diff qq_manhattan.xml @ 0:7a8a21c5a57f draft default tip

"planemo upload commit 3126d8d1bdf88d13a8d168020bdf03dbb2dd1c0b"

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/qq_manhattan.xml	Thu Oct 08 17:28:43 2020 +0000
@@ -0,0 +1,32 @@
+<tool id="qq_manhattan" name="Manhattan Plots" version="0.1.0" profile="19.05">
+    <requirements>
+        <requirement type="package" version="0.1.4">r-qqman</requirement>
+        <requirement type="package" version="1.6.4">r-optparse</requirement>
+    </requirements>
+    <command detect_errors='exit_code'><![CDATA[
+        Rscript $__tool_directory__/manhattan.R --file '$data' --pval '$pval' --chr '$chr' --bp '$bp' --snp '$snp' --name '$name'
+    ]]></command>
+    <inputs>
+        <param name="data" type="data" format="tabular,tsv" label="Data file"/>
+        <param name="pval" type="text" value="P" label="P-value column name in input file"/>
+        <param name="chr" type="text" value="CHR" label="Chromosome column name in input file"/>
+        <param name="bp" type="text" value="BP" label="Base pair coordinate column name in input file"/>
+        <param name="snp" type="text" value="SNP" label="SNP ID column name in input file"/>
+        <param name="name" type="text" value="Manhattan Plot" label="Plot title"/>
+    </inputs>
+    <outputs>
+        <data format="pdf" name="manhattan" from_work_dir="manhattan.pdf"/>
+    </outputs>
+    <tests>
+        <test expect_num_outputs="1">
+            <param name="data" value="test.tsv"/>
+            <output name="manhattan" file="manhattan.pdf" compare="sim_size"/>
+        </test>
+    </tests>
+    <help><![CDATA[
+        Simple manhattan plot wrapper usinng the qqman bioconductor package.
+    ]]></help>
+    <citations>
+        <citation type="doi">https://doi.org/10.1101/005165</citation>
+    </citations>
+</tool>