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Commit message:
Uploaded |
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added:
miRPlant.xml |
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| diff -r 9ae0d25e4169 -r 45d9b0f6a0d6 miRPlant.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/miRPlant.xml Thu Jul 31 03:09:14 2014 -0400 |
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| @@ -0,0 +1,90 @@ +<tool id="plant_microRNA_v1" name="miRPlant" veision="1.0.0"> + <description>tool for plant microRNA 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="2.1.7">ViennaRNA</requirement> + </requirements> + + <!--command interpreter="perl">miPlant.pl -i $input -format $format -gfa $gfa -idx $index -pre $pre -mat $mat -rfam $rfam -idx2 $idx2 -D $D -a $a -M $M -min $min -max $max -mis $mis -e $e -f $f -v $v -r $r -dis $dis -flank $flank -mfe $mfe -t $t -o $output</command--> + + <command interpreter="perl">miRPlant.pl + ## Change this to accommodate the number of threads you have available. + -t \${GALAXY_SLOTS:-4} + ## Do or not delet rfam mapped tags + #if $params.delet_rfam == "yes": + -D + #end if + -path \$SCRIPT_PATH + + #for $j, $s in enumerate( $series ) + ##rank_of_series=$j + -i ${s.input} + -tag ${s.tag} + #end for + + -format $format -gfa $gfa -pre $pre -mat $mat -rfam $rfam -a $a -M $mapnt -min $min -max $max -mis $mismatch -e $e -f $f -v $v -r $r -dis $dis -flank $flank -mfe $mfe + </command> + + <inputs> + + <repeat name="series" title="Series"> + <param name="input" type="data" label="Raw data"/> + <param name="tag" type="text" data_ref="input" label="Sample name of raw data"/> + </repeat> + + <conditional name="params"> + <param name="delet_rfam" type="select" label="delet rfam mapped reads"> + <option value="yes" selected="true">yes</option> + <option value="no">no</option> + </param> + </conditional> <!-- params --> + + <!--param name="input" format="tabular" type="data" label="input config file" /--> + + <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="gfa" type="data" label="genome sequence fasta file"/> + <!--param type="data" name="index" label="genome sequence bowtie index"/--> + <param name="mat" type="data" label="mature microRNA sequence file" /> + <param name="pre" type="data" label="precursor microRNA sequence fie" /> + <param name="rfam" type="data" label="rfam sequence file" /> + <!--param type="data" name="idx2" label="rfam sequence bowtie index " --> + <param name="a" type="text" value="ATCTCGTATG" label="3' adapter sequence" /> + <param name="mapnt" type="integer" value="8" label="minimum adapter map nts" /> + <param name="min" type="integer" value="19" label="minimum microRNA length" /> + <param name="max" type="integer" value="28" label="maximum microRNA length" /> + <param name="mismatch" type="integer" value="0" label="number of allowed mismatches when mapping reads to precursors" /> + <param name="e" type="integer" value="2" label="number of nucleotides upstream of the mature sequence to consider" /> + <param name="f" type="integer" value="5" label="number of nucleotides downstream of the mature sequence to consider" /> + <param name="v" type="integer" value="0" label="report end-to-end hits less than v mismatches"/> + <param name="r" type="integer" value="25" label="a read is allowed to map up to this number of positions in the genome" /> + <param name="dis" type="integer" value="200" label="Maximal space between miRNA and miRNA*" /> + <param name="flank" type="integer" value="10" label="Flank sequence length of miRNA precursor" /> + <param name="mfe" type="float" value="-30" label="Maximal free energy allowed for a miRNA precursor" /> + <param name="thread" type="integer" value="1" label="number of threads" /> + </inputs> + + <outputs> + <data format="txt" name="known microRNA express list" from_work_dir="miRPlant_out/known_microRNA_express.txt"/> + <data format="txt" name="known microRNA express alignment" from_work_dir="miRPlant_out/known_microRNA_express.aln"/> + <data format="txt" name="known microRNA moRs result" from_work_dir="miRPlant_out/known_microRNA_express.moRs"/> + <data format="txt" name="known microRNA precursor file" from_work_dir="miRPlant_out/known_microRNA_precursor.fa"/> + <data format="txt" name="known microRNA mature file" from_work_dir="miRPlant_out/known_microRNA_mature.fa"/> + <data format="txt" name="novel microRNA prediction file" from_work_dir="miRPlant_out/known_microRNA_mature.fa"/> + <data format="txt" name="novel microRNA express list" from_work_dir="miRPlant_out/novel_microRNA_express.txt"/> + <data format="txt" name="novel microRNA precursor file" from_work_dir="miRPlant_out/novel_microRNA_precursor.fa"/> + <data format="txt" name="novel microRNA mature sequence file" from_work_dir="miRPlant_out/novel_microRNA_mature.fa"/> + <data format="txt" name="analysis result" from_work_dir="miRPlant_out/result.html"/> + </outputs> + + <help> + + </help> + </tool> |