diff filter.seqs.xml @ 3:3ced7f00e40b draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4

--- a/filter.seqs.xml	Tue Sep 05 16:21:39 2017 -0400
+++ b/filter.seqs.xml	Wed Feb 14 09:40:41 2018 -0500
@@ -7,51 +7,55 @@
     <expand macro="stdio"/>
     <expand macro="version_command"/>
     <command><![CDATA[
-        @SHELL_OPTIONS@
+@SHELL_OPTIONS@
 
-        ## create symlinks to input datasets
-        ln -s "$fasta" fasta.dat &&
-        #for $i in $inputs:
-            ln -s "$i.fasta" fasta${inputs.index($i)}.dat &&
-        #end for
-        ln -s "$hard" hard.dat &&
+## create symlinks to input datasets
+ln -s '$fasta' fasta.dat &&
+#for $i in $inputs:
+    ln -s '$i.fasta' fasta${inputs.index($i)}.dat &&
+#end for
+ln -s '$hard' hard.dat &&
 
-        echo 'filter.seqs(
-            fasta=fasta.dat#for $i in $inputs#-fasta${inputs.index($i)}.dat#end for#,
-            vertical=$vertical,
-            #if $trump:
-                trump=$trump,
-            #end if
-            soft=$soft,
-            #if $hard:
-                hard=hard.dat,
-            #end if
-            processors='\${GALAXY_SLOTS:-8}'
-        )'
-        | sed 's/ //g'  ## mothur trips over whitespace
-        | mothur
-        | tee mothur.out.log &&
+echo 'filter.seqs(
+    fasta=fasta.dat#for $i in $inputs#-fasta${inputs.index($i)}.dat#end for#,
+    vertical=$vertical,
+    #if $trump:
+        trump=$trump,
+    #end if
+    soft=$soft,
+    #if $hard:
+        hard=hard.dat,
+    #end if
+    processors='\${GALAXY_SLOTS:-8}'
+)'
+| sed 's/ //g'  ## mothur trips over whitespace
+| mothur
+| tee mothur.out.log &&
 
-        ## rename collection files for more transparent element naming
-        mv fasta.filter.fasta "${fasta.element_identifier}".filter.fasta
-        #for i in $inputs:
-            && mv fasta${inputs.index($i)}.filter.fasta "${i.fasta.element_identifier}".filter.fasta
-        #end for
+## rename collection files for more transparent element naming
+mv fasta.filter.fasta "${fasta.element_identifier}".filter.fasta
+#for i in $inputs:
+    && mv fasta${inputs.index($i)}.filter.fasta "${i.fasta.element_identifier}".filter.fasta
+#end for
     ]]></command>
     <inputs>
         <param name="fasta" type="data" format="mothur.align" label="fasta - Alignment Fasta"/>
         <repeat name="inputs" title="Additional Alignment File">
             <param name="fasta" type="data" format="mothur.align" label="fasta - Alignment Fasta"/>
         </repeat>
-        <param name="vertical" type="boolean" checked="true" truevalue="true" falsevalue="false" label="vertical - Vertical column" help="Ignore any column that only contains gap characters (i.e. '-' or '.')"/>
-        <param name="trump" type="select" label="trump - Trump character" help="Remove a column if the trump character is found at that position in any sequence of the alignment">
+        <param name="vertical" type="boolean" checked="true" truevalue="true" falsevalue="false" label="vertical - Vertical column"
+            help="Ignore any column that only contains gap characters (i.e. '-' or '.')"/>
+        <param name="trump" type="select" label="trump - Trump character"
+            help="Remove a column if the trump character is found at that position in any sequence of the alignment">
             <option value="">Off</option>
             <option value=".">.</option>
             <option value="-">-</option>
             <option value="N">N</option>
         </param>
-        <param name="soft" type="integer" value="0" min="0" max="100" label="soft - percentage required to retain column. (0-100)" help="Removes any column where the dominant base (i.e. A, T, G, C, or U) does not occur in at least a designated percentage of sequences"/>
-        <param name="hard" type="data" format="mothur.filter" optional="True" label="hard - Hard Column Filter" help="A file should only contain one line consisting of 0's and 1's"/>
+        <param name="soft" type="integer" value="0" min="0" max="100" label="soft - percentage required to retain column. (0-100)"
+            help="Removes any column where the dominant base (i.e. A, T, G, C, or U) does not occur in at least a designated percentage of sequences"/>
+        <param name="hard" type="data" format="mothur.filter" optional="True" label="hard - Hard Column Filter"
+            help="A file should only contain one line consisting of 0's and 1's"/>
     </inputs>
     <outputs>
         <expand macro="logfile-output"/>
@@ -83,20 +87,23 @@
             <expand macro="logfile-test"/>
         </test>
     </tests>
-    <help>
-<![CDATA[
+    <help><![CDATA[
 
 @MOTHUR_OVERVIEW@
 
 **Command Documentation**
 
-The filter.seqs_ command removes columns from alignments based on a criteria defined by the user. For example, alignments generated against reference alignments (e.g. from RDP, SILVA, or greengenes) often have columns where every character is either a '.' or a '-'. These columns are not included in calculating distances because they have no information in them. By removing these columns, the calculation of a large number of distances is accelerated. Also, people also like to mask their sequences to remove variable regions using a soft or hard mask (e.g. Lane's mask). This type of masking is only encouraged for deep-level phylogenetic analysis, not fine level analysis such as that needed with calculating OTUs.
+The filter.seqs_ command removes columns from alignments based on a criteria defined by the user. For example, alignments
+generated against reference alignments (e.g. from RDP, SILVA, or greengenes) often have columns where every character is
+either a '.' or a '-'. These columns are not included in calculating distances because they have no information in them.
+By removing these columns, the calculation of a large number of distances is accelerated. Also, people also like to mask
+their sequences to remove variable regions using a soft or hard mask (e.g. Lane's mask). This type of masking is only
+encouraged for deep-level phylogenetic analysis, not fine level analysis such as that needed with calculating OTUs.
 
 .. _filter.seqs: https://www.mothur.org/wiki/Filter.seqs
 
 v.1.20.0: Updated to Mothur 1.33
 
-]]>
-    </help>
+    ]]></help>
     <expand macro="citations"/>
 </tool>