diff collect.shared.xml @ 2:152f67f91fb6 draft

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

--- a/collect.shared.xml	Tue Sep 05 17:09:33 2017 -0400
+++ b/collect.shared.xml	Tue Mar 20 22:06:36 2018 -0400
@@ -7,29 +7,29 @@
     <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 'collect.shared(
-            shared=otu.dat,
-            #if $label:
-                label=${ str($label).replace(",","-") },
-            #end if
-            #if $calc:
-                calc=${ str($calc).replace(",","-") },
-            #end if
-            #if $groups:
-                groups=${ str($groups).replace(",","-") },
-            #end if
-            freq=$freq,
-            all=true
-        )'
-        | sed 's/ //g'  ## mothur trips over whitespace
-        | mothur
-        | tee mothur.out.log
-        && rm otu.dat  ## don't want this collected into datacollection
+echo 'collect.shared(
+    shared=otu.dat,
+    #if $label:
+        label=${ str($label).replace(",","-") },
+    #end if
+    #if $calc:
+        calc=${ str($calc).replace(",","-") },
+    #end if
+    #if $groups:
+        groups=${ str($groups).replace(",","-") },
+    #end if
+    freq=$freq,
+    all=true
+)'
+| sed 's/ //g'  ## mothur trips over whitespace
+| mothur
+| tee mothur.out.log
+&& rm otu.dat  ## don't want this collected into datacollection
     ]]></command>
     <inputs>
         <param name="otu" type="data" format="mothur.shared" label="shared - OTU Shared"/>
@@ -56,7 +56,9 @@
             <option value="thetan" selected="true">thetan - Community Structure Similarity the Smith theta similarity coefficient</option>
             <option value="thetayc" selected="true">thetayc - Community Structure Similarity the Yue &amp; Clayton theta similarity coefficient</option>
         </param>
-        <param name="freq" type="float" value="100" label="freq - indicates when to output your data" help="by default it is set to 100. But you can set it to a percentage of the number of sequence. For example freq=0.10, means 10%" min="0.0" max="100.0"/>
+        <param name="freq" type="float" value="100" label="freq - indicates when to output your data"
+            help="by default it is set to 100. But you can set it to a percentage of the number of sequence. For example freq=0.10, means 10%" min="0.0" max="100.0"/>
+        <expand macro="param-savelog"/>
     </inputs>
     <outputs>
         <expand macro="logfile-output"/>
@@ -70,6 +72,7 @@
             <output_collection name="calcfiles" count="11">
                 <element name="jest" md5="22e97fbdbdadf3c4748d0f7c4d526855" ftype="tabular"/>
             </output_collection>
+            <param name="savelog" value="true"/>
             <expand macro="logfile-test"/>
         </test>
         <test><!-- test with group and label select and all calculators -->
@@ -80,11 +83,11 @@
             <output_collection name="calcfiles" count="39">
                 <element name="jest" md5="1289eac7fdcfb42eaf4ee35deb6fb0a4" ftype="tabular"/>
             </output_collection>
+            <param name="savelog" value="true"/>
             <expand macro="logfile-test"/>
         </test>
     </tests>
-    <help>
-<![CDATA[
+    <help><![CDATA[
 
 @MOTHUR_OVERVIEW@
 
@@ -94,7 +97,7 @@
 
 .. _calculators: https://www.mothur.org/wiki/Calculators
 .. _collect.shared: https://www.mothur.org/wiki/Collect.shared
-]]>
-    </help>
+
+    ]]></help>
     <expand macro="citations"/>
 </tool>