Mercurial > repos > greg > multigps
diff multigps.xml @ 18:e3d9e74cae68 draft
Uploaded
| author | greg |
|---|---|
| date | Tue, 13 Dec 2016 13:02:36 -0500 |
| parents | 426f8753acb2 |
| children | 0ea6413d66b2 |
line wrap: on
line diff
--- a/multigps.xml Fri Jan 15 10:07:58 2016 -0500 +++ b/multigps.xml Tue Dec 13 13:02:36 2016 -0500 @@ -1,14 +1,128 @@ -<tool id="multigps" name="MultiGPS" version="0.5.0.0"> +<tool id="multigps" name="MultiGPS" version="0.72.0"> <description>analyzes collections of multi-condition ChIP-seq data</description> <macros> - <import>multigps_macros.xml</import> + <import>macros.xml</import> </macros> <expand macro="requirements" /> + <command detect_errors="aggressive"> <command> <![CDATA[ + ## java -Xmx15G org.seqcode.projects.multigps.MultiGPS + ## --species "Saccharomyces cerevisiae;sacCer3" + ## --threads 2 + ## --expt $bampath/$name.bam + ## --ctrl $control + ## --format BAM + ## --scalewin 500 + ## --q 0.05 + ## --nodifftests + ## --verbose + ## --mappability + ## --jointinmodel + ## --fixedmodelrange + ## --gaussmodelsmoothing + ## --gausssmoothparam 1 + ## --minmodelupdateevents 50 + ## --memepath $memePath + ## --mememinw 6 + ## --mememaxw 18 + ## --seq $genome + ## --exclude $exclude + ## --out $name > $name.out 2>&1 + ## + + multigps + ############################ + ## General options + ############################ + --input "$input" + --format "$input.ext" + #if str($verbose) == 'yes': + --verbose + #end if + --threads="\${GALAXY_SLOTS:-4}" + ############################ + ## Advanced options + ############################ #set aoc = $advanced_options_cond #if str($aoc.advanced_options) == "display": + #set bmsc = $aoc.binding_model_smoothing_cond + #set gmsc = $aoc.gauss_model_smoothing_cond + #set rbec = $aoc.report_binding_events_cond + #set rloc = $aoc.reads_limits_options_cond + #set sdc = $aoc.scale_data_cond #set umc = $aoc.use_motif_cond + ############################ + ## Limits on how many reads + ############################ + #if str($rloc.reads_limits) == "yes": + --fixedpb $rloc.fixedpb + --poissongausspb $rloc.poissongausspb + #if str($rloc.nonunique) == "yes": + --nonunique + #end if + --mappability $rloc.mappability + #end if + #if str($rloc.nocache) == "yes": + --nocache + #end if + ############################ + ## Scaling data + ############################ + #if str($sdc.scale_data) == "yes": + #if str($sdc.scaling) == 'no': + --noscaling $sdc.scaling + #end if + #if str($sdc.medianscale) == 'yes': + --medianscale $sdc.medianscale + #end if + #if str($sdc.regressionscale) == 'yes': + --regressionscale $sdc.regressionscale + #endif + #if str($sdc.sessscale) == 'yes': + --sesscale $sdc.sesscale + #end if + #if $sdc.fixedscaling > 0: + ‒‒fixedscaling $sdc.fixedscaling + #end if + --scalewin $sdc.scalewin + #if str($sdc.plotscaling) == 'yes': + --plotscaling $sdc.plotscaling + #end if + #end if + ############################ + ## Running MultiGPS + ############################ + #if str($aoc.nomodelupdate) == "no": + --nomodelupdate + #end if + --minmodelupdateevents $aoc.minmodelupdateevents + #if str($bmsc.nomodelsmoothing) == "no": + --nomodelsmoothing + #end if + --splinesmoothparam $aoc.splinesmoothparam + #if str($gmsc.gaussmodelsmoothing) == "yes": + --gaussmodelsmoothing + --gausssmoothparam $gmsc.gausssmoothparam + #end if + #if str($aoc.jointinmodel) == "yes": + --jointinmodel + #end if + #if str($aoc.fixedmodelrange) == "yes": + --fixedmodelrange + #end if + --prlogconf $aoc.prlogconf + #if $aoc.fixedalpha > 0: + --fixedalpha $aoc.fixedalpha + #end if + --alphascale $aoc.alphascale + #if str($aoc.mlconfignotshared) == "no": + --mlconfignotshared + #end if + --exclude "$aoc.exclude" + ############################ + ## MultiGPS priors + ############################ #if str($umc.use_motif) == "yes": #set rgc = $umc.reference_genome_cond #if str($rgc.reference_genome_source) == "cached": @@ -23,165 +137,197 @@ #set tmp_seq_file = os.path.join($seq_dir, $tmp_filename) ln -f -s $tmp_seq_file $seq_file && #end if - #end if - #end if - python $__tool_directory__/multigps.py - --multigps_jar $__tool_directory__/multigps_v0.5.jar - #for $i in $input_items: - #set replicate_name = "" - #set read_distribution_file = "" - #set fixed_read = "" - #set sccond = $i.signal_control_cond - #set sorc = $sccond.signal_control - #if str($sorc) == "Signal": - #set replicate_name = $sccond.replicate_name - #set rdcond = $sccond.read_distribution_cond - #if str($rdcond.read_distribution) == "yes": - #set read_distribution_file = "$rdcond.read_distribution_file" - #end if - #if str($sccond.fixed_read_count) == "yes": - #set fixed_read = "P" - #end if - #else if str($sorc) == "Control": - #set rncond = $sccond.replicate_name_cond - #if str($rncond.specify_replicate_name) == "yes": - #set replicate_name = $rncond.replicate_name - #set rdcond = $rncond.read_distribution_cond - #if str($rdcond.read_distribution) == "yes": - #set read_distribution_file = "$rdcond.read_distribution_file" - #end if - #if str($rncond.fixed_read_count) == "yes": - #set fixed_read = "P" - #end if - #end if - #end if - --input_item "${i.input}" "${i.input.ext}" "${i.signal_control_cond.signal_control}" "${i.condition_name}" "$replicate_name" "$read_distribution_file" "$fixed_read" - #end for - --threads="\${GALAXY_SLOTS:-4}" - --geninfo $chromInfo - #if str($aoc.advanced_options) == "display": - #set rbec = $aoc.report_binding_events_cond - #set bmsc = $aoc.binding_model_smoothing_cond - #set rloc = $aoc.reads_limits_options_cond - #set sdc = $aoc.scale_data_cond - --use_motif $umc.use_motif - #if str($umc.use_motif) == "yes": #set mpc = $umc.multigps_priors_cond - --seq_dir $seq_dir + --seq $seq_dir + --geninfo ${chromInfo} #if str($mpc.multigps_priors) == "yes": #set bmc = $mpc.both_motifs_cond - --positional_prior $mpc.positional_prior - --events_shared_probability $mpc.events_shared_probability - --motifs $bmc.motifs - #if str($bmc.motifs) == "yes": - --num_motifs $bmc.num_motifs - --mememinw $bmc.min_motif_width - --mememaxw $bmc.max_motif_width + #if str($mpc.noposprior) == "no": + --noposprior + #end if + --probshared $mpc.probshared + #if str($bmc.nomotifs) == "yes": + --memenmotifs $bmc.memenmotifs + --mememinw $bmc.mememinw + --mememaxw $bmc.mememaxw #else: - #set mfoc = $bmc.motif_finding_only_cond - --motif_finding_only $mfoc.motif_finding_only - #if str($mfoc.motif_finding_only) == "yes": - --num_motifs $mfoc.num_motifs - --mememinw $mfoc.min_motif_width - --mememaxw $mfoc.max_motif_width + --nomotifs + #set mfoc = $bmc.nomotifprior_cond + --nomotifprior $mfoc.nomotifprior + #if str($mfoc.nomotifprior) == "yes": + --memenmotifs $mfoc.memenmotifs + --mememinw $mfoc.mememinw + --mememaxw $mfoc.mememaxw #end if #end if #end if #end if - --max_training_rounds $aoc.max_training_rounds - --exclude_file $aoc.exclude_file - --binding_model_updates $aoc.binding_model_updates - --minmodelupdateevents $aoc.minmodelupdateevents - --binding_model_smoothing $bmsc.binding_model_smoothing - #if str($bmsc.binding_model_smoothing) == "yes": - --spline_smooth $bmsc.spline_smooth - #else: - #set gmsc = $bmsc.gauss_model_smoothing_cond - #if str($gmsc.gauss_model_smoothing) == "yes": - --gauss_smooth $gmsc.gauss_smooth + ############################ + ## Reporting binding events + ############################ + #if str($rbec.report_binding_events) == "yes": + --q $rbec.minqvalue + --minfold $rbec.minfold + #if str($rbec.nodifftests) == "no": + --nodifftests #end if - #end if - --joint_in_model $aoc.joint_in_model - --ml_config_not_shared $aoc.ml_config_not_shared - #if str($rloc.reads_limits) == "yes": - --fixedpb $rloc.fixedpb - --poissongausspb $rloc.poissongausspb - --non_unique_reads $rloc.non_unique_reads - #end if - #if str($rbec.report_binding_events) == "yes": - --minqvalue $rbec.minqvalue - --minfold $rbec.minfold - --diff_enrichment_tests $rbec.diff_enrichment_tests --edgerod $rbec.edgerod --diffp $rbec.diffp #end if - #if str($sdc.scale_data) == "yes": - --noscaling $sdc.scaling - --medianscale $sdc.medianscale - --sesscale $sdc.sesscale - --scalewin $sdc.scalewin - #end if #end if - --output_html_path "$output_html" - --output_html_files_path "$output_html.files_path" - #if str($output_process_log) == "yes": - --output_process_path "$output_process" - #end if + --out "$output_html.files_path" + > "$output_html" + ##if str($output_process_log) == "yes": + ## --output_process_path "$output_process" + ###end if ]]> </command> <inputs> - <repeat name="input_items" title="Input files, attributes and options" min="1"> - <param name="input" type="data" format="bam,bed,scidx" label="Add input file" help="Supported formats are bam, bed and scidx"> - <validator type="unspecified_build" /> - </param> - <conditional name="signal_control_cond"> - <param name="signal_control" type="select" label="Is this experiment signal or control?"> - <option value="Signal" selected="True">Signal</option> - <option value="Control">Control</option> - </param> - <when value="Signal"> - <param name="replicate_name" type="text" label="Replicate name" /> - <expand macro="rd_cond" /> - <expand macro="frc_param" /> - </when> - <when value="Control"> - <conditional name="replicate_name_cond"> - <param name="specify_replicate_name" type="select" label="Specify replicate name?" help="Optional for control experiments. If used, the control will only be used for the corresponding named signal replicate"> - <option value="no" selected="True">No</option> - <option value="yes">Yes</option> - </param> - <when value="yes"> - <param name="replicate_name" type="text" optional="True" label="Replicate name" /> - <expand macro="rd_cond" /> - <expand macro="frc_param" /> - </when> - <when value="no" /> - </conditional> - </when> - </conditional> - <param name="condition_name" type="text" label="Condition name" /> - </repeat> + <param name="input" type="data" format="bam,bed,scidx" label="Add input file" help="Supported formats are bam, bed and scidx"> + <validator type="unspecified_build" /> + </param> + <param name="verbose" type="select" label="Generate intermediate files and extra output?" help="Verbose flag"> + <option value="no" selected="True">No</option> + <option value="yes">Yes</option> + </param> + <!-- + ############################ + ## Advanced options + ############################ + --> <conditional name="advanced_options_cond"> <param name="advanced_options" type="select" label="Advanced options"> <option value="hide" selected="true">Hide</option> <option value="display">Display</option> </param> <when value="display"> + <!-- + ############################ + ## Limits on how many reads + ############################ + --> + <conditional name="reads_limits_options_cond"> + <param name="reads_limits" type="select" label="Set limits on how many reads can have their 5′ end at the same position in each replicate?" help="Default behavior is to estimate a global per-base limit from a Poisson distribution parameterized by the number of reads divided by the number of mappable bases in the genome. The per-base limit is set as the count corresponding to the 10^-7 probability level from the Poisson."> + <option value="no" selected="True">No</option> + <option value="yes">Yes</option> + </param> + <when value="no" /> + <when value="yes"> + <param name="fixedpb" type="integer" value="0" min="0" label="Fixed per-base limit" help="Zero value estimates from background model"/> + <param name="poissongausspb" type="integer" value="0" min="0" label="Poisson threshold for filtering per base" help="Filter per base using the specified Poisson threshold parameterized by a local Gaussian sliding window" /> + <param name="nonunique" type="select" label="Use non-unique reads?"> + <option value="no" selected="True">No</option> + <option value="yes">Yes</option> + </param> + <param name="mappability" type="float" value="0.0" min="0.8" label="Fraction of the genome that is mappable for these experiments" /> + <param name="nocache" type="select" label="Turn off caching of the entire set of experiments?" help="Run slower with less memory" > + <option value="no" selected="True">No</option> + <option value="yes">Yes</option> + </param> + </when> + </conditional> + <!-- + ############################ + ## Scaling data + ############################ + --> + <conditional name="scale_data_cond"> + <param name="scale_data" type="select" label="Set data scaling parameters?" help="Default behavior is to scale signal to corresponding controls using regression on the set of signal/control ratios in 10Kbp windows."> + <option value="no" selected="True">No</option> + <option value="yes">Yes</option> + </param> + <when value="yes"> + <param name="scaling" type="select" label="Use signal vs control scaling?"> + <option value="yes" selected="True">Yes</option> + <option value="no">No</option> + </param> + <param name="medianscale" type="select" label="Use the median signal/control ratio as the scaling factor?"> + <option value="no" selected="True">No</option> + <option value="yes">Yes</option> + </param> + <param name="regressionscale" type="select" label="Use scaling by regression on binned tag counts?"> + <option value="no" selected="True">No</option> + <option value="yes">Yes</option> + </param> + <param name="sesscale" type="select" label="Estimate scaling factor by SES?" help="SES: Diaz, et al. Stat Appl Genet Mol Biol. 2012"> + <option value="no" selected="True">No</option> + <option value="yes">Yes</option> + </param> + <param name="fixedscaling" type="float" value="0.0" min="0.0" label="Multiply control counts by total tag count ratio and then by this factor" help="Set as 0 to skip" /> + <param name="scalewin" type="integer" min="0" value="500" label="Window size for estimating scaling ratios" help="The value is the number of base pairs. Use something much smaller than the default if scaling via SES (e.g. 200)." /> + <param name="plotscaling" type="select" label="Plot diagnostic information for the chosen scaling method?"> + <option value="no" selected="True">No</option> + <option value="yes">Yes</option> + </param> + </when> + <when value="no" /> + </conditional> + <!-- + ############################ + ## Running MultiGPS + ############################ + --> + <param name="nomodelupdate" type="select" label="Perform binding model updates?"> + <option value="yes" selected="True">Yes</option> + <option value="no">No</option> + </param> + <param name="minmodelupdateevents" type="integer" value="500" min="0" label="Minimum number of events to support an update of the read distribution" /> + <param name="nomodelsmoothing" type="select" label="Perform binding model smoothing?" help="Smoothing performed with a cubic spline."> + <option value="yes" selected="True">Yes</option> + <option value="no">No</option> + </param> + <param name="splinesmoothparam" type="integer" value="30" min="0" label="Spline smoothing parameter" /> + <conditional name="gauss_model_smoothing_cond"> + <param name="gaussmodelsmoothing" type="select" label="Use Gaussian model smoothing?" help="Select No to smooth with a cubic spline."> + <option value="no" selected="True">No</option> + <option value="yes">Yes</option> + </param> + <when value="no" /> + <when value="yes"> + <param name="gausssmoothparam" type="integer" value="3" min="0" label="Smoothing factor" help="Gaussian smoothing standard deviation." /> + </when> + </conditional> + <param name="jointinmodel" type="select" label="Allow joint events in model updates?"> + <option value="no" selected="True">No</option> + <option value="yes">Yes</option> + </param> + <param name="fixedmodelrange" type="select" label="Keep binding model range fixed to inital size?" help="Select No to vary automatically"> + <option value="no" selected="True">No</option> + <option value="yes">Yes</option> + </param> + <param name="prlogconf" type="integer" value="-6" label="Poisson log threshold for potential region scanning" /> + <param name="fixedalpha" type="integer" value="0" min="0" label="Impose this alpha" help="This is a sparse prior on binding events in the MultiGPS model. It can be interpreted as a minimum number of reads that each binding event must be responsible for in the model. A zero value will estimate the alpha automatically." /> + <param name="alphascale" type="float" value="1.0" min="0" label="Alpha scaling factor" /> + <param name="mlconfignotshared" type="select" label="Share component configs in the ML step?" help="Mainly affects the quantification of binding levels for binding events that are not shared but are located at nearby locations across experiments."> + <option value="yes" selected="True">Yes</option> + <option value="no">No</option> + </param> + <param name="exclude" type="data" optional="True" format="txt" label="Optional file containing a set of regions to ignore during MultiGPS training" help="Ideally exclude the mitochondrial genome and other blacklisted regions that contain artifactual accumulations of reads in both ChIP-seq and control experiments." /> + <!-- + ############################ + ## MultiGPS priors + ############################ + --> <conditional name="use_motif_cond"> <param name="use_motif" type="select" label="Perform motif-finding or use a motif-prior?"> <option value="no" selected="True">No</option> <option value="yes">Yes</option> </param> <when value="yes"> + <!-- + ############################ + ## Specifying the genome + ############################ + --> <conditional name="reference_genome_cond"> <param name="reference_genome_source" type="select" label="Choose the source for the reference genome"> - <option value="cached">Locally Cached</option> - <option value="history">From History</option> + <option value="cached">locally cached</option> + <option value="history">from history</option> </param> <when value="cached"> <param name="reference_genome" type="select" label="Using reference genome"> <options from_data_table="all_fasta"> - <filter type="data_meta" key="dbkey" ref="input_items.input" column="1"/> + <filter type="data_meta" key="dbkey" ref="input" column="1"/> </options> <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file"/> </param> @@ -189,12 +335,17 @@ <when value="history"> <param name="reference_genome" type="data" format="fasta" label="Using reference genome"> <options> - <filter type="data_meta" key="dbkey" ref="input_items.input"/> + <filter type="data_meta" key="dbkey" ref="input"/> </options> <validator type="no_options" message="The current history does not include a fasta dataset with the build associated with the selected input file"/> </param> </when> </conditional> + <!-- + ############################ + ## MultiGPS priors options + ############################ + --> <conditional name="multigps_priors_cond"> <param name="multigps_priors" type="select" label="Specify MultiGPS priors options?"> <option value="no" selected="True">No</option> @@ -202,13 +353,13 @@ </param> <when value="no" /> <when value="yes"> - <param name="positional_prior" type="select" label="Perform inter-experiment positional prior?"> + <param name="noposprior" type="select" label="Perform inter-experiment positional prior?"> <option value="yes" selected="True">Yes</option> <option value="no">No</option> </param> - <param name="events_shared_probability" type="float" value="0.9" min="0.0" label="Probability that events are shared across conditions" /> + <param name="probshared" type="float" value="0.9" min="0.0" label="Probability that events are shared across conditions" /> <conditional name="both_motifs_cond"> - <param name="motifs" type="select" label="Perform both motif-finding and motif priors?"> + <param name="nomotifs" type="select" label="Perform both motif-finding and motif priors?"> <option value="yes" selected="True">Yes</option> <option value="no">No</option> </param> @@ -216,8 +367,8 @@ <expand macro="motif_finding_params" /> </when> <when value="no"> - <conditional name="motif_finding_only_cond"> - <param name="motif_finding_only" type="select" label="Perform motif-finding only?" help="Selecting Yes turns off motif priors."> + <conditional name="nomotifprior_cond"> + <param name="nomotifprior" type="select" label="Perform motif-finding only?" help="Selecting Yes turns off motif priors."> <option value="no" selected="True">No</option> <option value="yes">Yes</option> </param> @@ -233,79 +384,11 @@ </when> <when value="no" /> </conditional> - <param name="max_training_rounds" type="integer" value="3" min="0" label="Maximum number of training rounds for updating binding event read distributions" /> - <param name="exclude_file" type="data" optional="True" format="txt" label="Optional file containing a set of regions to ignore during MultiGPS training" help="Ideally exclude the mitochondrial genome and other blacklisted regions that contain artifactual accumulations of reads in both ChIP-seq and control experiments." /> - <param name="binding_model_updates" type="select" label="Perform binding model updates?"> - <option value="yes" selected="True">Yes</option> - <option value="no">No</option> - </param> - <param name="minmodelupdateevents" type="integer" value="0" min="0" label="Minimum number of events to support an update of the read distribution" /> - <conditional name="binding_model_smoothing_cond"> - <param name="binding_model_smoothing" type="select" label="Perform binding model smoothing?" help="Smoothing performed with a cubic spline."> - <option value="yes" selected="True">Yes</option> - <option value="no">No</option> - </param> - <when value="yes"> - <param name="spline_smooth" type="integer" value="0" min="0" label="Smoothing factor" /> - </when> - <when value="no"> - <conditional name="gauss_model_smoothing_cond"> - <param name="gauss_model_smoothing" type="select" label="Use Gaussian model smoothing?" help="Select No to smooth with a cubic spline."> - <option value="no" selected="True">No</option> - <option value="yes">Yes</option> - </param> - <when value="yes"> - <param name="gauss_smooth" type="integer" value="3" min="0" label="Smoothing factor" help="Gaussian smoothing standard deviation." /> - </when> - <when value="no" /> - </conditional> - </when> - </conditional> - <param name="joint_in_model" type="select" label="Allow joint events in model updates?"> - <option value="no" selected="True">No</option> - <option value="yes">Yes</option> - </param> - <param name="ml_config_not_shared" type="select" label="Share component configs in the ML step?"> - <option value="yes" selected="True">Yes</option> - <option value="no">No</option> - </param> - <conditional name="reads_limits_options_cond"> - <param name="reads_limits" type="select" label="Set limits on how many reads can have their 5′ end at the same position in each replicate?" help="Default behavior is to estimate a global per-base limit from a Poisson distribution parameterized by the number of reads divided by the number of mappable bases in the genome. The per-base limit is set as the count corresponding to the 10^-7 probability level from the Poisson."> - <option value="no" selected="True">No</option> - <option value="yes">Yes</option> - </param> - <when value="no" /> - <when value="yes"> - <param name="fixedpb" type="integer" value="0" min="0" label="Fixed per-base limit" /> - <param name="poissongausspb" type="integer" value="0" min="0" label="Poisson threshold for filtering per base" help="Filter per base using the specified Poisson threshold parameterized by a local Gaussian sliding window" /> - <param name="non_unique_reads" type="select" label="Use non-unique reads"> - <option value="no" selected="True">No</option> - <option value="yes">Yes</option> - </param> - </when> - </conditional> - <conditional name="scale_data_cond"> - <param name="scale_data" type="select" label="Set data scaling parameters?" help="Default behavior is to scale signal to corresponding controls using regression on the set of signal/control ratios in 10Kbp windows."> - <option value="no" selected="True">No</option> - <option value="yes">Yes</option> - </param> - <when value="yes"> - <param name="scaling" type="select" label="Use signal vs control scaling?"> - <option value="yes" selected="True">Yes</option> - <option value="no">No</option> - </param> - <param name="medianscale" type="select" label="Use the median signal/control ratio as the scaling factor?"> - <option value="yes" selected="True">Yes</option> - <option value="no">No</option> - </param> - <param name="sesscale" type="select" label="Estimate scaling factor by SES?" help="SES: Diaz, et al. Stat Appl Genet Mol Biol. 2012"> - <option value="yes" selected="True">Yes</option> - <option value="no">No</option> - </param> - <param name="scalewin" type="integer" min="0" value="10000" label="Window size for estimating scaling ratios" help="The value is the number of base pairs. Use something much smaller than the default if scaling via SES (e.g. 200)." /> - </when> - <when value="no" /> - </conditional> + <!-- + ############################ + ## Reporting binding events + ############################ + --> <conditional name="report_binding_events_cond"> <param name="report_binding_events" type="select" label="Report binding events?"> <option value="no" selected="True">No</option> @@ -313,49 +396,46 @@ </param> <when value="no" /> <when value="yes"> - <param name="minqvalue" type="integer" min="0" value="0" label="Minimum Q-value (corrected p-value) of reported binding events" /> - <param name="minfold" type="integer" min="0" value="0" label="Minimum event fold-change vs scaled control" /> - <param name="diff_enrichment_tests" type="select" label="Run differential enrichment tests?"> + <param name="minqvalue" type="float" min="0" value="0.001" label="Minimum Q-value (corrected p-value) of reported binding events" /> + <param name="minfold" type="float" min="0" value="1.5" label="Minimum event fold-change vs scaled control" /> + <param name="nodifftests" type="select" label="Run differential enrichment tests?"> <option value="yes" selected="True">Yes</option> <option value="no">No</option> </param> - <param name="edgerod" type="integer" min="0" value="0" label="EdgeR over-dispersion parameter value" /> - <param name="diffp" type="integer" min="0" value="0" label="Minimum p-value for reporting differential enrichment" /> + <param name="edgerod" type="float" min="0" value="0.15" label="EdgeR over-dispersion parameter value" /> + <param name="diffp" type="float" min="0" value="0.01" label="Minimum p-value for reporting differential enrichment" /> </when> </conditional> </when> <when value="hide"/> </conditional> + <!-- <param name="output_process_log" type="select" label="Output MultiGPS process log?"> <option value="no" selected="True">No</option> <option value="yes">Yes</option> </param> + --> </inputs> <outputs> + <!-- <data name="output_process" format="txt" label="${tool.name} on ${on_string} (process log)"> <filter>output_process_log == "yes"</filter> </data> + --> <data name="output_html" format="html"/> </outputs> <tests> <test> - <repeat name="input_items"> - <param name="input" value="sacCer3_1.scidx" ftype="scidx" dbkey="sacCer3"/> - <param name="signal_control" value="Signal"/> - <param name="condition_name" value="Abf1"/> - <param name="replicate_name" value="1"/> - <param name="read_distribution" value="no"/> - <param name="fixed_read_count" value="no"/> - </repeat> + <param name="input" value="sacCer3_1.scidx" ftype="scidx" dbkey="sacCer3"/> <param name="binding_model_smoothing" value="no"/> - <param name="gauss_model_smoothing" value="yes"/> - <param name="gauss_smooth" value="3"/> + <param name="gaussmodelsmoothing" value="yes"/> + <param name="gausssmoothparam" value="3"/> <param name="use_motif" value="yes"/> <param name="reference_genome_source" value="history"/> <param name="reference_genome" value="phiX.fasta" dbkey="phiX"/> - <param name="num_motifs" value="3"/> - <param name="min_motif_width" value="6"/> - <param name="max_motif_width" value="16"/> + <param name="memenmotifs" value="3"/> + <param name="mememinw" value="6"/> + <param name="mememaxw" value="16"/> <param name="output_process_log" value="yes"/> <output name="output_process" file="output_process1.txt" ftype="txt" lines_diff="12"/> <output name="output_html" file="output_html1.html" ftype="html" lines_diff="12"/>