view transposetest/transposetest.xml @ 0:bf814ef1c04d draft default tip

testing

<tool id="transposetest" name="transposetest" version="0.01">
<description>Transpose test</description>
<command interpreter="python">
            transposetest.py --script_path "$runMe" --interpreter "Rscript" 
            --tool_name "transposetest" --input_tab "$input1"   --output_tab "$tab_file" 
            </command>
<inputs>
<param name="input1"  type="data" format="tabular" label="Select a suitable input file from your history"/> 
<param name="job_name" type="text" label="Supply a name for the outputs to remind you what they contain" value="transposetest"/> 

</inputs>
<outputs>
 <data format="tabular" name="tab_file" label="${job_name}"/>

</outputs>
<configfiles>
<configfile name="runMe">
<![CDATA[   
# transpose a tabular input file and write as a tabular output file
ourargs = commandArgs(TRUE)
inf = ourargs[1]
outf = ourargs[2]
inp = read.table(inf,head=F,row.names=NULL,sep='\t',colClasses="character")
outp = t(inp)
write.table(outp,outf, quote=FALSE, sep="\t",row.names=F,col.names=F)
]]>
</configfile>
</configfiles>
<tests><test>
        <param name="input1" value="transposetest_test1_input.xls" ftype="tabular"/>
        <param name="job_name" value="test1"/>
        <param name="runMe" value="$runMe"/>
        <output name="tab_file" file="transposetest_test1_output.xls" ftype="tabular"/>
        </test></tests>
<help>
<![CDATA[   

**What it Does**
Tests the toolfactory
Transposes a file


**Script**
Pressing execute will run the following code over your input file and generate some outputs in your history::

 # transpose a tabular input file and write as a tabular output file
 ourargs = commandArgs(TRUE)
 inf = ourargs[1]
 outf = ourargs[2]
 inp = read.table(inf,head=F,row.names=NULL,sep='\t',colClasses="character")
 outp = t(inp)
 write.table(outp,outf, quote=FALSE, sep="\t",row.names=F,col.names=F)



**Attribution** This Galaxy tool was created by [e-mail] at 22/03/2013 01:13:57
using the Galaxy Tool Factory.
See https://bitbucket.org/fubar/galaxytoolfactory for details of that project
Please cite: Creating re-usable tools from scripts: The Galaxy Tool Factory. Ross Lazarus; Antony Kaspi; Mark Ziemann; The Galaxy Team. 
Bioinformatics 2012; doi: 10.1093/bioinformatics/bts573


]]>

</help>
</tool>