change your tool to use explicitly named output folder and files<div><br></div><div>bash mytool.sh $input $output1.extra_files_path $output1 $output2</div><div><br></div><div>where $output1.extra_files_path will be a folder (e.g. working dir)</div>

<div><br></div><div>$output1, $output2, etc. are files that are to be brought into your history in galaxy, to be used by other tools or viewable by the user.  mv files from working dir to these locations before exiting.</div>

<div><br></div><div>files in the folder that are not moved to the $output1 location will be saved but not visible to the user</div><div><br></div><div>also see compound datatypes (although they&#39;re usually not necessary).</div>

<br><div class="gmail_quote">On Sun, May 6, 2012 at 2:56 AM, 張詩婷 <span dir="ltr">&lt;<a href="mailto:jhang23020@gmail.com" target="_blank">jhang23020@gmail.com</a>&gt;</span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">

<span style="color:rgb(44,49,67);font-family:Verdana,sans-serif;font-size:15px;line-height:20px">Hi,</span><div><font color="#2c3143" face="Verdana, sans-serif"><span style="font-size:15px;line-height:20px"><br></span></font><div>


<div><span style="line-height:25px;color:rgb(44,49,67);font-size:16px;font-family:Verdana,sans-serif">A</span><span style="line-height:24px;color:rgb(44,49,67);font-size:15px;font-family:Verdana,sans-serif">fter execution, m</span><span style="line-height:25px;color:rgb(44,49,67);font-size:16px;font-family:Verdana,sans-serif">y tool created many files in a directory </span><span style="line-height:25px;color:rgb(44,49,67);font-size:16px;font-family:Verdana,sans-serif">, how </span><span style="line-height:25px;color:rgb(44,49,67);font-size:16px;font-family:Verdana,sans-serif">can I to find this directory? </span></div>


<div><span style="line-height:25px;color:rgb(44,49,67);font-size:16px;font-family:Verdana,sans-serif"><br></span></div><div><font color="#2c3143" face="Verdana, sans-serif"><span style="font-size:15px;line-height:23px">command:  bash mytool.sh $input</span></font></div>


<div><font color="#2c3143" face="Verdana, sans-serif"><span style="font-size:15px;line-height:22px"><br></span></font></div><div><span style="line-height:25px;color:rgb(44,49,67);font-size:16px;font-family:Verdana,sans-serif"><br>


</span></div><div><font color="#2c3143" face="Verdana, sans-serif"><span style="font-size:15px;line-height:20px"><br></span></font></div><div><span style="line-height:25px;color:rgb(44,49,67);font-size:16px;font-family:Verdana,sans-serif"><br>


</span></div><div><br></div><div><br></div><div><br></div></div></div>
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