Mercurial > repos > big-tiandm > sirna_plant
view siRNA.xml @ 3:a0c49a058bec draft
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author | big-tiandm |
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date | Thu, 23 Oct 2014 22:05:27 -0400 |
parents | 49ce0a59cbe1 |
children | 75180ba26dc1 |
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<tool id="plant_sirna_v1" name="siRNA" veision="1.0.0"> <description>tool for plant siRNA analisis</description> <requirements> <requirement type="set_environment">SCRIPT_PATH</requirement> <requirement type="package" version="0.12.7">bowtie</requirement> <requirement type="package" version="2.11.0">R</requirement> <requirement type="package" version="0.0.13">fastx_toolkit </requirement> <requirement type="perl-module">threads</requirement> <requirement type="perl-module">Parallel-ForkManager</requirement> <requirement type="perl-module">SVG</requirement> <requirement type="perl-module">Boost-Graph</requirement> </requirements> <command interpreter="perl">siRNA.pl ## Change this to accommodate the number of threads you have available. -t \${GALAXY_SLOTS:-4} -path \$SCRIPT_PATH #for $j, $s in enumerate( $series ) ##rank_of_series=$j -i ${s.input} -tag ${s.tag} #end for -format $format -g $genome -f $gff -mis $mis -rfam $rfam -v $v -a $a -n $mapnt -d $d -p $p -l $l -deg $deg -cen $cen -span $span ## Do or not annotate siRNAs by function #if $params.function_anno == "yes": -nat $params.nat -repeat $params.repeat #end if </command> <inputs> <repeat name="series" title="Series"> <param name="input" type="data" label="Raw data file"/> <param name="tag" type="text" data_ref="input" label="Sample name of raw data"/> </repeat> <param name="format" type="select" lable="raw data format" multiple="false"> <option value="fastq">Raw data is fastq. format</option> <option value="fasta">Raw data is fasta. format</option> </param> <param name="genome" type="data" label="genome sequence fasta file"/> <!--param type="data" name="index" label="genome sequence bowtie index"/--> <param name="gff" type="data" label="gff file" /> <param name="mis" type="integer" value="0" label="number of allowed mismatches when mapping reads to genome" /> <param name="rfam" type="data" label="rfam sequence file" /> <param name="v" type="integer" value="0" label="report end-to-end hits less than v mismatches"/> <param name="a" type="text" value="ATCTCGTATG" label="3' adapter sequence" /> <param name="mapnt" type="integer" value="25" label="a read is allowed to map up to this number of positions in the genome" /> <param name="d" type="integer" value="100" label="distance of tag to merged a cluster" /> <param name="p" type="select" lable="cluster method" multiple="false"> <option value="F">conventional</option> <option value="T">NIBLES</option> </param> <param name="l" type="integer" value="1000" label="the length of the upstream and downstream,used in position annotate" /> <conditional name="params"> <param name="function_anno" type="select" label="Do or not annotate siRNAs by function"> <option value="no" selected="true">no</option> <option value="yes">yes</option> </param> <when value="yes"> <param name="nat" type="data" label="atural antisense transcripts file" /> <param name="repeat" type="data" label="repeat information file out of Repeatmasker" /> </when> </conditional> <!-- params --> <param name="cen" type="data" label="centromere file input" /> <param name="span" type="integer" value="50000" label="plot span" /> <param name="deg" type="data" label="file config of de sample" /> </inputs> <outputs> <data format="txt" name="siRNA cluster" from_work_dir="./total.result"/> <data format="txt" name="analysis result" from_work_dir="./result.html"/> </outputs> <help> </help> </tool>