diff chimera.perseus.xml @ 2:1dab91d5c40e draft

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

--- a/chimera.perseus.xml	Tue Sep 05 16:52:09 2017 -0400
+++ b/chimera.perseus.xml	Tue Mar 20 22:27:06 2018 -0400
@@ -7,41 +7,43 @@
     <expand macro="stdio"/>
     <expand macro="version_command"/>
     <command><![CDATA[
-        @SHELL_OPTIONS@
+@SHELL_OPTIONS@
 
-        ## create symlinks to input datasets
-        ln -s "$fasta" fasta.dat &&
-        ln -s "$name" name.dat &&
-        ln -s "$group" group.dat &&
+## create symlinks to input datasets
+ln -s '$fasta' fasta.dat &&
+ln -s '$name' name.dat &&
+ln -s '$group' group.dat &&
 
-        echo 'chimera.perseus(
-            fasta=fasta.dat,
-            #if $name.is_of_type("mothur.names"):
-                name=name.dat,
-            #elif $name.is_of_type("mothur.count_table"):
-                count=name.dat,
-            #end if
-            #if $group:
-                group=group.dat,
-            #end if
-            alpha=$alpha,
-            beta=$beta,
-            cutoff=$cutoff,
-            dereplicate=$dereplicate,
-            processors='\${GALAXY_SLOTS:-8}'
-        )'
-        | sed 's/ //g'  ## mothur trips over whitespace
-        | mothur
-        | tee mothur.out.log
+echo 'chimera.perseus(
+    fasta=fasta.dat,
+    #if $name.is_of_type("mothur.names"):
+        name=name.dat,
+    #elif $name.is_of_type("mothur.count_table"):
+        count=name.dat,
+    #end if
+    #if $group:
+        group=group.dat,
+    #end if
+    alpha=$alpha,
+    beta=$beta,
+    cutoff=$cutoff,
+    dereplicate=$dereplicate,
+    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 - Candiate Aligned Sequences"/>
-        <param name="name" type="data" format="mothur.names,mothur.count_table" label="name - Names or count_table"/>
-        <param name="group" type="data" format="mothur.groups" optional="true" label="group - Sequences Name reference"/>
-        <param name="alpha" type="float" value="-5.54" label="alpha" help="The default is -5.54"/>
-        <param name="beta" type="float" value="0.33" label="beta" help="The default is 0.33"/>
-        <param name="cutoff" type="float" value="0.50" label="cutoff" help="The default is 0.50"/>
-        <param name="dereplicate" type="boolean" falsevalue="false" truevalue="true" checked="false" label="dereplicate - remove chimeric sequences from all groups" help="If parameter is false, then if one group finds the seqeunce to be chimeric, then all groups find it to be chimeric. default=false"/>
+        <param argument="fasta" type="data" format="mothur.align" label="fasta - Candiate Aligned Sequences"/>
+        <param argument="name" type="data" format="mothur.names,mothur.count_table" label="name - Names or count_table"/>
+        <param argument="group" type="data" format="mothur.groups" optional="true" label="group - Sequences Name reference"/>
+        <param argument="alpha" type="float" value="-5.54" label="alpha" help="The default is -5.54"/>
+        <param argument="beta" type="float" value="0.33" label="beta" help="The default is 0.33"/>
+        <param argument="cutoff" type="float" value="0.50" label="cutoff" help="The default is 0.50"/>
+        <param argument="dereplicate" type="boolean" falsevalue="false" truevalue="true" checked="false" label="dereplicate - remove chimeric sequences from all groups"
+            help="If parameter is false, then if one group finds the seqeunce to be chimeric, then all groups find it to be chimeric. default=false"/>
+        <expand macro="param-savelog"/>
     </inputs>
     <outputs>
         <expand macro="logfile-output"/>
@@ -53,12 +55,12 @@
             <param name="fasta" value="amazon.fasta" ftype="fasta"/>
             <param name="name" value="amazon1.names" ftype="mothur.names"/>
             <output name="out_chimeras" md5="bcd513127321a32035764a2087c23528" ftype="tabular"/>
+            <param name="savelog" value="true"/>
             <expand macro="logfile-test"/>
         </test>
         <!-- TODO: find/create test dataset with chimera present -->
     </tests>
-    <help>
-<![CDATA[
+    <help><![CDATA[
 
 @MOTHUR_OVERVIEW@
 
@@ -68,7 +70,6 @@
 
 .. _chimera.perseus: https://www.mothur.org/wiki/Chimera.perseus
 
-]]>
-    </help>
+    ]]></help>
     <expand macro="citations"/>
 </tool>