Mercurial > repos > diego > rtg_investigator
view tools/rtg/readsim.xml @ 1:8593828f91e7 default tip
Full galaxy wrapper
author | diego |
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date | Sat, 21 Apr 2012 21:36:15 -0400 |
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<tool id="rtg_readsim" name="Simulate reads"> <description>with RTG readsim</description> <command interpreter="bash">galaxy-rtg-wrapper.sh readsim -t ${input.extra_files_path} #if str($input2) != "None": -T ${input2.extra_files_path} #end if #if $limit.sType == "numreads": -n $limit.n #else -c $limit.c #end if -m $m -M $M --machine $machine.sMachine #if $machine.sMachine == "illumina_se": -r $machine.r #else if $machine.sMachine == "illumina_pe": -L $machine.L -R $machine.R #else if $machine.sMachine == "454_pe": --454-min-total-size $machine.454-min --454-max-total-size $machine.454-max #end if --seed $seed -o ${output.extra_files_path} >$output</command> <inputs> <param name="input" type="data" format="rtg_sdf" label="SDF containing input genome"/> <param name="input2" type="data" format="rtg_sdf" label="SDF with second genome for simulating diploid genomes" optional="true" /> <param name="m" type="integer" value="200" label="Minimum fragment length" help="Total number of reads"/> <param name="M" type="integer" value="400" label="Minimum fragment length" help="Total number of reads"/> <conditional name="limit"> <param name="sType" type="select" label="Select read limit"> <option value="numreads">Fixed number of reads</option> <option value="coverage">Fixed coverage</option> </param> <when value="numreads"> <param name="n" type="integer" value="1000" label="Number of reads" help="Total number of reads"/> </when> <when value="coverage"> <param name="c" type="float" value="1" label="Coverage" help="Total coverage"/> </when> </conditional> <conditional name="machine"> <param name="sMachine" type="select" label="Select machine type"> <option value="illumina_pe">Illumina paired-end</option> <option value="illumina_se">Illumina single-end</option> <option value="454_pe">454 paired-end</option> </param> <when value="illumina_se"> <param name="r" type="integer" value="100" label="Read length" help="Target read length on left side"/> </when> <when value="illumina_pe"> <param name="L" type="integer" value="100" label="Left read length" help="Target read length on left side"/> <param name="R" type="integer" value="100" label="Right read length" help="Target read length on right side"/> </when> <when value="454_pe"> <param name="454-min" type="integer" value="500" label="Minimum total length" help="Minimum sum of left and right read lengths"/> <param name="454-max" type="integer" value="300" label="Maximum total length" help="Maximum sum of left and right read lengths"/> </when> </conditional> <param name="seed" type="integer" value="42" label="Seed" help="Seed for the random number generator"/> </inputs> <outputs> <data format="rtg_sdf" name="output" /> </outputs> <help> This tool creates an SDF containing randomly generated reads. </help> </tool>