diff tools/mothur/merge.taxsummary.xml @ 0:ee4fee239fe7 draft default tip

planemo upload commit 68a4fd4cc5332c57ac39bef73db224425af0706c-dirty

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/mothur/merge.taxsummary.xml	Fri Jun 03 09:32:47 2016 -0400
@@ -0,0 +1,49 @@
+<tool profile="16.07" id="mothur_merge_taxsummary" name="Merge.taxsummary" version="@WRAPPER_VERSION@.0">
+    <description>Merge tax.summary files</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements"/>
+    <expand macro="version_command"/>
+    <command detect_errors="aggressive"><![CDATA[
+        echo 'merge.taxsummary(
+            input=${ str($input).replace(",","-") },
+            output=$output
+        )'
+        | sed 's/ //g'  ## mothur trips over whitespace
+        | mothur &&
+
+        ## move output files to correct destination
+        mv mothur.*.logfile "$logfile"
+    ]]></command>
+    <inputs>
+        <param name="input" type="data" format="mothur.tax.summary" multiple="true" label="input - tax.summary files"/>
+    </inputs>
+    <outputs>
+        <data name="logfile" format="txt" label="${tool.name} on ${on_string}: logfile"/>
+        <data name="output" format="mothur.tax.summary" label="${tool.name} on ${on_string}: merged sff"/>
+    </outputs>
+    <tests>
+        <test>
+            <param name="input" value="amazon.wang.knn.tax.summary,amazon.silva.wang.tax.summary"/>
+            <output name="output" md5="6e1276cc740b03d5407a3707322e1ee3" ftype="mothur.tax.summary"/>
+            <expand macro="logfile-test"/>
+        </test>
+    </tests>
+    <help>
+<![CDATA[
+
+@MOTHUR_OVERVIEW@
+
+.. _Mothur: http://www.mothur.org/wiki/Main_Page
+
+**Command Documenation**
+
+The merge.taxsummary command takes a list of tax.summary files separated by dashes and merges them into one file.
+
+.. _merge.taxsummary: http://www.mothur.org/wiki/Merge.taxsummary
+
+]]>
+    </help>
+    <expand macro="citations"/>
+</tool>