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reparation.xml
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reparation.xml
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<tool id="reparation" name="REPARATION" version="0.1.0">
<requirements>
</requirements>
<stdio>
<exit_code range="1:" />
</stdio>
<command interpreter='perl'>
reparation.pl
--g $genome
--gtf $gtf
--a $Ribo_alignment
--en $experimentname
--p $occupancy
--mn $min_read_len
--mx $max_read_len
--db $blastdb
--mo $MINORF
--mr $MINREAD
--ost $OFFSET_START
--osp $OFFSET_STOP
--gcode $gcode
--by $by
--score $score
<!-- Shine dalgarno sequence -->
--sd $choose_sd.sd_usage
--osd $choose_sd.OFFSET_SD
--seed $choose_sd.SEED
--id $identity
--ev $evalue
--pg $pgm
<!-- pset $positive_set -->
--cdn $start_codons
--ncdn $start_codon_nset
--pcdn $start_codon_pset
<!-- output files -->
--bgS $bedgraphS
--bgAS $bedgraphAS
--orf $predicted_ORFs
--bed $predicted_ORFs_bed
--fa $predicted_ORFs_fasta
--ps $psite_offset
</command>
<inputs>
<param name="scripts" value="scripts/" type="text" hidden='true' />
<param type="data" name="genome" format="fasta" label="Genome fasta file" help="Fasta file of the bacterial genome"/>
<param type="data" name="gtf" format="gtf" label="Annotation file" help="Annotation " />
<param type="data" name="Ribo_alignment" format="sam" label="Alignment file (sam)" help=""/>
<param name="experimentname" size="20" type="text" label="enter the experiment name" />
<param type="data" name="blastdb" format="fasta" label="Fasta file of curated bacteria protein sequence" help=""/>
<param name="occupancy" type="select" label="Determin P-site offset" multiple="false">
<option value="3" selected="true">3'</option>
<option value="5">5'</option>
<option value="1">plastid</option>
</param>
<param name="min_read_len" size="3" value="22" type="integer" label="Minimum RPF read length"/>
<param name="max_read_len" size="3" value="40" type="integer" label="Maximum RPF read length"/>
<param name="MINORF" size="10" value="90" type="integer" label="Minimum ORF length" />
<param name="MINREAD" size="10" value="90" type="integer" label="Minimum RPF read counts per open reading frame" />
<param name="OFFSET_START" size="10" value="45" type="integer" label="Start region length" />
<param name="OFFSET_STOP" size="10" value="21" type="integer" label="Stop region length" />
<param name="start_codons" size="30" value="ATG,GTG,TTG" type="text" label="Start codons for open reading frame prediction" />
<param name="start_codon_pset" size="24" value="ATG,GTG,TTG" type="text" label="Start codons for the positive set" />
<param name="start_codon_nset" size="24" value="CTG" type="text" label="Start codons for the negative set" />
<param name="score" size="10" value="0.5" type="float" label="Prediction score threshold." />
<!-- Positive set generation -->
<param name="pgm" type="select" label="Tool for initial positive set" multiple="false">
<option value="1" selected="true">prodigal</option>
<option value="2">glimmer3</option>
</param>
<param name="by" size="1" value="N" type="text" label="bypass Shine-Dalgarno trainer in prodigal." />
<param name="gcode" size="10" value="11" type="integer" label="Genetic code" />
<param name="identity" value="0.75" type="float" label="Identity threshold for BLAST search" help=""/>
<param name="evalue" value="0.00001" type="float" label="E-value threshold for BLAST search" help=""/>
<!-- Shine dalgarno sequence -->
<conditional name="choose_sd">
<param name="sd_usage" type="select" label="Allow the use of Shine Dalgarno sequence in the analysis" multiple="false">
<option value="1" selected="true">Yes</option>
<option value="0">No</option>
</param>
<when value="1">
<param name="OFFSET_SD" size="2" value="5" type="integer" label="Distance of Shine dalgarno sequence start from ORF start" />
<param name="SEED" size="12" value="GGAGG" type="text" label="Shine Dalgarno seed sequence" />
</when>
</conditional>
</inputs>
<outputs>
<data format="bedGraph" name="bedgraphS" label="RIBOseq footprint count data (sense)" />
<data format="bedGraph" name="bedgraphAS" label="RIBOseq footprint count data (anti sense)" />
<data format="txt" name="predicted_ORFs" label="Predicted ORFs (list)" />
<data format="fasta" name="predicted_ORFs_fasta" label="Predicted ORFs (protein sequences)" />
<data format="bed" name="predicted_ORFs_bed" label="Predicted ORFs (bed file)" />
<data format="png" name="psite_offset" label="plastid estimated p-site offsets">
<filter>choose_sd['occupancy'] == '1'</filter>
</data>
</outputs>
<help>
</help>
</tool>