diff primer.design.xml @ 2:fb7c0871d8af draft

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

--- a/primer.design.xml	Tue Sep 05 17:10:26 2017 -0400
+++ b/primer.design.xml	Tue Mar 20 22:03:11 2018 -0400
@@ -7,43 +7,43 @@
     <expand macro="stdio"/>
     <expand macro="version_command"/>
     <command><![CDATA[
-        @SHELL_OPTIONS@
+@SHELL_OPTIONS@
 
-        ## create symlinks to input datasets
-        ln -s "$fasta" fasta.dat &&
-        ln -s "$otu" otu.dat &&
-        ln -s "$name" name.dat &&
-        ln -s "$count" count.dat &&
+## create symlinks to input datasets
+ln -s '$fasta' fasta.dat &&
+ln -s '$otu' otu.dat &&
+ln -s '$name' name.dat &&
+ln -s '$count' count.dat &&
 
-        echo 'primer.design(
-            fasta=fasta.dat,
-            list=otu.dat,
-            #if $label:
-                label=$label,
-            #end if
-                otulabel=$otulabel,
-            #if $name:
-                name=name.dat,
-            #end if
-            #if $count:
-                count=count.dat,
-            #end if
-            #if $cutoff:
-                cutoff=$cutoff,
-            #end if
-            #if $mintm:
-                mintm=$mintm,
-            #end if
-            #if $maxtm:
-                maxtm=$maxtm,
-            #end if
-            pdiffs=$pdiffs,
-            length=$length,
-            processors='\${GALAXY_SLOTS:-8}'
-        )'
-        | sed 's/ //g'  ## mothur trips over whitespace
-        | mothur
-        | tee mothur.out.log
+echo 'primer.design(
+    fasta=fasta.dat,
+    list=otu.dat,
+    #if $label:
+        label=$label,
+    #end if
+        otulabel=$otulabel,
+    #if $name:
+        name=name.dat,
+    #end if
+    #if $count:
+        count=count.dat,
+    #end if
+    #if $cutoff:
+        cutoff=$cutoff,
+    #end if
+    #if $mintm:
+        mintm=$mintm,
+    #end if
+    #if $maxtm:
+        maxtm=$maxtm,
+    #end if
+    pdiffs=$pdiffs,
+    length=$length,
+    processors='\${GALAXY_SLOTS:-8}'
+)'
+| sed 's/ //g'  ## mothur trips over whitespace
+| mothur
+| tee mothur.out.log
     ]]></command>
     <inputs>
         <param name="fasta" type="data" format="mothur.align" label="fasta - provide aligned fasta file"/>
@@ -63,6 +63,7 @@
         <param name="mintm" type="integer" value="" optional="true" label="mintm - indicate minimum melting temperature" help=""/>
         <param name="maxtm" type="integer" value="" optional="true" label="maxtm - indicate maximum melting temperature" help=""/>
         <param name="cutoff" type="integer" value="" optional="true" min="0" max="100" label="cutoff - set a percentage of sequences that support the base" help="For example: cutoff=97 would only return a sequence that only showed ambiguities for bases that were not supported by at least 97% of sequences."/>
+        <expand macro="param-savelog"/>
     </inputs>
     <outputs>
         <expand macro="logfile-output"/>
@@ -79,11 +80,11 @@
             <output name="fasta_out" md5="a5c8c17814f02124194dba2e37f566c7" ftype="mothur.align"/>
             <output name="summary_out" md5="8dd341c49c26c6d0f8026b34cb7bc925" ftype="tabular"/>
             <output name="list_out" md5="0a73804f3d48c668b4dab85c76d2c767" ftype="mothur.list"/>
+            <param name="savelog" value="true"/>
             <expand macro="logfile-test"/>
         </test>
     </tests>
-    <help>
-<![CDATA[
+    <help><![CDATA[
 
 @MOTHUR_OVERVIEW@
 
@@ -93,8 +94,7 @@
 
 .. _primer.design: https://www.mothur.org/wiki/Primer.design
 
-]]>
-    </help>
+    ]]></help>
     <citations>
         <citation type="doi">10.1128/AEM.01541-09</citation>
     </citations>