diff daa2rma.xml @ 0:2ac9f9b9dd63 draft

planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/megan commit b3dd3f0e8765048f093748d46df5d29af7d88850-dirty

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/daa2rma.xml	Mon Nov 05 03:40:10 2018 -0500
@@ -0,0 +1,64 @@
+<tool id="daa2rma" name="daa2rma" version="2.2.4">
+    <description>Compute a MEGAN rma6 file from a DIAMOND daa file</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements"/>
+    <expand macro="stdio"/>
+    <expand macro="version_command"/>
+    <command detect_errors="aggressive"><![CDATA[
+@CLASSIFICATION_UTILS@
+
+#set CATEGORIES=['gi2', 'acc2', 'syn2', 'tags4']
+#set TARGETS=['taxa', 'eggnog', 'interpro2go', 'seed', 'kegg']
+
+ln -s $in input.daa &&
+daa2rma
+-i input.daa
+-o '$rma'
+
+@MDF_CLI@
+@READS_CLI@
+--pairedReadsInOneFile $reads.pairedReadsInOneFile
+@PARAMETERS_CLI@
+--maxMatchesPerRead $params.maxMatchesPerRead
+@CLASSIFICATION_CLI@
+@OTHER_CLI@
+    ]]></command>
+    <inputs>
+        <param argument="--in" type="data" format="daa" label="Input DAA file"/>
+        <expand macro="mdf_macro"/>
+        <expand macro="reads_macro">
+            <param argument="--pairedReadsInOneFile" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Paired reads in one file" help="usually they are in two" />
+        </expand>
+        <expand macro="params_macro">
+            <param argument="--maxMatchesPerRead" type="integer" value="100" label="Max matches per read" />
+        </expand>
+        <expand macro="classification_macro"/>
+        <expand macro="other_macro"/>
+    </inputs>
+    <outputs>
+        <data name="rma" format="rma6" label="${tool.name} on ${on_string}"/>
+    </outputs>
+    <tests>
+        <test>
+            <param name="in" ftype="daa" value="diamond_results.daa"/>
+            <output name="rma" ftype="rma6" value="diamond_results.rma" />
+       </test>
+    </tests>
+    <help><![CDATA[
+Compute a MEGAN RMA6 file from a DIAMOND DAA file
+
+**Input**
+
+- DAA file
+- metadata mapping file (as defined in http://qiime.org/documentation/file_formats.html
+- BIOM 1 format (see http://biom-format.org/documentation/format-versions/biom-1.0.html
+
+**Output**
+
+- RMA6 file
+
+    ]]></help>
+    <expand macro="citations"/>
+</tool>