I am a student of Bs Bioinformatics. I have been using the open source galaxy platform to integrate tool and make a work flow as my Final semester project. My supervisor happens to be ill and thus is unable to facilitate me in any respect. I here by take this opportunity to request that If any of you could help me fixing my problem. I would extremely grateful.

PROBLEM
My project problem is that , first of all i am using perl code tools for galaxy because galaxy dose not support installed tools from command prompt. so m using perl code tools for example clustalw, wublast, muscle and many more. sir these perl code tools are running correctly on command prompt and give me desire output, but when i put them it to the galaxy by making there xml file it gives an error that error occour while running this job.. and sir actually galaxy took tool's correct output as an error. i dnt know how to resolve it i tried alot but couldnt resolve it..
sir breifly m telling you that how m embedding perl code tools into galaxy:
1.go to ebi site, there are some perl code tools like clustalw, muscle,ncbiblast etc
2.i took them and download them
3. go to command prompt and try to run them by giving commands like
   perl ncbiblast.pl -S aemanzahra@comsats.edu.pk -D uniprot -P blastp
4.when it runs correctly i put them and embed them into the galaxy.
now in galaxy
1. insatlled galaxy
2. go in to tools directory
3. make a new directory of new tool ito tools directory e.g clustalw tool
4.go into clustalw tool and made two files in it. clustalw.pl in which perl code of clustalw tool is present.
   and secondly clustalw.xml is present of this tool that i made.
5.then run galaxy by sh run.sh command
6.galaxy web page opens
7. and i clicked on my added tool clustalw there and give it an input file of multiple sequences.
8. it runs. but after running it gives me an error that "error occour while running this job" but it took the output files of this tool as an error.
"The tools  run and three output files are created but the Galaxy takes them as errors."
WHAT PROBLEM IS THERE?
 
waitin for your reply
regards aeman