| Previous changeset 40:6a273db77b9b (2014-10-28) Next changeset 42:3b9a6381e6bf (2014-10-28) |
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Commit message:
Deleted selected files |
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removed:
siRNA.xml |
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| diff -r 6a273db77b9b -r 58b9d9a0d832 siRNA.xml --- a/siRNA.xml Tue Oct 28 01:33:03 2014 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,90 +0,0 @@ -<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="package" version="1.96">threads</requirement> - <requirement type="package" version="1.06">Parallel-ForkManager</requirement> - <requirement type="package" version="2.59">SVG</requirement> - <requirement type="package" version="1.4">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> |