Hi all,
I'm Venice and I'm working on a local galaxy instance here at IRRI. This
question might sound really naive but I really can't work around it. I'm
creating an xml for a tool where the user will select a list of file names
from the drop-down as input. I stored these files in a directory within
galaxy-dist. Based on the user input, Galaxy must output the user-selected
file.
I created this xml:
<tool id="matrix2flapjack" name="NT Matrix to Flapjack">
<description>file conversion</description>
<command interpreter="perl">matrix2flapjack.pl $inputFile $outputFile
$snp_map</command>
<inputs>
<param format="tabular" name="inputFile" type="data" label="Nucleotide
Matrix file"/>
<param name="snp_map" type="select" label="SNP map file">
<option
value="/home/galaxy/galaxy-dist/SNP_maps/11861_snp_map.txt">11861</option>
<option
value="/home/galaxy/galaxy-dist/SNP_maps/11862_snp_map.txt">11862</option>
<option
value="/home/galaxy/galaxy-dist/SNP_maps/13033_snp_map.txt">13033</option>
</param>
</inputs>
<outputs>
<data format="tabular" name="outputFile" label="Flapjack Format of
${inputFile.name} ">
</data>
<data format="tabular" name="snp_map" label="SNP Map"/>
</outputs>
<help>
This tool converts a SNP NT matrix file to Flapjack file format.
</help>
</tool>
However, it doesn't output the file. Instead, it prompts, "Either the
dataset does not exist or you don't have permission to access it."
Thanks in advance for your reply.
Thanks and Best regards,
Venice
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