diff tools/mothur/deunique.seqs.xml @ 0:ee4fee239fe7 draft default tip

planemo upload commit 68a4fd4cc5332c57ac39bef73db224425af0706c-dirty

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/mothur/deunique.seqs.xml	Fri Jun 03 09:32:47 2016 -0400
@@ -0,0 +1,97 @@
+<tool profile="16.07" id="mothur_deunique_seqs" name="Deunique.seqs" version="@WRAPPER_VERSION@.0">
+    <description>Return all sequences</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements"/>
+    <expand macro="version_command"/>
+    <command detect_errors="aggressive"><![CDATA[
+         echo 'deunique.seqs(
+            #if $inputtype.intype == "countfile":
+                count=$names,
+            #else
+                name=$names,
+            #end if
+            fasta=$fasta
+        )'
+        | sed 's/ //g'  ## mothur trips over whitespace
+        | mothur &&
+
+        ## move output files to correct destination
+        prefix="$fasta" &&
+        prefix2="$names" &&
+        mv \${prefix%.dat}*.redundant.fasta "$out_fasta" &&
+        mv mothur.*.logfile "$logfile";
+        #if $inputtype.intype == 'countfile':
+            if [[ -f \${prefix2%.dat}.redundant.groups ]];
+            then
+                mv \${prefix2%.dat}.redundant.groups "$groups_file";
+            fi
+        #end if
+    ]]></command>
+    <inputs>
+        <param name="fasta" type="data" format="fasta" label="fasta - Sequences to filter"/>
+        <conditional name="inputtype">
+            <param name="intype" type="select" label="type of file to provide, may be either a names or a count file" help="">
+                <option value="namesfile">names</option>
+                <option value="countfile">count table</option>
+            </param>
+            <when value="namesfile">
+                <param name="names" type="data" format="mothur.names" label="provide a names file" help="A names file will generate a new faste file containing all the sequences."/>
+            </when>
+            <when value="countfile">
+                <param name="names" type="data" format="mothur.count_table" label="provide a count table" help="A counts table will generate a new faste file containing all the sequences. If the file contains group information, a group file will also be created."/>
+            </when>
+        </conditional>
+    </inputs>
+    <outputs>
+        <data name="logfile" format="txt" label="${tool.name} on ${on_string}: logfile"/>
+        <data name="out_fasta" format_source="fasta" label="${tool.name} on ${on_string}: fasta"/>
+        <!-- groups file is created when a count file is used as input, but will be empty if the count file did not contain group information -->
+        <data name="groups_file" format="mothur.groups" label="${tool.name} on ${on_string}: groups">
+            <filter>inputtype.intype == 'countfile'</filter>
+        </data>
+    </outputs>
+    <tests>
+        <test><!-- test names file input -->
+            <param name="fasta" value="amazon.unique.fasta"/>
+            <param name="intype" value="namesfile"/>
+            <param name="names" value="amazon.unique.names"/>
+            <output name="out_fasta" md5="579698b8037ee939dd730e2cf0dd018d" ftype="fasta"/>
+            <expand macro="logfile-test"/>
+        </test>
+        <test><!-- test count file input with group file output -->
+            <param name="fasta" value="amazon.unique.fasta"/>
+            <param name="intype" value="countfile"/>
+            <param name="names" value="amazon_withgroups.count_table"/>
+            <output name="out_fasta" md5="177f5cf92a84ab3aef0a665e06178bbe" ftype="fasta"/>
+            <output name="groups_file" file="amazon_withgroups.redundant.groups" ftype="mothur.groups"/>
+            <expand macro="logfile-test"/>
+        </test>
+        <test><!-- test count file input without group file output -->
+            <param name="fasta" value="amazon.unique.fasta"/>
+            <param name="intype" value="countfile"/>
+            <param name="names" value="amazon.count_table"/>
+            <output name="out_fasta" md5="177f5cf92a84ab3aef0a665e06178bbe" ftype="fasta"/>
+            <output name="groups_file" md5="d41d8cd98f00b204e9800998ecf8427e" ftype="mothur.groups"/> <!--empty-->
+            <expand macro="logfile-test"/>
+        </test>
+    </tests>
+    <help>
+<![CDATA[
+
+@MOTHUR_OVERVIEW@
+
+**Command Documenation**
+
+The deunique.seqs_ command is the reverse of the unique.seqs command, and creates a fasta file from a fasta and name_ file.
+
+.. _name: http://www.mothur.org/wiki/Name_file
+.. _deunique.seqs: http://www.mothur.org/wiki/Deunique.seqs
+
+v.1.21.0: Updated to Mothur 1.33, added option to provide count instead of names file, new groups file as output
+
+]]>
+    </help>
+    <expand macro="citations"/>
+</tool>