>
     <command><![CDATA[
-        @SHELL_OPTIONS@
+@SHELL_OPTIONS@
 
-        ## create symlinks to input datasets
-        ln -s "$otu" otu.dat &&
+## create symlinks to input datasets
+ln -s '$otu' otu.dat &&
 
-        echo 'dist.shared(
-            shared=otu.dat,
-            #if $label:
-                label=${ str($label).replace(",","-") },
-            #end if
-            #if $groups:
-                groups=${ str($groups).replace(",","-") },
-            #end if
-            #if $calc:
-                calc=${ str($calc).replace(",","-") },
-            #end if
-            #if $subsampling.use == "yes":
-                #if $subsampling.subsample:
-                    subsample=$subsampling.subsample,
-                #end if
-                iters=$subsampling.iters,
-            #end if
-            output=$output,
-            processors='\${GALAXY_SLOTS:-8}'
-        )'
-        | sed 's/ //g'  ## mothur trips over whitespace
-        | mothur
-        | tee mothur.out.log
+echo 'dist.shared(
+    shared=otu.dat,
+    #if $label:
+        label=${ str($label).replace(",","-") },
+    #end if
+    #if $groups:
+        groups=${ str($groups).replace(",","-") },
+    #end if
+    #if $calc:
+        calc=${ str($calc).replace(",","-") },
+    #end if
+    #if $subsampling.use == "yes":
+        #if $subsampling.subsample:
+            subsample=$subsampling.subsample,
+        #else
+            subsample=T,
+        #end if
+        iters=$subsampling.iters,
+    #end if
+    output=$output,
+    processors='\${GALAXY_SLOTS:-8}'
+)'
+| sed 's/ //g'  ## mothur trips over whitespace
+| mothur
+| tee mothur.out.log
     ]]></command>
     <inputs>
         <param name="otu" type="data" format="mothur.shared" label="shared - OTU Shared"/>
@@ -58,7 +60,8 @@
                 <option value="yes">yes</option>
             </param>
             <when value="yes">
-                <param name="subsample" type="integer" value="" min="0" optional="true" label="subsample (defaults to the size of the smallest group)" help="Should not exceed the number of sequences in any group"/>
+                <param name="subsample" type="integer" value="" min="0" optional="true" label="subsample (defaults to the size of the smallest group)"
+                    help="Should not exceed the number of sequences in any group"/>
                 <param name="iters" type="integer" value="1000" min="1" optional="true" label="iters - Number of iterations to try (default 1000)"/>
             </when>
             <when value="no"/>
@@ -67,6 +70,7 @@
             <option value="lt" selected="true">Phylip formatted Lower Triangle Matrix</option>
             <option value="square">Phylip formatted Square Matrix</option>
         </param>
+        <expand macro="param-savelog"/>
     </inputs>
     <outputs>
         <expand macro="logfile-output"/>
@@ -80,6 +84,7 @@
             <output_collection name="distfiles" count="72">
                 <element name="thetayc.0.33.lt" md5="c707e43f14c2022f4027e6a2495cbae8" ftype="mothur.dist"/>
             </output_collection>
+            <param name="savelog" value="true"/>
             <expand macro="logfile-test"/>
         </test>
         <test><!-- test with label,group select and all calculators -->
@@ -90,14 +95,13 @@
             <output_collection name="distfiles" count="74">
                 <element name="gower.0.22.lt" md5="209dbf7e9f1e13753524905f64c8e3b7" ftype="mothur.dist"/>
             </output_collection>
+            <param name="savelog" value="true"/>
             <expand macro="logfile-test"/>
         </test>
-        <test><!-- test with subsampling -->
+        <test><!-- test with subsampling without specifying size -->
             <param name="otu" value="amazon.an.shared" ftype="mothur.shared"/>
+            <param name="label" value="0.03,0.33"/>
             <param name="use" value="yes"/>
-            <param name="subsample" value="10"/>
-            <param name="iters" value="42"/>
-            <param name="label" value="0.03,0.33"/>
             <param name="calc" value="canberra"/>
             <param name="output" value="square"/>
             <output_collection name="distfiles" count="6">
@@ -108,11 +112,30 @@
                     </assert_contents>
                 </element>
             </output_collection>
+            <param name="savelog" value="true"/>
+            <expand macro="logfile-test"/>
+        </test>
+        <test><!-- test with subsampling with specifying size-->
+            <param name="otu" value="amazon.mothur.shared" ftype="mothur.shared"/>
+            <param name="use" value="yes"/>
+            <param name="subsample" value="2"/>
+            <param name="iters" value="42"/>
+            <param name="label" value="0.10"/>
+            <param name="calc" value="canberra"/>
+            <param name="output" value="square"/>
+            <output_collection name="distfiles" count="3">
+                <element name="canberra.0.10.square.std" ftype="mothur.dist">
+                    <assert_contents>
+                        <has_text text="forest"/>
+                        <has_text text="pasture"/>
+                    </assert_contents>
+                </element>
+            </output_collection>
+            <param name="savelog" value="true"/>
             <expand macro="logfile-test"/>
         </test>
     </tests>
-    <help>
-<![CDATA[
+    <help><![CDATA[
 
 @MOTHUR_OVERVIEW@
 
@@ -126,7 +149,6 @@
 
 v1.26.0: Updated to Mothur 1.33. Omitted calculators since they do not appear to be available.
 
-]]>
-    </help>
+    ]]></help>
     <expand macro="citations"/>
 </tool>