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1 <tool id="transposetest" name="transposetest" version="0.01">
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2 <description>Transpose test</description>
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3 <command interpreter="python">
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4 transposetest.py --script_path "$runMe" --interpreter "Rscript"
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5 --tool_name "transposetest" --input_tab "$input1" --output_tab "$tab_file"
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6 </command>
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7 <inputs>
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8 <param name="input1" type="data" format="tabular" label="Select a suitable input file from your history"/>
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9 <param name="job_name" type="text" label="Supply a name for the outputs to remind you what they contain" value="transposetest"/>
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10
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11 </inputs>
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12 <outputs>
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13 <data format="tabular" name="tab_file" label="${job_name}"/>
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14
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15 </outputs>
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16 <configfiles>
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17 <configfile name="runMe">
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18 <![CDATA[
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19 # transpose a tabular input file and write as a tabular output file
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20 ourargs = commandArgs(TRUE)
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21 inf = ourargs[1]
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22 outf = ourargs[2]
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23 inp = read.table(inf,head=F,row.names=NULL,sep='\t',colClasses="character")
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24 outp = t(inp)
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25 write.table(outp,outf, quote=FALSE, sep="\t",row.names=F,col.names=F)
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26 ]]>
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27 </configfile>
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28 </configfiles>
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29 <tests><test>
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30 <param name="input1" value="transposetest_test1_input.xls" ftype="tabular"/>
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31 <param name="job_name" value="test1"/>
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32 <param name="runMe" value="$runMe"/>
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33 <output name="tab_file" file="transposetest_test1_output.xls" ftype="tabular"/>
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34 </test></tests>
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35 <help>
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36 <![CDATA[
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37
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38 **What it Does**
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39 Tests the toolfactory
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40 Transposes a file
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41
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42
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43 **Script**
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44 Pressing execute will run the following code over your input file and generate some outputs in your history::
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45
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46 # transpose a tabular input file and write as a tabular output file
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47 ourargs = commandArgs(TRUE)
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48 inf = ourargs[1]
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49 outf = ourargs[2]
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50 inp = read.table(inf,head=F,row.names=NULL,sep='\t',colClasses="character")
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51 outp = t(inp)
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52 write.table(outp,outf, quote=FALSE, sep="\t",row.names=F,col.names=F)
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53
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54
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55
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56 **Attribution** This Galaxy tool was created by admin@here.now at 22/03/2013 01:13:57
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57 using the Galaxy Tool Factory.
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58 See https://bitbucket.org/fubar/galaxytoolfactory for details of that project
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59 Please cite: Creating re-usable tools from scripts: The Galaxy Tool Factory. Ross Lazarus; Antony Kaspi; Mark Ziemann; The Galaxy Team.
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60 Bioinformatics 2012; doi: 10.1093/bioinformatics/bts573
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61
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62
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63 ]]>
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64
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65 </help>
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66 </tool>
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