diff get.lineage.xml @ 2:c5034189eb03 draft

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

--- a/get.lineage.xml	Tue Sep 05 17:11:46 2017 -0400
+++ b/get.lineage.xml	Tue Mar 20 22:27:20 2018 -0400
@@ -7,63 +7,63 @@
     <expand macro="stdio"/>
     <expand macro="version_command"/>
     <command><![CDATA[
-        @SHELL_OPTIONS@
+@SHELL_OPTIONS@
 
-        #import re
-        ## create symlinks to input datasets
-        ln -s "$file.taxonomy" file.taxonomy.dat &&
-        #if $file.filetype == "useconstaxonomy":
-            ln -s "$file.shared" file.shared.dat &&
-            ln -s "$file.list" file.list.dat &&
-        #end if
-        ln -s "$fasta_in" fasta_in.dat &&
-        ln -s "$group_in" group_in.dat &&
-        ln -s "$alignreport_in" alignreport_in.dat &&
-        ln -s "$list_in" list_in.dat &&
-        ln -s "$name_in" name_in.dat &&
-        ln -s "$count" count.dat &&
+#import re
+## create symlinks to input datasets
+ln -s '$file.taxonomy' file.taxonomy.dat &&
+#if $file.filetype == "useconstaxonomy":
+    ln -s '$file.shared' file.shared.dat &&
+    ln -s '$file.list' file.list.dat &&
+#end if
+ln -s '$fasta_in' fasta_in.dat &&
+ln -s '$group_in' group_in.dat &&
+ln -s '$alignreport_in' alignreport_in.dat &&
+ln -s '$list_in' list_in.dat &&
+ln -s '$name_in' name_in.dat &&
+ln -s '$count' count.dat &&
 
-        echo 'get.lineage(
-            #if $file.filetype == "usetaxonomy":
-                taxonomy=file.taxonomy.dat
-            #else
-                constaxonomy=file.taxonomy.dat
-                #if $file.shared:
-                    ,shared=file.shared.dat
-                #end if
-                #if $file.list:
-                    ,list=file.list.dat
-                #end if
-            #end if
-            #if $file.taxons:
-                #set taxonstring=str($file.taxons).replace(",","-")
-                ,taxon='"'$re.sub("(\s|,)+",",",$re.sub("\(\d+\)","", $taxonstring ))'"'
-            #elif $taxon:
-                ,taxon='"'$re.sub("(\s|,)+",",",$re.sub("\(\d+\)","", $taxon.value )).replace(",","-")'"'
-            #end if
-            #if $fasta_in:
-                ,fasta=fasta_in.dat
-            #end if
-            #if $group_in:
-                ,group=group_in.dat
-            #end if
-            #if $alignreport_in:
-                ,alignreport=alignreport_in.dat
-            #end if
-            #if $list_in:
-                ,list=list_in.dat
-            #end if
-            #if $name_in:
-                ,name=name_in.dat
-                ,dups=$dups
-            #end if
-            #if $count:
-                ,count=count.dat
-            #end if
-        )'
-        | sed 's/ //g'  ## mothur trips over whitespace
-        | mothur
-        | tee mothur.out.log
+echo 'get.lineage(
+    #if $file.filetype == "usetaxonomy":
+        taxonomy=file.taxonomy.dat
+    #else
+        constaxonomy=file.taxonomy.dat
+        #if $file.shared:
+            ,shared=file.shared.dat
+        #end if
+        #if $file.list:
+            ,list=file.list.dat
+        #end if
+    #end if
+    #if $file.taxons:
+        #set taxonstring=str($file.taxons).replace(",","-")
+        ,taxon='"'$re.sub("(\s|,)+",",",$re.sub("\(\d+\)","", $taxonstring ))'"'
+    #elif $taxon:
+        ,taxon='"'$re.sub("(\s|,)+",",",$re.sub("\(\d+\)","", $taxon.value )).replace(",","-")'"'
+    #end if
+    #if $fasta_in:
+        ,fasta=fasta_in.dat
+    #end if
+    #if $group_in:
+        ,group=group_in.dat
+    #end if
+    #if $alignreport_in:
+        ,alignreport=alignreport_in.dat
+    #end if
+    #if $list_in:
+        ,list=list_in.dat
+    #end if
+    #if $name_in:
+        ,name=name_in.dat
+        ,dups=$dups
+    #end if
+    #if $count:
+        ,count=count.dat
+    #end if
+)'
+| sed 's/ //g'  ## mothur trips over whitespace
+| mothur
+| tee mothur.out.log
     ]]></command>
     <inputs>
         <conditional name="file">
@@ -91,7 +91,8 @@
                 </param>
             </when>
             <when value="useconstaxonomy">
-                <param name="taxonomy" type="data" format="mothur.cons.taxonomy" label="constaxonomy - Constaxonomy file. Provide either a constaxonomy file or a taxonomy file" help="please make sure your file has no quotation marks in it"/>
+                <param name="taxonomy" type="data" format="mothur.cons.taxonomy" label="constaxonomy - Constaxonomy file. Provide either a constaxonomy file or a taxonomy file"
+                    help="please make sure your file has no quotation marks in it"/>
                 <param name="taxons" type="select" size="120" optional="true" multiple="true" label="Browse Taxons from Taxonomy">
                     <options from_dataset="taxonomy">
                         <column name="name" index="2"/>
@@ -112,14 +113,17 @@
                 <param name="list" type="data" format="mothur.list" optional="true" label="list - list file"/>
             </when>
         </conditional>
-        <param name="taxon" type="text" area="True" size="5x120" label="taxon - Manually select Taxons for filtering" help="If no taxons selected from file, Enter 1 or more taxons separated by dashes here, e.g. Bacteria;Firmicutes;-Bacteria;Actinobacteria; "/>
+        <param name="taxon" type="text" area="True" size="5x120" label="taxon - Manually select Taxons for filtering"
+            help="If no taxons selected from file, Enter 1 or more taxons separated by dashes here, e.g. Bacteria;Firmicutes;-Bacteria;Actinobacteria; "/>
         <param name="fasta_in" type="data" format="fasta" optional="true" label="fasta - Fasta Sequences"/>
         <param name="group_in" type="data" format="mothur.groups" optional="true" label="group - Groups"/>
         <param name="alignreport_in" type="data" format="mothur.align.report" optional="true" label="alignreport - Align Report"/>
         <param name="list_in" type="data" format="mothur.list" optional="true" label="list - OTU List"/>
         <param name="name_in" type="data" format="mothur.names" optional="true" label="name - Sequences Name reference"/>
         <param name="dups" type="boolean" truevalue="true" falsevalue="false" checked="true" label="dups - Apply to duplicate names"/>
-        <param name="count" type="data" format="mothur.count_table" optional="true" help="The count file is similar to the name file in that it is used to represent the number of duplicate sequences for a given representative sequence. It can also contain group information"/>
+        <param name="count" type="data" format="mothur.count_table" optional="true"  label="Count Table"
+            help="The count file is similar to the name file in that it is used to represent the number of duplicate sequences for a given representative sequence. It can also contain group information"/>
+        <expand macro="param-savelog"/>
     </inputs>
     <outputs>
         <expand macro="logfile-output"/>
@@ -185,8 +189,7 @@
             <output name="taxonomy_out" md5="0ea2511f40073a95c0812268da0cf727"/>
         </test>
     </tests>
-    <help>
-<![CDATA[
+    <help><![CDATA[
 
 @MOTHUR_OVERVIEW@
 
@@ -201,7 +204,6 @@
 .. _align.report: https://www.mothur.org/wiki/Align.seqs
 .. _get.lineage: https://www.mothur.org/wiki/Get.lineage
 
-]]>
-    </help>
+    ]]></help>
     <expand macro="citations"/>
 </tool>