diff chimera.bellerophon.xml @ 2:d8fdd5448cda draft

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

--- a/chimera.bellerophon.xml	Tue Sep 05 17:15:47 2017 -0400
+++ b/chimera.bellerophon.xml	Tue Mar 20 22:07:34 2018 -0400
@@ -7,45 +7,48 @@
     <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 'chimera.bellerophon(
-            fasta=fasta.dat,
-            filter=$filter,
-            correction=$correction,
-            #if int($window) > 0:
-                window=$window,
-            #end if
-            #if $increment:
-                increment=$increment,
-            #end if
-            processors='\${GALAXY_SLOTS:-8}'
-        )'
-        | sed 's/ //g'  ## mothur trips over whitespace
-        | mothur
-        | tee mothur.out.log
+echo 'chimera.bellerophon(
+    fasta=fasta.dat,
+    filter=$filter,
+    correction=$correction,
+    #if int($window) > 0:
+        window=$window,
+    #end if
+    #if $increment:
+        increment=$increment,
+    #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="fasta" label="fasta - Candiate Sequences"/>
-        <param name="filter" type="boolean" falsevalue="False" truevalue="True" checked="false" label="filter - Apply a 50% soft vertical filter"/>
-        <param name="correction" type="boolean" falsevalue="False" truevalue="True" checked="true" label="correction - Use the square root of the distances instead of the distance value"/>
-        <param name="window" type="integer" value="0" label="window - Length of sequence you want in each window analyzed (uses default if &lt; 1)" help="Default is 25% of the sequence length."/>
-        <param name="increment" type="integer" value="25" min="0" label="increment - Increment for window slide on each iteration" help="Default is 25, but you may set it up to sequence length minus twice the window."/>
+        <param argument="fasta" type="data" format="fasta" label="fasta - Candiate Sequences"/>
+        <param argument="filter" type="boolean" falsevalue="False" truevalue="True" checked="false" label="filter - Apply a 50% soft vertical filter"/>
+        <param argument="correction" type="boolean" falsevalue="False" truevalue="True" checked="true" label="correction - Use the square root of the distances instead of the distance value"/>
+        <param argument="window" type="integer" value="0" label="window - Length of sequence you want in each window analyzed"
+            help="Default is 25% of the sequence length. Uses default if &lt; 1"/>
+        <param argument="increment" type="integer" value="25" min="0" label="increment - Increment for window slide on each iteration"
+            help="Default is 25, but you may set it up to sequence length minus twice the window."/>
+        <expand macro="param-savelog"/>
     </inputs>
     <outputs>
         <expand macro="logfile-output"/>
-        <data name="out_file" format="txt" from_work_dir="fasta.bellerophon.chimeras" label="${tool.name} on ${on_string}: bellerophon.chimeras"/>
-        <data name="out_accnos" format="mothur.accnos" from_work_dir="fasta.bellerophon.accnos" label="${tool.name} on ${on_string}: bellerophon.accnos"/>
+        <data name="bellerophon.chimeras" format="txt" from_work_dir="fasta.bellerophon.chimeras" label="${tool.name} on ${on_string}: bellerophon.chimeras"/>
+        <data name="bellerophon.accnos" format="mothur.accnos" from_work_dir="fasta.bellerophon.accnos" label="${tool.name} on ${on_string}: bellerophon.accnos"/>
     </outputs>
     <tests>
         <test>
             <param name="fasta" value="Mock_S280_L001_R1_001_small.trim.contigs.good.fasta"/>
             <param name="window" value="-1"/> <!-- don't use window if negative -->
-            <output name="out_file" md5="435ff11d15d6c117e29747ab8ac36c75" ftype="txt"/>
-            <output name="out_accnos" ftype="mothur.accnos" file="Mock_S280_L001_R1_001_small.trim.contigs.good.bellerophon.accnos"/>
+            <output name="bellerophon.chimeras" md5="435ff11d15d6c117e29747ab8ac36c75" ftype="txt"/>
+            <output name="bellerophon.accnos" ftype="mothur.accnos" file="Mock_S280_L001_R1_001_small.trim.contigs.good.bellerophon.accnos"/>
             <output name="logfile" ftype="txt"> <!-- outputs some results to the log file -->
                 <assert_contents>
                     <has_text text="Minimum"/>
@@ -53,11 +56,11 @@
                     <has_text text="Maximum"/>
                 </assert_contents>
             </output>
+            <param name="savelog" value="true"/>
             <expand macro="logfile-test"/>
         </test>
     </tests>
-    <help>
-<![CDATA[
+    <help><![CDATA[
 
 @MOTHUR_OVERVIEW@
 
@@ -84,7 +87,6 @@
 .. _bellerophon: http://comp-bio.anu.edu.au/Bellerophon/doc/doc.html
 .. _chimera.bellerophon: https://www.mothur.org/wiki/Chimera.bellerophon
 
-]]>
-    </help>
+    ]]></help>
     <expand macro="citations"/>
 </tool>