Question: Re: [Galaxy-Dev] Tool Integration: Soapaligner/Soap2
gravatar for Kelly Vincent
8.3 years ago by
Kelly Vincent340
Kelly Vincent340 wrote:
Branden, Are you currently calling a script file (Python Perl, etc.) in your command tag, or calling the tool directly? If you are running it only with an XML file, you cannot do what you want here. The command that will be run is generated by converting the variable values you put in the <command> tag to the names of the actual input and output files that Galaxy creates when the tool is run. However, this is not particularly difficult if you are calling a script in the <command> tag, though it's a little convoluted. There are several tools that deal with this situation (the NGS tools again, in particular). There are a couple of basic situations. If you just need to have a single file with a certain extension, simply create a temp file with the extension specified (in Python "tempfile.mkstemp( suffix='.ext' )" will do it). It's slightly more complicated if you need associated files in the same directory (for instance, Samtools expects a fasta file like "hg19.fa" plus its index "hg19.fa.fai" to be in the same place. When you call the indexing command with the name of the fasta file, it automatically creates the index file with that name plus ".fai"). In this case, you should symlink the original file to a temp file (with or without a specified extension, as appropriate) and then get the name of that temp file. The name of the other file is that name PLUS the appropriate extension. For example, does this in lines 73 through 76. Note that the reason for symlinking to a temp file is that otherwise the tool will create a new file in a database/files subdirectory, which is not the right way to do things. So in the Samtools case, if the uploaded fasta file is "database/files/000/dataset_23.dat", a new file "database/files/000/dataset_23.dat.fai" will be created, but the database won't know about it and it will not be deleted after the tool finishes (but it still won't be available to future use, either). The paster.log contains the command as generated by the <command> tag, but it's not possible to print to that log from a tool script. You can simply print the relevant command to sdtout or stderr from the script and when you run it in the browser, you will see it in the info section. Hopefully this makes sense--let us know if you need further assistance. Regards, Kelly
samtools bam • 954 views
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