Mercurial > repos > diego > rtg_investigator
diff 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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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tools/rtg/readsim.xml Sat Apr 21 21:36:15 2012 -0400 @@ -0,0 +1,75 @@ +<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>