Hi,<div><br></div><div>Is there a way to pipe in the same xml wrapper two scripts in different languages, the output of the first script becoming the input of the second ?</div><div>I know that the spirit of galaxy would be to make a workflow, but the intermediate output in the present case is not interesting at all and may confuse the user.</div>
<div><br></div><div>I am testing something like :</div><div><div>        &lt;command interpreter=&quot;python&quot;&gt;plotter.py $input $minsize $maxsize $factor $output&lt;/command&gt;</div><div>        &lt;command interpreter=&quot;bash&quot;&gt;r_wrapper.sh $Rplotter&lt;/command&gt;</div>
<div><div>        &lt;inputs&gt;</div><div>                &lt;param name=&quot;input&quot; type=&quot;data&quot; format=&quot;tabular&quot; label=&quot;Compute Plot table from this bowtie standard output&quot;/&gt;</div>
<div>                &lt;param name=&quot;minsize&quot; type=&quot;integer&quot; size=&quot;3&quot; value=&quot;20&quot; label=&quot;Min size of small RNA to plot&quot; help=&quot;&#39;20&#39; = 20 nucleotides&quot;/&gt;</div>
<div>                &lt;param name=&quot;maxsize&quot; type=&quot;integer&quot; size=&quot;3&quot; value=&quot;22&quot; label=&quot;Max size of small RNA to plot&quot; help=&quot;&#39;22&#39; = 22 nucleotides&quot;/&gt;</div>
<div>                &lt;param name=&quot;factor&quot; type=&quot;float&quot; size=&quot;6&quot; value=&quot;1.00&quot; label=&quot;Normalization factort&quot; help=&quot;leave at 1.00 for no normalization&quot;/&gt;</div>
<div>                &lt;param name=&quot;title&quot; type=&quot;text&quot; size=&quot;15&quot; value=&quot;Main Title&quot; label=&quot;Main Titles&quot;/&gt;</div><div>                &lt;param name=&quot;xlabel&quot; type=&quot;text&quot; size=&quot;15&quot; value=&quot;Coordinates (nt)&quot; label=&quot;x axis label&quot;/&gt;</div>
<div>                &lt;param name=&quot;ylabel&quot; type=&quot;text&quot; size=&quot;15&quot; value=&quot;Normalized number of reads&quot; label=&quot;y axis label&quot;/&gt;</div><div>                &lt;param name=&quot;yrange&quot; type=&quot;integer&quot; size=&quot;6&quot; value=&quot;400&quot; label=&quot;y axis range&quot;/&gt;</div>
<div><br></div><div>        &lt;/inputs&gt;</div><div>  &lt;configfiles&gt;</div><div>    &lt;configfile name=&quot;Rplotter&quot;&gt;</div><div>      ## Setup R error handling to go to stderr</div><div>      options( show.error.messages=F,</div>
<div>               error = function () { cat( geterrmessage(), file=stderr() ); q( &quot;no&quot;, 1, F ) } )</div><div>      tab = read.delim(&quot;${output}&quot;, header=TRUE)</div><div>      ## Open output PDF file</div>
<div>      pdf( &quot;${outputFinal}&quot; )</div><div><br></div><div>      #determining y and x axis ranges</div><div>      MAXcoord =  max(tab[,1]) + 100</div><div>      MINcoord = min(tab[,1])</div><div>      MMAX = ${yrange}</div>
<div>      plot(tab[,1], tab[,2], type=&quot;h&quot;, xaxt=&quot;n&quot;, xlim=c(MINcoord , MAXcoord), ylim=c(-MMAX , MMAX), frame.plot=FALSE, lwd=2, las=2, xlab= &quot;${xlabel}&quot;, ylab=&quot;${ylabel}&quot;, main = &quot;${title}&quot;)</div>
<div>      lines(tab[,1], tab[,3], type=&quot;h&quot;, lwd=2)</div><div>      axis(1)</div><div><br></div><div>      ## Close the PDF file</div><div>      devname = dev.off()</div><div>    &lt;/configfile&gt;</div><div>  &lt;/configfiles&gt;</div>
<div><br></div><div>        &lt;outputs&gt;</div><div>                &lt;data name=&quot;output&quot; format=&quot;tabular&quot; label= &quot;Data Frame&quot;/&gt;</div><div>                &lt;data name=&quot;outputFinal&quot; format=&quot;pdf&quot; label= &quot;PDF plot&quot;/&gt;</div>
<div>        &lt;/outputs&gt;</div></div><div><br></div><div>but the second script output is empty. I suspect that the second script is launched when the output of the first script is not available yet.</div><div><br></div>
<div><br></div><div>Thanks for the help</div><div><br></div><div>Chris</div>
</div>