diff dist.seqs.xml @ 2:189b742d2434 draft

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

--- a/dist.seqs.xml	Tue Sep 05 16:51:56 2017 -0400
+++ b/dist.seqs.xml	Tue Mar 20 22:23:36 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 "$fasta" fasta.dat &&
+## create symlinks to input datasets
+ln -s '$fasta' fasta.dat &&
 
-        echo 'dist.seqs(
-            fasta=fasta.dat,
-            #if $calc:
-                calc=$calc,
-            #end if
-            countends=$countends,
-            #if $cutoff:
-                cutoff=$cutoff,
-            #end if
-            #if $output:
-                output=$output,
-            #end if
-            processors='\${GALAXY_SLOTS:-8}'
-        )'
-        | sed 's/ //g'  ## mothur trips over whitespace
-        | mothur
-        | tee mothur.out.log
+echo 'dist.seqs(
+    fasta=fasta.dat,
+    #if $calc:
+        calc=$calc,
+    #end if
+    countends=$countends,
+    #if $cutoff:
+        cutoff=$cutoff,
+    #end if
+    #if $output:
+        output=$output,
+    #end if
+    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,fasta" label="fasta - Alignment Fasta"/>
@@ -39,12 +39,14 @@
             <option value="eachgap ">eachgap - penalize each gap</option>
         </param>
         <param name="countends" type="boolean" checked="true" truevalue="true" falsevalue="false" label="countends - Penalize terminal gaps"/>
-        <param name="cutoff" type="float" value="" min="0.0" optional="true" label="cutoff - Distance Cutoff threshold - ignored if not > 0" help="Do not save any distances larger than this, a common value would be 0.10"/>
+        <param name="cutoff" type="float" value="" min="0.0" optional="true" label="cutoff - Distance Cutoff threshold - ignored if not > 0"
+            help="Do not save any distances larger than this, a common value would be 0.10"/>
         <param name="output" type="select" label="output - Distance Matrix Output Format" help="">
             <option value="" selected="true">Default Column-Formatted Matrix</option>
             <option value="lt">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"/>
@@ -59,6 +61,7 @@
         <test><!-- test with default params -->
             <param name="fasta" value="HMP_MOCK.v35.align" ftype="mothur.align"/>
             <output name="out_dist" md5="2c4817bb8657b4df2dcb1f2a019f505e" ftype="mothur.pair.dist"/>
+            <param name="savelog" value="true"/>
             <expand macro="logfile-test"/>
         </test>
         <test><!-- test with all params custom -->
@@ -68,11 +71,11 @@
             <param name="cutoff" value="0.3"/>
             <param name="output" value="lt"/>
             <output name="out_dist" md5="8a5ccf1ad8f1c344cf4d3e2c97d4cdc6" ftype="mothur.lower.dist"/>
+            <param name="savelog" value="true"/>
             <expand macro="logfile-test"/>
         </test>
     </tests>
-    <help>
-<![CDATA[
+    <help><![CDATA[
 
 @MOTHUR_OVERVIEW@
 
@@ -86,7 +89,6 @@
 
 v.1.20.0: Updated to Mothur 1.33
 
-]]>
-    </help>
+    ]]></help>
     <expand macro="citations"/>
 </tool>