annotate basicplot.xml @ 0:da8c70a64f0c draft default tip

planemo upload for repository https://github.com/chamaelj/tools-artbio/tree/master/tools/basicplot commit 09c37709000f22d9fb378ec1a4ec0e8f46e6bf73-dirty

<tool id="Basicplot" name="basicplot" version="0.9.0">
	<description>Basic plot</description>
        <requirements>
            <requirement type="package" version="3.1.2">R</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**

Take on 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>