Hello Yoong,

I quickly see 3 mistakes :
- you use interpreter="python" but if so, you need to put your scripts in the same directory of your .xml. If you really want to use the full absolute path, delete the interpreter argument. - you don't need $alignments.files_path in your command. $alignments seems enough. - you describe many outputs although you just use one of them ($alignments). So, try to comment the others.


Some clues for you :)

Gildas


Le 28/10/2015 12:27, Greg Von Kuster a écrit :
Hello Yoong,

The best place to ask questions like this is the Galaxy Dev mailing list (galaxy-dev@lists.galaxyproject.org <mailto:galaxy-dev@lists.galaxyproject.org>). There are many developers that support this mailing list, so you will undoutedly receive optimal answers to any of your questions. I’ve forwarded your current questions to the mailing list.

Regards,

Greg Von Kuster

On Oct 28, 2015, at 12:56 AM, 홍윤지 <yoong0...@gmail.com <mailto:yoong0...@gmail.com>> wrote:

hey, my name is yoong in korean student .
i'd like to run the program name Mapsplice2, so i made a xml file, and submit that

this is my xml file..


<tool id="mapsplice" name="Mapsplice" version="2.2.0">

<description>MapSplice2 Description</description>

<command interpreter="python">
/home/yoong/galaxy/tools/MapSplice-v2.1.9/mapsplice.py -o $alignments.files_path -p 20 --qual-scale phred33 --bam --fusion -c /home/yoong/1_reference/hg19 -x /home/yoong/1_reference/BowtieIndex -1 $input_reads_1 -2 $input_reads_2
</command>

<inputs>
<param format="fastq" name="input_reads_1" type="data" label="Source file1"/> <param format="fastq" name="input_reads_2" type="data" label="Source file2"/>
</inputs>
<outputs>
<data format="bam" name="alignments" label="alignments.bam"/>
<data format="txt" name="deletions" label="deletions.txt"/>
<data format="txt" name="fusions_candidates" label="fusions_candidates.txt"/>
<data format="txt" name="fusions_raw" label="fusions_raw"/>
<data format="txt" name="insertions" label="insertions.txt"/>
<data format="txt" name="junctions" label="junctions.txt"/>
<data format="txt" name="stats" label="stats.txt"/>
</outputs>
<help>
        Help
</help>
</tool>

and, look at the report error, there is no special error... what's was the problom..? Do I something wrong ?...
plz help me...!! Thank you ...



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