comparison trinityrnaseq.xml @ 4:d5580071d910

Update commandline to detect successful completion

3:a9d882069cd4

			--min_kmer_cov $additional_params.min_kmer_cov --max_reads_per_graph $additional_params.max_reads_per_graph --bflyHeapSpaceMax $additional_params.bflyHeapSpaceMax
			#if $additional_params.bfly_opts != 'None':
				--bfly_opts " $additional_params.bfly_opts "
			#end if
        #end if
	
                
        ## direct to output
        | tee $trinity_log | grep -q 'All commands completed successfully.'
 
    </command>
    <inputs>
        <param name="JM" type="select" label="JM" help="Amount of memory to allocate to Jellyfish for Kmer catalog construction">
            <option value="1G">1G</option>
            <option value="10G">10G</option>

        <exit_code range="1:"  level="fatal" description="Failed" />
        <regex match="command not found" 
               source="both" 
               level="fatal" 
               description="Trinity.pl not found" />
        <regex match="Error" 
               source="both" 
               level="fatal" 
               description="A trinity process failed" />
    </stdio>
    <outputs>
        <data format="txt" name="trinity_log" label="${tool.name} on ${on_string}: log" />
        <data format="fasta" name="assembled_transcripts" label="${tool.name} on ${on_string}: Assembled Transcripts" from_work_dir="trinity_out_dir/Trinity.fasta"/>
    </outputs>

4:d5580071d910

			--min_kmer_cov $additional_params.min_kmer_cov --max_reads_per_graph $additional_params.max_reads_per_graph --bflyHeapSpaceMax $additional_params.bflyHeapSpaceMax
			#if $additional_params.bfly_opts != 'None':
				--bfly_opts " $additional_params.bfly_opts "
			#end if
        #end if

        ## direct output to the log file
        | tee $trinity_log 
        ## Check output for success message (direct grep output to dev null, -q option quits early leaving tee error messages)
        | grep 'All commands completed successfully.' > /dev/null
        ## Print the stats to output to provide info on galaxy history item
        && \$TRINITY_HOME/util/TrinityStats.pl trinity_out_dir/Trinity.fasta
    </command>
    <inputs>
        <param name="JM" type="select" label="JM" help="Amount of memory to allocate to Jellyfish for Kmer catalog construction">
            <option value="1G">1G</option>
            <option value="10G">10G</option>

        <exit_code range="1:"  level="fatal" description="Failed" />
        <regex match="command not found" 
               source="both" 
               level="fatal" 
               description="Trinity.pl not found" />
    </stdio>
    <outputs>
        <data format="txt" name="trinity_log" label="${tool.name} on ${on_string}: log" />
        <data format="fasta" name="assembled_transcripts" label="${tool.name} on ${on_string}: Assembled Transcripts" from_work_dir="trinity_out_dir/Trinity.fasta"/>
    </outputs>