diff tools/mothur/bin.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/bin.seqs.xml	Fri Jun 03 09:32:47 2016 -0400
@@ -0,0 +1,84 @@
+<tool profile="16.07" id="mothur_bin_seqs" name="Bin.seqs" version="@WRAPPER_VERSION@.0">
+    <description>Order Sequences by OTU</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements"/>
+    <expand macro="version_command"/>
+    <command detect_errors="aggressive"><![CDATA[
+        echo 'bin.seqs(
+            #if $name:
+                name=$name,
+            #end if
+            #if $group:
+                group=$group,
+            #end if
+            #if $label:
+                label=${ str($label).replace(",","-") },
+            #end if
+            #if $count:
+                count=$count,
+            #end if
+            fasta=$fasta,
+            list=$otu
+        )'
+        | sed 's/ //g'  ## mothur trips over whitespace
+        | mothur &&
+
+        ## move output files to correct destination
+        prefix="$otu" &&
+        mv mothur.*.logfile "$logfile" &&
+        mv \${prefix%.dat}*.fasta .
+    ]]></command>
+    <inputs>
+        <param name="fasta" type="data" format="fasta" label="fasta - Sequences to Bin"/>
+        <param name="otu" type="data" format="mothur.list" label="list - OTU List"/>
+        <param name="name" type="data" format="mothur.names" optional="true" label="name - Sequences Name reference"/>
+        <param name="label" type="select" label="label - OTU Labels" multiple="true">
+            <expand macro="labeloptions"/>
+        </param>
+        <param name="group" type="data" format="group" optional="true" label="group - Sequences Name reference"/>
+        <param name="count" type="data" format="mothur.count_table" optional="true" label="count - Represents the number of duplicate sequences for a given representitive sequence"/>
+    </inputs>
+    <outputs>
+        <data name="logfile" format="txt" label="${tool.name} on ${on_string}: logfile"/>
+        <collection name="fastafiles" type="list" label="${tool.name} on ${on_string}: fastafiles per label">
+            <discover_datasets pattern=".*?\.(?P&lt;designation&gt;.*)\.fasta" format="fasta"/>
+        </collection>
+    </outputs>
+    <tests>
+        <test><!-- test with defaults -->
+            <param name="otu" value="amazon.an.list"/>
+            <param name="fasta" value="amazon.fasta"/>
+            <output_collection name="fastafiles" count="36">
+                <element name="0.22" md5="8fd8dd141561dc3e574e0c3f356e7e84" ftype="fasta"/>
+            </output_collection>
+            <expand macro="logfile-test"/>
+        </test>
+        <test><!-- test with group and name file and label select -->
+            <param name="otu" value="amazon.an.list"/>
+            <param name="fasta" value="amazon.fasta"/>
+            <param name="name" value="amazon.names"/>
+            <param name="group" value="amazon.groups" ftype="mothur.groups"/>
+            <param name="label" value="0.03,0.05,0.22"/>
+            <output_collection name="fastafiles" count="3">
+                <element name="0.22" md5="02755d06b535fdcdb5a70b6eb767d1f6" ftype="fasta"/>
+            </output_collection>
+            <expand macro="logfile-test"/>
+        </test>
+    </tests>
+    <help>
+<![CDATA[
+
+@MOTHUR_OVERVIEW@
+
+**Command Documenation**
+
+The bin.seqs_ command generates fasta-formatted files where sequences are ordered according to the OTU from the list_file_ that they belong to. Such an output may be helpful for generating primers specific to an OTU or for classification of sequences.
+
+.. _list_file: http://www.mothur.org/wiki/List_file
+.. _bin.seqs: http://www.mothur.org/wiki/Bin.seqs
+]]>
+    </help>
+    <expand macro="citations"/>
+</tool>