diff rarefaction.single.xml @ 2:871f24df79d8 draft

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

--- a/rarefaction.single.xml	Tue Sep 05 17:07:42 2017 -0400
+++ b/rarefaction.single.xml	Tue Mar 20 22:07:50 2018 -0400
@@ -7,38 +7,38 @@
     <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 'rarefaction.single(
-            #if $otu.is_of_type("mothur.rabund"):
-                rabund=otu.dat,
-            #elif $otu.is_of_type("mothur.sabund"):
-                sabund=otu.dat,
-            #elif $otu.is_of_type("mothur.shared"):
-                shared=otu.dat,
-            #elif $otu.is_of_type("mothur.list"):
-                list=otu.dat,
-            #end if
-            #if $label:
-                label=${ str($label).replace(",","-") },
-            #end if
-            calc=${ str($calc).replace(",","-") },
-            abund=$abund,
-            iters=$iters,
-            freq=$freq,
-            processors='\${GALAXY_SLOTS:-8}'
-        )'
-        | sed 's/ //g'  ## mothur trips over whitespace
-        | mothur
-        | tee mothur.out.log
+echo 'rarefaction.single(
+    #if $otu.is_of_type("mothur.rabund"):
+        rabund=otu.dat,
+    #elif $otu.is_of_type("mothur.sabund"):
+        sabund=otu.dat,
+    #elif $otu.is_of_type("mothur.shared"):
+        shared=otu.dat,
+    #elif $otu.is_of_type("mothur.list"):
+        list=otu.dat,
+    #end if
+    #if $label:
+        label=${ str($label).replace(",","-") },
+    #end if
+    calc=${ str($calc).replace(",","-") },
+    abund=$abund,
+    iters=$iters,
+    freq=$freq,
+    processors='\${GALAXY_SLOTS:-8}'
+)'
+| sed 's/ //g'  ## mothur trips over whitespace
+| mothur
+| tee mothur.out.log
 
-        ## rename output from sobs calculator to be consistent with others
-        #if 'sobs' in str($calc).split(','):
-            && mv otu\.*rarefaction otu.r_sobs
-        #end if
+## rename output from sobs calculator to be consistent with others
+#if 'sobs' in str($calc).split(','):
+    && mv otu\.*rarefaction otu.r_sobs
+#end if
     ]]></command>
     <inputs>
         <param name="otu" type="data" format="mothur.list,mothur.rabund,mothur.sabund,mothur.shared" label="list,rabund,sabund,shared - OTU List"/>
@@ -65,6 +65,7 @@
         <param name="abund" type="integer" value="10" min="0" label="abund - ACE Estimator threshold for abundant versus rare OTUs"/>
         <param name="iters" type="integer" value="1000" min="0" label="iters - Number of randomizations"/>
         <param name="freq" type="float" value="100" min="0" max="100" label="freq - Reporting frequency" help="if between 0 and 1 the fraction of sequences to sample, if greater than one - report every n iterations"/>
+        <expand macro="param-savelog"/>
     </inputs>
     <outputs>
         <expand macro="logfile-output"/>
@@ -78,6 +79,7 @@
             <output_collection name="rarefactioncurves" count="1">
                 <element name="sobs" md5="c4c1f1970edf87ea5103e0704130f079" ftype="tabular"/>
             </output_collection>
+            <param name="savelog" value="true"/>
             <expand macro="logfile-test"/>
         </test>
         <test><!-- test with all calculators and subset of labels -->
@@ -87,11 +89,11 @@
             <output_collection name="rarefactioncurves" count="15">
                 <element name="simpson" md5="8d6b7ad9a68c30c882e93b17d343042a" ftype="tabular"/>
             </output_collection>
+            <param name="savelog" value="true"/>
             <expand macro="logfile-test"/>
         </test>
     </tests>
-    <help>
-<![CDATA[
+    <help><![CDATA[
 
 @MOTHUR_OVERVIEW@
 
@@ -100,7 +102,7 @@
 The rarefaction.single_ command generates intra-sample rarefaction curves using a re-sampling without replacement approach. Rarefaction curves provide a way of comparing the richness observed in different samples.  For calc parameter choices see: https://www.mothur.org/wiki/Calculators
 
 .. _rarefaction.single: https://www.mothur.org/wiki/Rarefaction.single
-]]>
-    </help>
+
+    ]]></help>
     <expand macro="citations"/>
 </tool>