Hello, I am defining some tools for my own galaxy installation and I would like to know if there is a more elegant solution for redirecting error output than the one in the next config file: <tool id="gatk_mio" name="calling with gatk"> <description>calling with gatk</description> <command> ln -s "${input}" input.bam ; samtools index input.bam; java -jar /home/ralonso/software/GenomeAnalysisTK-3.3-0/GenomeAnalysisTK.jar -T UnifiedGenotyper -R /home/ralonso/BiB/Galaxy/data/Cclementina_v1.0_scaffolds.fa -I input.bam -o $output *2>/dev/null;* </command> <inputs> <param format="bam" name="input" type="data" label="bam"/> </inputs> <outputs> <data format="vcf" name="output" /> </outputs> <help> bwa </help> </tool> Best regards many thanks -- Roberto Alonso Functional Genomics Unit Bioinformatics and Genomics Department Prince Felipe Research Center (CIPF) C./Eduardo Primo Yúfera (Científic), nº 3 (junto Oceanografico) 46012 Valencia, Spain Tel: +34 963289680 Ext. 1021 Fax: +34 963289574 E-Mail: ralonso@cipf.es
Two things - if you really want to just hide standard output - you can use the XML CDATA idiom to eliminate the need for escaping < and >. <command><![CDATA[ comand > /dev/null ]]></command If you want to allow the standard error to just be printed and use the exit code of the tool to determine whether the job has failed - you can add the following block to your tool XML: <stdio> <exit_code range="1:" /> </stdio> I think this is a saner default and I would just add this block to all new tools. You may want to check out the planemo tool builder - it will bootstrap new tool definitions that do both of these (use CDATA for the command and set a default stdio). http://planemo.readthedocs.org/en/latest/writing_standalone.html Hope this helps. -John On Thu, Apr 16, 2015 at 6:55 AM, Roberto Alonso CIPF <ralonso@cipf.es> wrote:
Hello,
I am defining some tools for my own galaxy installation and I would like to know if there is a more elegant solution for redirecting error output than the one in the next config file:
<tool id="gatk_mio" name="calling with gatk"> <description>calling with gatk</description> <command> ln -s "${input}" input.bam ; samtools index input.bam; java -jar /home/ralonso/software/GenomeAnalysisTK-3.3-0/GenomeAnalysisTK.jar -T UnifiedGenotyper -R /home/ralonso/BiB/Galaxy/data/Cclementina_v1.0_scaffolds.fa -I input.bam -o $output 2>/dev/null; </command>
<inputs> <param format="bam" name="input" type="data" label="bam"/> </inputs> <outputs> <data format="vcf" name="output" /> </outputs>
<help> bwa </help>
</tool>
Best regards
many thanks
-- Roberto Alonso Functional Genomics Unit Bioinformatics and Genomics Department Prince Felipe Research Center (CIPF) C./Eduardo Primo Yúfera (Científic), nº 3 (junto Oceanografico) 46012 Valencia, Spain Tel: +34 963289680 Ext. 1021 Fax: +34 963289574 E-Mail: ralonso@cipf.es
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participants (2)
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John Chilton -
Roberto Alonso CIPF