diff tools/mothur/summary.tax.xml @ 0:ee4fee239fe7 draft default tip

planemo upload commit 68a4fd4cc5332c57ac39bef73db224425af0706c-dirty

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/mothur/summary.tax.xml	Fri Jun 03 09:32:47 2016 -0400
@@ -0,0 +1,110 @@
+<tool profile="16.07" id="mothur_summary_tax" name="Summary.tax" version="@WRAPPER_VERSION@.0">
+    <description>Assign sequences to taxonomy</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements"/>
+    <expand macro="version_command"/>
+    <command detect_errors="aggressive"><![CDATA[
+        ## if reftaxonomy option chosen, link tree.sum file to have same basename as reftaxonomy
+        #if $reftax.source2:
+            ln -s "$reftax.reftaxonomy" myreftax.taxonomy &&
+            ln -s "$sum" myreftax.tree.sum &&
+        #end if
+        echo 'summary.tax(
+            taxonomy=$tax.taxonomy,
+            #if $name:
+                name=$name,
+            #end if
+            #if $group:
+                group=$group,
+            #end if
+            #if $reftax.source2:
+                reftaxonomy=myreftax.taxonomy,
+            #end if
+            #if $count:
+                count=$count,
+            #end if
+            relabund=$relabund
+        )'
+        | sed 's/ //g'  ## mothur trips over whitespace
+        | mothur &&
+
+        ## move output files to correct destination
+        prefix="$tax.taxonomy" &&
+        mv \${prefix%.dat}*.tax.summary "$taxsummary" &&
+        mv mothur.*.logfile "$logfile"
+    ]]></command>
+    <inputs>
+        <conditional name="tax">
+            <param name="source" type="select" label="Select Taxonomy from" help="">
+                <option value="hist">History</option>
+                <option value="ref">Cached Reference</option>
+            </param>
+            <when value="ref">
+                <param name="taxonomy" type="select" format="mothur.seq.taxonomy" label="taxonomy - Taxonomy Reference">
+                    <options from_data_table="mothur_taxonomy"/>
+                </param>
+            </when>
+            <when value="hist">
+                <param name="taxonomy" type="data" format="mothur.seq.taxonomy" label="taxonomy - Taxonomy Reference"/>
+            </when>
+        </conditional>
+        <param name="name" type="data" format="mothur.names" optional="true" label="name - taxonomy sequence names"/>
+        <param name="group" type="data" format="mothur.groups" optional="true" label="group - Groups for summary file"/>
+        <conditional name="reftax">
+            <param name="source2" type="select" label="Select Reference Taxonomy used in Summary.seqs from" help="Including the reference taxonomy file used when you classified your sequences keep the rankIDs in the summary file static.">
+                <option value="" selected="true">Selection is Optional</option>
+                <option value="hist">History</option>
+                <option value="ref">Cached Reference</option>
+            </param>
+            <when value="ref">
+                <param name="reftaxonomy" type="select" format="mothur.seq.taxonomy" label="reftaxonomy - Taxonomy Reference used when sequences were classified">
+                    <options from_data_table="mothur_taxonomy"/>
+                </param>
+                <param name="sum" type="data" format="tabular" label="tree.sum - summary file produced when sequences were classified" help="run classify.seqs to get this file"/>
+            </when>
+            <when value="hist">
+                <param name="reftaxonomy" type="data" format="mothur.seq.taxonomy" label="reftaxonomy - Taxonomy Reference used when sequences were classified"/>
+                <param name="sum" type="data" format="tabular" label="tree.sum - summary file produced when sequences were classified" help="run classify.seqs to get this file"/>
+            </when>
+            <when value=""/>
+        </conditional>
+        <param name="count" type="data" format="mothur.count_table" optional="true" label="count - a count_table" help="generated by count.seqs"/>
+        <param name="relabund" type="boolean" falsevalue="false" truevalue="true" checked="false" label="relabund - allows you to indicate that you want the summary files to be relative abundances rather than raw abundances. default=f"/>
+    </inputs>
+    <outputs>
+        <data name="logfile" format="txt" label="${tool.name} on ${on_string}: logfile"/>
+        <data name="taxsummary" format="mothur.summary" label="${tool.name} on ${on_string}: summary"/>
+    </outputs>
+    <tests>
+        <test>
+            <param name="source" value="hist"/>
+            <param name="taxonomy" value="abrecovery.pds.wang.taxonomy" ftype="mothur.seq.taxonomy"/>
+            <output name="taxsummary" md5="1019aae0e68b2ee102565c535a8e03cf" ftype="mothur.summary"/>
+            <expand macro="logfile-test"/>
+        </test>
+        <test>
+            <param name="source" value="hist"/>
+            <param name="taxonomy" value="abrecovery.pds.wang.taxonomy" ftype="mothur.seq.taxonomy"/>
+            <param name="source2" value="hist"/>
+            <param name="reftaxonomy" value="abrecovery.pds.wang.taxonomy" ftype="mothur.seq.taxonomy"/>
+            <param name="sum" value="abrecovery.pds.wang.tree.sum"/>
+            <output name="taxsummary" md5="1019aae0e68b2ee102565c535a8e03cf" ftype="mothur.summary"/>
+            <expand macro="logfile-test"/>
+        </test>
+    </tests>
+    <help>
+<![CDATA[
+
+@MOTHUR_OVERVIEW@
+
+**Command Documenation**
+
+The summary.tax_ command reads a taxonomy file and an optional name and or group file, and summarizes the taxonomy information.
+
+.. _summary.tax: http://www.mothur.org/wiki/Summary.otu
+]]>
+    </help>
+    <expand macro="citations"/>
+</tool>