diff trim.seqs.xml @ 2:baa3df51e2b7 draft

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

--- a/trim.seqs.xml	Tue Sep 05 17:02:03 2017 -0400
+++ b/trim.seqs.xml	Tue Mar 20 21:56:31 2018 -0400
@@ -7,64 +7,65 @@
     <expand macro="stdio"/>
     <expand macro="version_command"/>
     <command><![CDATA[
-        @SHELL_OPTIONS@
+@SHELL_OPTIONS@
 
-        ## create symlinks to input datasets
-        ln -s "$fasta" fasta.dat &&
-        ln -s "$names" names.dat &&
-        ln -s "$count" count.dat &&
-        #if $oligo.add == "yes":
-            ln -s "$oligo.oligos" oligo.oligos.dat &&
-        #end if
-        #if $qual.add2 == "yes":
-            ln -s "$qual.qfile" qual.qfile.dat &&
-        #end if
+## create symlinks to input datasets
+ln -s '$fasta' fasta.dat &&
+ln -s '$names' names.dat &&
+ln -s '$count' count.dat &&
+#if $oligo.add == "yes":
+    ln -s '$oligo.oligos' oligo.oligos.dat &&
+#end if
+#if $qual.add2 == "yes":
+    ln -s '$qual.qfile' qual.qfile.dat &&
+#end if
 
-        echo 'trim.seqs(
-            fasta=fasta.dat,
-            minlength=$minlength,
-            maxlength=$maxlength,
-            maxambig=$maxambig,
-            maxhomop=$maxhomop,
-            keepfirst=$keepfirst,
-            removelast=$removelast,
-            #if $oligo.add == "yes":
-                oligos=oligo.oligos.dat,
-                bdiffs=$oligo.bdiffs,
-                pdiffs=$oligo.pdiffs,
-                tdiffs=$oligo.tdiffs,
-                ldiffs=$oligo.ldiffs,
-                sdiffs=$oligo.sdiffs,
-                keepforward=$oligo.keepforward,
-                allfiles=$oligo.allfiles,
-            #end if
-            #if $qual.add2 == "yes":
-                qfile=qual.qfile.dat,
-                qaverage=$qual.qaverage,
-                qthreshold=$qual.qthreshold,
-                qwindowaverage=$qual.qwindowaverage,
-                qwindowsize=$qual.qwindowsize,
-                rollaverage=$qual.rollaverage,
-                qstepsize=$qual.qstepsize,
-                qtrim=$qual.qtrim,
-            #end if
-            flip=$flip,
-            #if $names:
-                name=names.dat,
-            #end if
-            logtransform=$logtransform,
-            checkorient=$checkorient,
-            #if $count:
-                count=count.dat,
-            #end if
-            processors='\${GALAXY_SLOTS:-8}'
-        )'
-        | sed 's/ //g'  ## mothur trips over whitespace
-        | mothur
-        | tee mothur.out.log
-        ## prevent these two files from being gathered into collection
-        && mv fasta.trim.fasta fasta.trim
-        && mv fasta.scrap.fasta fasta.scrap
+echo 'trim.seqs(
+    fasta=fasta.dat,
+    minlength=$minlength,
+    maxlength=$maxlength,
+    maxambig=$maxambig,
+    maxhomop=$maxhomop,
+    keepfirst=$keepfirst,
+    removelast=$removelast,
+    #if $oligo.add == "yes":
+        oligos=oligo.oligos.dat,
+        bdiffs=$oligo.bdiffs,
+        pdiffs=$oligo.pdiffs,
+        tdiffs=$oligo.tdiffs,
+        ldiffs=$oligo.ldiffs,
+        sdiffs=$oligo.sdiffs,
+        keepforward=$oligo.keepforward,
+        allfiles=$oligo.allfiles,
+    #end if
+    #if $qual.add2 == "yes":
+        qfile=qual.qfile.dat,
+        qaverage=$qual.qaverage,
+        qthreshold=$qual.qthreshold,
+        qwindowaverage=$qual.qwindowaverage,
+        qwindowsize=$qual.qwindowsize,
+        rollaverage=$qual.rollaverage,
+        qstepsize=$qual.qstepsize,
+        qtrim=$qual.qtrim,
+    #end if
+    flip=$flip,
+    #if $names:
+        name=names.dat,
+    #end if
+    logtransform=$logtransform,
+    checkorient=$checkorient,
+    #if $count:
+        count=count.dat,
+    #end if
+    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 fasta.trim.fasta fasta.trim
+&& mv fasta.scrap.fasta fasta.scrap
     ]]></command>
     <inputs>
         <param name="fasta" type="data" format="fasta" label="fasta - Sequences"/>
@@ -113,6 +114,7 @@
         <param name="count" type="data" format="mothur.count_table" optional="true" label="count - a 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. If you run trim.seqs with an oligos file that contains group labels, trim.seqs will create a new *.trim.count_table with the group information included. "/>
         <param name="logtransform" type="boolean" truevalue="true" falsevalue="false" checked="false" label="logtransform" help="allows you to indicate you want the averages for the qwindowaverage, rollaverage and qaverage to be calculated using a logtransform."/>
         <param name="checkorient" type="boolean" truevalue="true" falsevalue="false" checked="false" label="checkorient - search the reverse complement?" help="If you are running the trim.seqs command with paired barcodes or primers, you can use the checkorient parameter. When checkorient=t and mothur can't find the barcodes and primers, it will search the reverse compliment. "/>
+        <expand macro="param-savelog"/>
     </inputs>
     <outputs>
         <expand macro="logfile-output"/>
@@ -157,6 +159,7 @@
             <output name="scrap_fasta" md5="4f791b7684662f1f962970af46429e24" ftype="fasta"/>
             <output name="trim_names" md5="1b8c6c47052bb69524ef56ebb764fb8f" ftype="mothur.names"/>
             <output name="scrap_names" md5="80f9252837e4b189f06ec00469b88e85" ftype="mothur.names"/>
+            <param name="savelog" value="true"/>
             <expand macro="logfile-test"/>
         </test>
         <test><!-- test with count table -->
@@ -167,6 +170,7 @@
             <output name="scrap_fasta" md5="4f791b7684662f1f962970af46429e24" ftype="fasta"/>
             <output name="trim_count" md5="836b4d72a8cda3741ef435741783b384" ftype="mothur.count_table"/>
             <output name="scrap_count" md5="04ae9f50c1b6f0d8d7e1ac28f845dd4c" ftype="mothur.count_table"/>
+            <param name="savelog" value="true"/>
             <expand macro="logfile-test"/>
         </test>
         <test><!-- test with oligos -->
@@ -178,6 +182,7 @@
             <output name="trim_fasta" md5="75a8a3ae2d1fe1ff2b860480b84e9bd6" ftype="fasta"/>
             <output name="scrap_fasta" md5="c4fd14e70ab7d1c21d238e87624829d7" ftype="fasta"/>
             <output name="groups_file" md5="198957282c234e825414e175d926046a" ftype="mothur.groups"/>
+            <param name="savelog" value="true"/>
             <expand macro="logfile-test"/>
         </test>
         <test><!-- test with oligos and allfiles parameter -->
@@ -195,6 +200,7 @@
             <output_collection name="fasta_allfiles" count="9">
                 <element name="F003D144" md5="025ff271ac24ecb898863d7fcbfabf10" ftype="fasta"/>
             </output_collection>
+            <param name="savelog" value="true"/>
             <expand macro="logfile-test"/>
         </test>
         <test><!-- test with qfile-->
@@ -206,11 +212,11 @@
             <output name="scrap_fasta" md5="a4d3ef3d91b4c0146ec84bb7aad3987c" ftype="fasta"/>
             <output name="trim_qual" md5="3d4e2d3c7dd43b90660ab9c923d9eab1" ftype="qual454"/>
             <output name="scrap_qual" md5="22931236d082c2b77811bbf912c1f4b1" ftype="qual454"/>
+            <param name="savelog" value="true"/>
             <expand macro="logfile-test"/>
         </test>
     </tests>
-    <help>
-<![CDATA[
+    <help><![CDATA[
 
 @MOTHUR_OVERVIEW@
 
@@ -220,7 +226,6 @@
 
 .. _trim.seqs: https://www.mothur.org/wiki/Trim.seqs
 
-]]>
-    </help>
+    ]]></help>
     <expand macro="citations"/>
 </tool>