diff vegan_fisher_alpha.xml @ 0:a5a453f92273 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vegan/vegan_fisher_alpha commit 0e04a4c237677c1f5be1950babcf8591097996a9

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/vegan_fisher_alpha.xml	Wed Dec 23 13:55:34 2015 -0500
@@ -0,0 +1,47 @@
+<tool id="vegan_fisher_alpha" name="Vegan Fisher Alpha" version="0.0.2">
+    <description>
+        index
+    </description>
+    <macros>
+        <import>vegan_macros.xml</import>
+    </macros>
+    <expand macro="requirements" />
+    <expand macro="stdio" />
+    <expand macro="version_command" />
+    <command><![CDATA[
+        Rscript "${vegan_fisher_alpha_script}"
+    ]]>
+    </command>
+    <configfiles>
+        <configfile name="vegan_fisher_alpha_script"><![CDATA[
+@RSCRIPT_PREAMBLE@
+@RSCRIPT_LOAD_TABULAR_FILE@
+
+write.table( fisher.alpha( input_abundance, MARGIN = ${margin} ), "${output_fisher_alpha}", col.names=NA, sep = "\t")
+    ]]>
+        </configfile>
+    </configfiles>
+    <inputs>
+        <expand macro="params_load_tabular_file" />
+        <param name="margin" type="integer" value="1" label="Margin for which the index is computed"/>
+    </inputs>
+    <outputs>
+        <data format="tabular" name="output_fisher_alpha" />
+    </outputs>
+    <tests>
+        <test>
+            <param name="input_abundance" ftype="tabular" value="vegan_in.tabular"/>
+            <param name="species_column" value="6"/>
+            <param name="sample_columns" value="2"/>
+            <param name="margin" value="1"/>
+            <output name="output_fisher_alpha" ftype="tabular" file="output_fisher_alpha.tabular" />
+        </test>
+    </tests>
+    <help>
+        <![CDATA[
+Calculate Diversity index using vegan and selected method.
+        ]]>
+    </help>
+    <citations>
+    </citations>
+</tool>
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