diff bum.xml @ 0:e41ec5af7472 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heinz commit b0b2c64a46bdd9beebdfb7fc5312f75346483763

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/bum.xml	Thu Aug 02 11:57:44 2018 -0400
@@ -0,0 +1,41 @@
+<tool id="heinz_bum" name="Fit a BUM model" version="1.0">
+    <description>with p-values</description>
+    <requirements>
+        <requirement type="package" version="1.20.0">r-getopt</requirement>
+        <requirement type="package" version="1.34.0">bioconductor-bionet</requirement>
+    </requirements>
+    <command detect_errors="exit_code"><![CDATA[
+Rscript '$__tool_directory__/bum.R' --input '$p_values' --output '$dist_params'
+    ]]></command>
+    <inputs>
+        <param type="data" name="p_values" label="Input file" format="txt" help="
+        The input file should only contain p-values, one per line." />
+    </inputs>
+    <outputs>
+        <data name="dist_params" format="txt" label="${tool.name} on ${on_string}: BUM params"/>
+    </outputs>
+    <tests>
+      <!--Ensure the stochastic result is similar enough-->
+        <test>
+            <param name="p_values" value="BUM_input.txt" />
+            <output name="dist_params">
+                <assert_contents>
+                    <has_text text="0.684" />
+                    <has_text text="0.376" />
+                </assert_contents>
+            </output>
+        </test>
+    </tests>
+    <help><![CDATA[
+BUM is the abbreviation for "Beta-Uniform Mixture (BUM) distribution."
+
+This tool (part of the package "Bionet") is used for fitting Beta-Uniform
+mixture model to a P-value distribution, the output of which is two model
+parameters: lambda and alpha, kept in a text file, the first line is
+lambda; the second, alpha.
+    ]]></help>
+    <citations>
+        <citation type="doi">10.1093/bioinformatics/btq089</citation>
+        <citation type="doi">10.1093/bioinformatics/btn161</citation>
+    </citations>
+</tool>