diff filter.seqs.xml @ 1:74e541cb0f87 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit ea40e3d84e7850eb4226d6c85f709dcad18d4ba9

--- a/filter.seqs.xml	Fri Jun 24 16:30:23 2016 -0400
+++ b/filter.seqs.xml	Thu May 18 18:36:18 2017 -0400
@@ -4,8 +4,11 @@
         <import>macros.xml</import>
     </macros>
     <expand macro="requirements"/>
+    <expand macro="stdio"/>
     <expand macro="version_command"/>
-    <command detect_errors="aggressive"><![CDATA[
+    <command><![CDATA[
+        @SHELL_OPTIONS@
+
         ## create symlinks to input datasets
         ln -s "$fasta" fasta.dat &&
         #for $i in $inputs:
@@ -26,17 +29,18 @@
             processors='\${GALAXY_SLOTS:-8}'
         )'
         | sed 's/ //g'  ## mothur trips over whitespace
-        | mothur &&
+        | mothur
+        | tee mothur.out.log &&
 
         ## rename collection files for more transparent element naming
-        mv fasta.filter.fasta "${fasta.element_identifier}".filter.fasta &&
+        mv fasta.filter.fasta "${fasta.element_identifier}".filter.fasta
         #for i in $inputs:
-            mv fasta${inputs.index($i)}.filter.fasta ${i.fasta.element_identifier}.filter.fasta
+            && mv fasta${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" optional="true">
+        <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 '.')"/>
@@ -54,10 +58,14 @@
         <data name="out_filter" format="mothur.filter" from_work_dir="fasta*.filter" label="${tool.name} on ${on_string}: filter"/>
         <collection name="filteredfastas" type="list" label="${tool.name} on ${on_string}: filtered fastas">
             <discover_datasets pattern="(?P&lt;designation&gt;.*)\.filter\.fasta" format="fasta"/>
+            <filter>inputs</filter> <!-- only output collection if multiple outputs-->
         </collection>
+        <data name="filteredfasta" format="fasta" from_work_dir="*.filter.fasta" label="${tool.name} on ${on_string}: filtered fasta">
+            <filter>not inputs</filter>
+        </data>
     </outputs>
     <tests>
-        <test>
+        <test><!-- test with multiple inputs and collection output -->
             <param name="fasta" value="HMP_MOCK.v35.align" ftype="mothur.align"/>
             <repeat name="inputs">
                 <param name="fasta" value="Mock_S280_L001_R1_001_small.trim.contigs.good.align_head" ftype="mothur.align"/>
@@ -68,17 +76,23 @@
             </output_collection>
             <expand macro="logfile-test"/>
         </test>
+        <test><!-- test with single input and non-collection output -->
+            <param name="fasta" value="HMP_MOCK.v35.align" ftype="mothur.align"/>
+            <output name="out_filter" md5="3e6c2cfef46baf35d2a8b5cafe53e3a4"/>
+            <output name="filteredfasta" md5="ef4c6c2d9a882f7a22e5fa3c814af7cc"/>
+            <expand macro="logfile-test"/>
+        </test>
     </tests>
     <help>
 <![CDATA[
 
 @MOTHUR_OVERVIEW@
 
-**Command Documenation**
+**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.
 
-.. _filter.seqs: http://www.mothur.org/wiki/Filter.seqs
+.. _filter.seqs: https://www.mothur.org/wiki/Filter.seqs
 
 v.1.20.0: Updated to Mothur 1.33