diff macros.xml @ 0:a94f4d96045c draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit a933cd08ace9778a03e575e54f2b69bc5315e14c

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/macros.xml	Thu Dec 08 06:27:47 2016 -0500
@@ -0,0 +1,90 @@
+<macros>
+    <token name="@WRAPPER_VERSION@">1.0.1</token>
+    <xml name="requirements">
+        <requirements>
+            <requirement type="package" version="1.0.1">picrust</requirement>
+        </requirements>
+    </xml>
+
+    <xml name="version_command">
+        <version_command>predict_metagenomes.py --version | cut -d" " -f3 </version_command>
+    </xml>
+
+    <xml name="otu-reference-precalculated">
+        <!-- selection of "gg" picrust parameter reference data file -->
+        <conditional name="gg">
+           <param name="source" type="select" label="Select precalculated file from" help="">
+               <option value="ref">Cached Reference</option>
+               <option value="hist">History</option>
+           </param>
+           <when value="ref">
+               <param name="precalc" type="select" label="Precalculated input marker gene copy number predictions on per-otu basis">
+                   <options from_data_table="picrust_precalculated"/>
+               </param>
+           </when>
+           <when value="hist">
+               <param name="precalc" type="data" format="tabular" label="Precalculated input marker gene copy number predictions on per-otu basis"
+                      help="files may be downloaded from PICRUSt website (see tool help below)" />
+           </when>
+       </conditional>
+    </xml>
+
+    <xml name="biom_format_select">
+        <param name="output_type" type="select" label="Format of the output BIOM file">
+            <option value="json" selected="true">JSON</option>
+            <option value="hdf5">HDF5</option>
+            <option value="tsv">Classic (tab-separated text)</option>
+        </param>
+    </xml>
+
+    <xml name="biom_output">
+        <data name="out_biom" format="tabular" label="${tool.name} on ${on_string}: Normalized OTUs">
+            <change_format>
+                <when input="output_type" value="json" format="json"/>
+                <when input="output_type" value="tsv" format="tabular"/>
+                <when input="output_type" value="hdf5" format="hdf5"/>
+            </change_format>
+        </data>
+    </xml>
+
+    <token name="@OUTPUT_CONVERSION_COMMANDS@"><![CDATA[
+        #if $output_type == "json":
+            && biom convert -i tempbiom -o '$out_biom' --to-json
+        #elif $output_type == "tsv":
+            && biom convert -i tempbiom -o '$out_biom' --to-tsv
+        #else
+            && biom convert -i tempbiom -o '$out_biom' --to-hdf5
+        #end if
+    ]]></token>
+
+    <token name="@PICRUST_OVERVIEW@">
+<![CDATA[
+**PICRUSt: Phylogenetic Investigation of Communities by Reconstruction of Unobserved States**
+
+The PICRUSt project aims to support prediction of the unobserved character states in a community of
+organisms from phylogenetic information about the organisms in that community. The primary application
+is to predict gene family abundance (e.g. the metagenome) in environmental DNA samples for which only
+marker gene (e.g. 16S rRNA gene) data are available. This is an open source, international, collaborative
+bioinformatics project developed in the Huttenhower, Beiko, Langille, Vega Thurber, Knight and Caporaso labs.
+
+For more information please visit:
+
+- Picrust Documentation: https://picrust.github.io/picrust/
+- Picrust GitHub: http://picrust.github.com/
+- Picrust Support: https://groups.google.com/d/forum/picrust-users
+
+**Reference Data**
+
+Precalculated files: ftp://ftp.microbio.me/pub/picrust-references/picrust-1.0.0/
+
+]]>
+    </token>
+
+    <xml name="citations">
+        <citations>
+            <citation type="doi">10.1038/nbt.2676</citation>
+            <yield/>
+        </citations>
+    </xml>
+
+</macros>