diff pca.xml @ 2:1fdf1610e7dc draft

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

--- a/pca.xml	Tue Sep 05 16:50:31 2017 -0400
+++ b/pca.xml	Tue Mar 20 22:02:11 2018 -0400
@@ -7,28 +7,28 @@
     <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 'pca(
-            #if $otu.is_of_type("mothur.relabund"):
-                relabund=otu.dat,
-            #elif $otu.is_of_type("mothur.shared"):
-                shared=otu.dat,
-            #end if
-            #if $label:
-                label=${ str($label).replace(",","-") },
-            #end if
-            #if $groups:
-                groups=${ str($groups).replace(",","-") },
-            #end if
-            metric=$metric
-        )'
-        | sed 's/ //g'  ## mothur trips over whitespace
-        | mothur
-        | tee mothur.out.log
+echo 'pca(
+    #if $otu.is_of_type("mothur.relabund"):
+        relabund=otu.dat,
+    #elif $otu.is_of_type("mothur.shared"):
+        shared=otu.dat,
+    #end if
+    #if $label:
+        label=${ str($label).replace(",","-") },
+    #end if
+    #if $groups:
+        groups=${ str($groups).replace(",","-") },
+    #end if
+    metric=$metric
+)'
+| sed 's/ //g'  ## mothur trips over whitespace
+| mothur
+| tee mothur.out.log
     ]]></command>
     <inputs>
         <param name="otu" type="data" format="mothur.shared,mothur.relabund" label="shared,relabund - OTU Shared or Relabund file"/>
@@ -41,6 +41,7 @@
             </options>
         </param>
         <param name="metric" type="boolean" truevalue="true" falsevalue="false" checked="true" label="metric - Calculate pearson correlation coefficient"/>
+        <expand macro="param-savelog"/>
     </inputs>
     <outputs>
         <expand macro="logfile-output"/>
@@ -62,11 +63,11 @@
             <output_collection name="pca_loadings" count="2">
                 <element name="0.55" md5="8c76b60484ffcab2ef7230e29071dd51" ftype="txt"/>
             </output_collection>
+            <param name="savelog" value="true"/>
             <expand macro="logfile-test"/>
         </test>
     </tests>
-    <help>
-<![CDATA[
+    <help><![CDATA[
 
 @MOTHUR_OVERVIEW@
 
@@ -77,7 +78,7 @@
 .. _shared: https://www.mothur.org/wiki/Shared_file
 .. _relabund: https://www.mothur.org/wiki/Get.relabund
 .. _pca: https://www.mothur.org/wiki/Pca
-]]>
-    </help>
+
+    ]]></help>
     <expand macro="citations"/>
 </tool>