diff basicplot.xml @ 0:4b684a42d677 draft

"planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/basicplot commit 0dff19dd491024012ea5145323c9f8c527578ca7"

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/basicplot.xml	Mon Jan 06 12:47:07 2020 -0500
@@ -0,0 +1,89 @@
+<tool id="Basicplot" name="basicplot" version="0.9.1">
+	<description>Basic plot</description>
+        <requirements>
+            <requirement type="package" version="3.5.0">r-base</requirement>
+        </requirements>
+        <command><![CDATA[
+            Rscript '$basicplot' "\${GALAXY_SLOTS:-1}"
+    ]]></command>
+  <configfiles>
+    <configfile name="basicplot">
+    <![CDATA[
+      ## Setup R error handling to go to stderr
+      options( show.error.messages=F,  error = function () { cat( geterrmessage(), file=stderr() ); q( "no", 1, F ) } )
+      options(warn=-1)
+      Table = read.delim("${input}", header=TRUE)
+      pdf("${output}")
+      pairs(Table[ ,-1], main="${title}", log="xy", pch = 20)
+      dev.off()
+    ]]>
+    </configfile>
+  </configfiles>
+        <inputs>
+                <param name="input" type="data" format="tabular" label="tabular file"/>
+                <param name="title" type="text" size="25" value="Title" label="Main Title"/>
+        </inputs>
+        <outputs>
+                <data name="output" format="pdf" label="plot" />
+        </outputs>
+<tests>
+    <test>
+        <param name="input" value="data.tab" ftype="tabular"/>
+        <param name="title" value="Title"/>
+        <output name="output" file="basicplot.pdf" ftype="pdf"/>
+    </test>
+</tests>
+<help>
+
+**What it does**
+
+Takes a tabular file of numerical data as input and produces pairwise plots of numerical data, in log-log scale.
+The first column of the data frame is ignored.
+
+Example of input data:
+
+<![CDATA[
+
+gene	sample1	sample2	sample3	sample4	sample5	sample6
+
+tRNA:Ala-AGC-2-3	4407	4506	2267	2423	2736	1153
+
+tRNA:Asp-GTC-1-10	2111	2931	3302	3499	3809	1682
+
+tRNA:Asp-GTC-1-11	2099	2936	3349	3556	4124	1629
+
+tRNA:Glu-TTC-1-6	1095	1376	1189	1162	1120	561
+
+tRNA:Glu-TTC-1-5	1022	1415	1156	1081	1120	578
+
+tRNA:Glu-TTC-1-4	1047	1336	1156	1182	1127	602
+
+tRNA:Glu-CTC-3-4	3613	3414	8161	9021	9776	5248
+
+tRNA:Glu-CTC-3-5	3741	3292	7893	8845	9833	5074
+
+tRNA:Glu-CTC-3-6	3619	3379	7663	8737	9513	5021
+
+tRNA:Glu-CTC-3-8	7249	5809	80760	39479	62652	27404
+
+tRNA:Glu-CTC-3-9	3770	3367	8007	8969	9976	5100
+
+]]>
+
+
+</help>
+<citations>
+        <citation type="bibtex">
+@Manual{,
+     title = {R: A Language and Environment for Statistical Computing},
+     author = {{R Core Team}},
+     organization = {R Foundation for Statistical Computing},
+     address = {Vienna, Austria},
+     year = {2014},
+     url = {http://www.R-project.org/},
+   }
+        </citation>
+    </citations>
+    
+</tool>
+