diff summary.shared.xml @ 2:88aa9d575274 draft

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

--- a/summary.shared.xml	Tue Sep 05 17:06:22 2017 -0400
+++ b/summary.shared.xml	Tue Mar 20 22:12:56 2018 -0400
@@ -7,40 +7,40 @@
     <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 'summary.shared(
-            shared=otu.dat,
-            #if $groups:
-                label=${ str($label).replace(",","-") },
-            #end if
-            #if $label:
-                groups=${ str($groups).replace(",","-") },
-            #end if
-            #if $calc:
-                calc=${ str($calc).replace(",","-") },
-            #end if
-            all=$all,
-            distance=$distance,
-            #if $subsample.use == "yes":
-                #if $subsample.subsample:
-                    subsample=$subsample.subsample,
-                #else
-                    subsample=T,
-                #end if
-                #if $subsample.iters:
-                    iters=$subsample.iters,
-                #end if
-            #end if
-            output=$output,
-            processors='\${GALAXY_SLOTS:-8}'
-        )'
-        | sed 's/ //g'  ## mothur trips over whitespace
-        | mothur
-        | tee mothur.out.log
+echo 'summary.shared(
+    shared=otu.dat,
+    #if $groups:
+        label=${ str($label).replace(",","-") },
+    #end if
+    #if $label:
+        groups=${ str($groups).replace(",","-") },
+    #end if
+    #if $calc:
+        calc=${ str($calc).replace(",","-") },
+    #end if
+    all=$all,
+    distance=$distance,
+    #if $subsample.use == "yes":
+        #if $subsample.subsample:
+            subsample=$subsample.subsample,
+        #else
+            subsample=T,
+        #end if
+        #if $subsample.iters:
+            iters=$subsample.iters,
+        #end if
+    #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"/>
@@ -84,6 +84,7 @@
             <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"/>
@@ -103,10 +104,11 @@
         <test><!-- test with defaults -->
             <param name="otu" value="amazon.an.shared"/>
             <output name="summary" md5="29384359e341721b3519fba35b9301e4" ftype="tabular"/>
+            <param name="savelog" value="true"/>
             <expand macro="logfile-test"/>
         </test>
         <test><!-- test with subsample -->
-            <param name="otu" value="amazon.an.shared"/>
+            <param name="otu" value="amazon.mothur.shared"/>
             <param name="use" value="yes"/>
             <param name="subsample" value="10"/>
             <param name="iters" value="42"/>
@@ -116,6 +118,7 @@
                     <has_text text="pasture"/>
                 </assert_contents>
             </output>
+            <param name="savelog" value="true"/>
             <expand macro="logfile-test"/>
         </test>
         <test><!-- test with label and groups select and all calculators -->
@@ -124,6 +127,7 @@
             <param name="groups" value="forest,pasture"/>
             <param name="calc" value="sharedsobs,sharedchao,sharedace,anderberg,jclass,jest,kulczynski,kulczynskicody,kstest,lennon,ochiai,sorclass,sorest,whittaker,hamming,memchi2,memchord,memeuclidean,mempearson,braycurtis,jabund,morisitahorn,sorabund,thetan,thetayc,canberra,gower,hellinger,manhattan,odum,soergel,spearman,speciesprofile,structchi2,structchord,structeuclidean,structkulczynski,structpearson,sharednseqs,sharedobserved"/>
             <output name="summary" md5="acd56d4ab09ec1c2117f5e4840a875a1" ftype="tabular"/>
+            <param name="savelog" value="true"/>
             <expand macro="logfile-test"/>
         </test>
         <test><!-- test with distance output collection -->
@@ -144,11 +148,11 @@
                     </assert_contents>
                 </element>
             </output_collection>
+            <param name="savelog" value="true"/>
             <expand macro="logfile-test"/>
         </test>
     </tests>
-    <help>
-<![CDATA[
+    <help><![CDATA[
 
 @MOTHUR_OVERVIEW@
 
@@ -159,7 +163,7 @@
 .. _shared: https://www.mothur.org/wiki/Shared_file
 .. _group: https://www.mothur.org/wiki/Group_file
 .. _summary.shared: https://www.mothur.org/wiki/Summary.shared
-]]>
-    </help>
+
+    ]]></help>
     <expand macro="citations"/>
 </tool>