diff trim.flows.xml @ 2:9d48c9a47566 draft

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

--- a/trim.flows.xml	Tue Sep 05 16:54:21 2017 -0400
+++ b/trim.flows.xml	Tue Mar 20 22:00:16 2018 -0400
@@ -7,41 +7,42 @@
     <expand macro="stdio"/>
     <expand macro="version_command"/>
     <command><![CDATA[
-        @SHELL_OPTIONS@
+@SHELL_OPTIONS@
 
-        ## create symlinks to input datasets
-        ln -s "$flow" flow.dat &&
-        #if $oligo.add == "yes":
-            ln -s "$oligo.oligos" oligo.oligos.dat &&
-        #end if
+## create symlinks to input datasets
+ln -s '$flow' flow.dat &&
+#if $oligo.add == "yes":
+    ln -s '$oligo.oligos' oligo.oligos.dat &&
+#end if
 
-        echo 'trim.flows(
-            flow=flow.dat,
-            minflows=$minflows,
-            maxflows=$maxflows,
-            #if $maxhomop:
-                maxhomop=$maxhomop,
-            #end if
-            order=$order,
-            signal=$signal,
-            noise=$noise,
-            #if $oligo.add == "yes":
-                oligos=oligo.oligos.dat,
-                bdiffs=$oligo.bdiffs,
-                pdiffs=$oligo.pdiffs,
-                tdiffs=$oligo.tdiffs,
-                ldiffs=$oligo.ldiffs,
-                sdiffs=$oligo.sdiffs,
-            #end if
-            fasta=$fasta,
-            processors='\${GALAXY_SLOTS:-8}'
-        )'
-        | sed 's/ //g'  ## mothur trips over whitespace
-        | mothur
-        | tee mothur.out.log
-        ## prevent these two files from being gathered into collection
-        && mv flow.trim.flow flow.trim
-        && mv flow.scrap.flow flow.scrap
+echo 'trim.flows(
+    flow=flow.dat,
+    minflows=$minflows,
+    maxflows=$maxflows,
+    #if $maxhomop:
+        maxhomop=$maxhomop,
+    #end if
+    order=$order,
+    signal=$signal,
+    noise=$noise,
+    #if $oligo.add == "yes":
+        oligos=oligo.oligos.dat,
+        bdiffs=$oligo.bdiffs,
+        pdiffs=$oligo.pdiffs,
+        tdiffs=$oligo.tdiffs,
+        ldiffs=$oligo.ldiffs,
+        sdiffs=$oligo.sdiffs,
+    #end if
+    fasta=$fasta,
+    processors='\${GALAXY_SLOTS:-8}'
+)'
+| sed 's/ //g'  ## mothur trips over whitespace
+| mothur
+| tee mothur.out.log
+
+## prevent these two files from being gathered into collection
+&& mv flow.trim.flow flow.trim
+&& mv flow.scrap.flow flow.scrap
     ]]></command>
     <inputs>
         <param name="flow" type="data" format="mothur.sff.flow" label="flow - flowgram data" help="Use sffinfo to generate flow data from an sff file"/>
@@ -71,6 +72,7 @@
             <option value="I"> I </option>
         </param>
         <param name="fasta" type="boolean" truevalue="true" falsevalue="false" checked="false" label="fasta - translate the flowgram data to fasta sequence format"/>
+        <expand macro="param-savelog"/>
     </inputs>
     <outputs>
         <expand macro="logfile-output"/>
@@ -95,6 +97,7 @@
                     <has_text text="flow"/>
                 </assert_contents>
             </output>
+            <param name="savelog" value="true"/>
             <expand macro="logfile-test"/>
         </test>
         <test><!-- test with oligos file and fasta output -->
@@ -116,11 +119,11 @@
                 <element name="F003D006" md5="5ea6613d7aa26f87ca9b983152e14a4b" ftype="mothur.sff.flow"/>
             </output_collection>
             <output name="flow_fasta" md5="0725967a9ed731c049d48ea876b0e308" ftype="fasta"/>
+            <param name="savelog" value="true"/>
             <expand macro="logfile-test"/>
         </test>
     </tests>
-    <help>
-<![CDATA[
+    <help><![CDATA[
 
 @MOTHUR_OVERVIEW@
 
@@ -130,7 +133,6 @@
 
 .. _trim.flows: https://www.mothur.org/wiki/Trim.flows
 
-]]>
-    </help>
+    ]]></help>
     <expand macro="citations"/>
 </tool>