multigps: multigps.xml annotate

annotate multigps.xml @ 2:028fafca04fa draft default tip

"planemo upload commit 9e4d2776d6b3276e2849943439799b82d989bc3b"

author	iuc
date	Sun, 22 Dec 2019 12:11:33 -0500
parents	7e0a12282c7f
children

rev	line source
2 028fafca04fa "planemo upload commit 9e4d2776d6b3276e2849943439799b82d989bc3b" iuc parents: 1 diff changeset	1 <tool id="multigps" name="MultiGPS" version="0.74.0">
0 4aa531981208 Uploaded iuc parents: diff changeset	2 <description>analyzes collections of multi-condition ChIP-seq data</description>
4aa531981208 Uploaded iuc parents: diff changeset	3 <macros>
4aa531981208 Uploaded iuc parents: diff changeset	4 <import>macros.xml</import>
4aa531981208 Uploaded iuc parents: diff changeset	5 </macros>
2 028fafca04fa "planemo upload commit 9e4d2776d6b3276e2849943439799b82d989bc3b" iuc parents: 1 diff changeset	6 <expand macro="requirements" />
0 4aa531981208 Uploaded iuc parents: diff changeset	7 <command detect_errors="aggressive">
4aa531981208 Uploaded iuc parents: diff changeset	8 <![CDATA[
4aa531981208 Uploaded iuc parents: diff changeset	9 #set output_dir = $output_html.files_path
4aa531981208 Uploaded iuc parents: diff changeset	10 mkdir -p $output_dir &&
4aa531981208 Uploaded iuc parents: diff changeset	11 multigps
4aa531981208 Uploaded iuc parents: diff changeset	12 ## General options
2 028fafca04fa "planemo upload commit 9e4d2776d6b3276e2849943439799b82d989bc3b" iuc parents: 1 diff changeset	13 --design '$build_design_file'
0 4aa531981208 Uploaded iuc parents: diff changeset	14 ## Append .txt extensions to events hrefs
4aa531981208 Uploaded iuc parents: diff changeset	15 ## in output dataset so files will render
4aa531981208 Uploaded iuc parents: diff changeset	16 ## in the browser.
4aa531981208 Uploaded iuc parents: diff changeset	17 --eventsaretxt
2 028fafca04fa "planemo upload commit 9e4d2776d6b3276e2849943439799b82d989bc3b" iuc parents: 1 diff changeset	18 ## Do not run the parallel version of meme.
0 4aa531981208 Uploaded iuc parents: diff changeset	19 --meme1proc
2 028fafca04fa "planemo upload commit 9e4d2776d6b3276e2849943439799b82d989bc3b" iuc parents: 1 diff changeset	20 --threads \${GALAXY_SLOTS:-4}
028fafca04fa "planemo upload commit 9e4d2776d6b3276e2849943439799b82d989bc3b" iuc parents: 1 diff changeset	21 #if str($in_test_mode) == "no":
028fafca04fa "planemo upload commit 9e4d2776d6b3276e2849943439799b82d989bc3b" iuc parents: 1 diff changeset	22 --geninfo '$chromInfo'
028fafca04fa "planemo upload commit 9e4d2776d6b3276e2849943439799b82d989bc3b" iuc parents: 1 diff changeset	23 #else:
028fafca04fa "planemo upload commit 9e4d2776d6b3276e2849943439799b82d989bc3b" iuc parents: 1 diff changeset	24 --geninfo '$__tool_directory__/tool-data/hg19.len'
0 4aa531981208 Uploaded iuc parents: diff changeset	25 #end if
4aa531981208 Uploaded iuc parents: diff changeset	26 ## Advanced options
4aa531981208 Uploaded iuc parents: diff changeset	27 #set aoc = $advanced_options_cond
4aa531981208 Uploaded iuc parents: diff changeset	28 #if str($aoc.advanced_options) == 'display':
4aa531981208 Uploaded iuc parents: diff changeset	29 #set bmsc = $aoc.binding_model_smoothing_cond
4aa531981208 Uploaded iuc parents: diff changeset	30 #set gmsc = $aoc.gauss_model_smoothing_cond
4aa531981208 Uploaded iuc parents: diff changeset	31 #set rbec = $aoc.report_binding_events_cond
4aa531981208 Uploaded iuc parents: diff changeset	32 #set rloc = $aoc.reads_limits_options_cond
4aa531981208 Uploaded iuc parents: diff changeset	33 #set sdc = $aoc.scale_data_cond
4aa531981208 Uploaded iuc parents: diff changeset	34 #set umc = $aoc.use_motif_cond
4aa531981208 Uploaded iuc parents: diff changeset	35 #if str($umc.use_motif) == 'yes':
4aa531981208 Uploaded iuc parents: diff changeset	36 #set rgc = $umc.reference_genome_cond
4aa531981208 Uploaded iuc parents: diff changeset	37 --seq
4aa531981208 Uploaded iuc parents: diff changeset	38 #if str($rgc.reference_genome_source) == 'cached':
2 028fafca04fa "planemo upload commit 9e4d2776d6b3276e2849943439799b82d989bc3b" iuc parents: 1 diff changeset	39 '${rgc.reference_genome.fields.path}'
0 4aa531981208 Uploaded iuc parents: diff changeset	40 #else:
2 028fafca04fa "planemo upload commit 9e4d2776d6b3276e2849943439799b82d989bc3b" iuc parents: 1 diff changeset	41 '${rgc.reference_genome}'
0 4aa531981208 Uploaded iuc parents: diff changeset	42 #end if
4aa531981208 Uploaded iuc parents: diff changeset	43 #end if
4aa531981208 Uploaded iuc parents: diff changeset	44 ## Limits on how many reads
4aa531981208 Uploaded iuc parents: diff changeset	45 #if str($rloc.reads_limits) == 'yes':
4aa531981208 Uploaded iuc parents: diff changeset	46 --fixedpb $rloc.fixedpb
4aa531981208 Uploaded iuc parents: diff changeset	47 --poissongausspb $rloc.poissongausspb
4aa531981208 Uploaded iuc parents: diff changeset	48 #if str($rloc.nonunique) == 'yes':
4aa531981208 Uploaded iuc parents: diff changeset	49 --nonunique
4aa531981208 Uploaded iuc parents: diff changeset	50 #end if
4aa531981208 Uploaded iuc parents: diff changeset	51 --mappability $rloc.mappability
4aa531981208 Uploaded iuc parents: diff changeset	52 #if str($rloc.nocache) == 'yes':
4aa531981208 Uploaded iuc parents: diff changeset	53 --nocache
4aa531981208 Uploaded iuc parents: diff changeset	54 #end if
4aa531981208 Uploaded iuc parents: diff changeset	55 #end if
4aa531981208 Uploaded iuc parents: diff changeset	56 ## Scaling data
4aa531981208 Uploaded iuc parents: diff changeset	57 #if str($sdc.scale_data) == 'yes':
4aa531981208 Uploaded iuc parents: diff changeset	58 #if str($sdc.scaling) == 'no':
4aa531981208 Uploaded iuc parents: diff changeset	59 --noscaling $sdc.scaling
4aa531981208 Uploaded iuc parents: diff changeset	60 #end if
4aa531981208 Uploaded iuc parents: diff changeset	61 #if str($sdc.medianscale) == 'yes':
4aa531981208 Uploaded iuc parents: diff changeset	62 --medianscale $sdc.medianscale
4aa531981208 Uploaded iuc parents: diff changeset	63 #end if
4aa531981208 Uploaded iuc parents: diff changeset	64 #if str($sdc.regressionscale) == 'yes':
4aa531981208 Uploaded iuc parents: diff changeset	65 --regressionscale $sdc.regressionscale
4aa531981208 Uploaded iuc parents: diff changeset	66 #end if
4aa531981208 Uploaded iuc parents: diff changeset	67 #if str($sdc.sesscale) == 'yes':
4aa531981208 Uploaded iuc parents: diff changeset	68 --sesscale $sdc.sesscale
4aa531981208 Uploaded iuc parents: diff changeset	69 #end if
4aa531981208 Uploaded iuc parents: diff changeset	70 #if $sdc.fixedscaling > 0:
4aa531981208 Uploaded iuc parents: diff changeset	71 ‒‒fixedscaling $sdc.fixedscaling
4aa531981208 Uploaded iuc parents: diff changeset	72 #end if
4aa531981208 Uploaded iuc parents: diff changeset	73 --scalewin $sdc.scalewin
4aa531981208 Uploaded iuc parents: diff changeset	74 #if str($sdc.plotscaling) == 'yes':
4aa531981208 Uploaded iuc parents: diff changeset	75 --plotscaling $sdc.plotscaling
4aa531981208 Uploaded iuc parents: diff changeset	76 #end if
4aa531981208 Uploaded iuc parents: diff changeset	77 #end if
4aa531981208 Uploaded iuc parents: diff changeset	78 ## Running MultiGPS
4aa531981208 Uploaded iuc parents: diff changeset	79 #if str($aoc.readdistributionfile) != 'None':
2 028fafca04fa "planemo upload commit 9e4d2776d6b3276e2849943439799b82d989bc3b" iuc parents: 1 diff changeset	80 --readdistributionfile '$aoc.readdistributionfile'
0 4aa531981208 Uploaded iuc parents: diff changeset	81 #end if
2 028fafca04fa "planemo upload commit 9e4d2776d6b3276e2849943439799b82d989bc3b" iuc parents: 1 diff changeset	82 --maxtrainingrounds $aoc.maxtrainingrounds
0 4aa531981208 Uploaded iuc parents: diff changeset	83 #if str($aoc.nomodelupdate) == 'no':
4aa531981208 Uploaded iuc parents: diff changeset	84 --nomodelupdate
4aa531981208 Uploaded iuc parents: diff changeset	85 #end if
4aa531981208 Uploaded iuc parents: diff changeset	86 --minmodelupdateevents $aoc.minmodelupdateevents
4aa531981208 Uploaded iuc parents: diff changeset	87 #if str($bmsc.nomodelsmoothing) == 'no':
4aa531981208 Uploaded iuc parents: diff changeset	88 --nomodelsmoothing
4aa531981208 Uploaded iuc parents: diff changeset	89 #else:
4aa531981208 Uploaded iuc parents: diff changeset	90 --splinesmoothparam $bmsc.splinesmoothparam
4aa531981208 Uploaded iuc parents: diff changeset	91 #end if
4aa531981208 Uploaded iuc parents: diff changeset	92 #if str($gmsc.gaussmodelsmoothing) == 'yes':
4aa531981208 Uploaded iuc parents: diff changeset	93 --gaussmodelsmoothing
4aa531981208 Uploaded iuc parents: diff changeset	94 --gausssmoothparam $gmsc.gausssmoothparam
4aa531981208 Uploaded iuc parents: diff changeset	95 #end if
4aa531981208 Uploaded iuc parents: diff changeset	96 #if str($aoc.jointinmodel) == 'yes':
4aa531981208 Uploaded iuc parents: diff changeset	97 --jointinmodel
4aa531981208 Uploaded iuc parents: diff changeset	98 #end if
4aa531981208 Uploaded iuc parents: diff changeset	99 #if str($aoc.fixedmodelrange) == 'yes':
4aa531981208 Uploaded iuc parents: diff changeset	100 --fixedmodelrange
4aa531981208 Uploaded iuc parents: diff changeset	101 #end if
4aa531981208 Uploaded iuc parents: diff changeset	102 --prlogconf $aoc.prlogconf
4aa531981208 Uploaded iuc parents: diff changeset	103 #if $aoc.fixedalpha > 0:
4aa531981208 Uploaded iuc parents: diff changeset	104 --fixedalpha $aoc.fixedalpha
4aa531981208 Uploaded iuc parents: diff changeset	105 #end if
4aa531981208 Uploaded iuc parents: diff changeset	106 --alphascale $aoc.alphascale
4aa531981208 Uploaded iuc parents: diff changeset	107 #if str($aoc.mlconfignotshared) == 'no':
4aa531981208 Uploaded iuc parents: diff changeset	108 --mlconfignotshared
4aa531981208 Uploaded iuc parents: diff changeset	109 #end if
4aa531981208 Uploaded iuc parents: diff changeset	110 #if str($aoc.exclude) != 'None':
4aa531981208 Uploaded iuc parents: diff changeset	111 --exclude '$aoc.exclude'
4aa531981208 Uploaded iuc parents: diff changeset	112 #end if
4aa531981208 Uploaded iuc parents: diff changeset	113 ## MultiGPS priors
4aa531981208 Uploaded iuc parents: diff changeset	114 #if str($umc.use_motif) == 'yes':
4aa531981208 Uploaded iuc parents: diff changeset	115 #set mpc = $umc.multigps_priors_cond
4aa531981208 Uploaded iuc parents: diff changeset	116 #if str($mpc.multigps_priors) == 'yes':
4aa531981208 Uploaded iuc parents: diff changeset	117 #set bmc = $mpc.both_motifs_cond
4aa531981208 Uploaded iuc parents: diff changeset	118 #if str($mpc.noposprior) == 'no':
4aa531981208 Uploaded iuc parents: diff changeset	119 --noposprior
4aa531981208 Uploaded iuc parents: diff changeset	120 #end if
4aa531981208 Uploaded iuc parents: diff changeset	121 --probshared $mpc.probshared
4aa531981208 Uploaded iuc parents: diff changeset	122 #if str($bmc.nomotifs) == 'yes':
4aa531981208 Uploaded iuc parents: diff changeset	123 --memenmotifs $bmc.memenmotifs
4aa531981208 Uploaded iuc parents: diff changeset	124 --mememinw $bmc.mememinw
4aa531981208 Uploaded iuc parents: diff changeset	125 --mememaxw $bmc.mememaxw
4aa531981208 Uploaded iuc parents: diff changeset	126 #else:
2 028fafca04fa "planemo upload commit 9e4d2776d6b3276e2849943439799b82d989bc3b" iuc parents: 1 diff changeset	127 #set nmpc = $bmc.nomotifprior_cond
0 4aa531981208 Uploaded iuc parents: diff changeset	128 --nomotifs
2 028fafca04fa "planemo upload commit 9e4d2776d6b3276e2849943439799b82d989bc3b" iuc parents: 1 diff changeset	129 #if str($nmpc.nomotifprior) == 'yes':
028fafca04fa "planemo upload commit 9e4d2776d6b3276e2849943439799b82d989bc3b" iuc parents: 1 diff changeset	130 --nomotifprior
028fafca04fa "planemo upload commit 9e4d2776d6b3276e2849943439799b82d989bc3b" iuc parents: 1 diff changeset	131 --memenmotifs $nmpc.memenmotifs
028fafca04fa "planemo upload commit 9e4d2776d6b3276e2849943439799b82d989bc3b" iuc parents: 1 diff changeset	132 --mememinw $nmpc.mememinw
028fafca04fa "planemo upload commit 9e4d2776d6b3276e2849943439799b82d989bc3b" iuc parents: 1 diff changeset	133 --mememaxw $nmpc.mememaxw
0 4aa531981208 Uploaded iuc parents: diff changeset	134 #end if
4aa531981208 Uploaded iuc parents: diff changeset	135 #end if
4aa531981208 Uploaded iuc parents: diff changeset	136 #end if
4aa531981208 Uploaded iuc parents: diff changeset	137 #end if
4aa531981208 Uploaded iuc parents: diff changeset	138 ## Reporting binding events
4aa531981208 Uploaded iuc parents: diff changeset	139 #if str($rbec.report_binding_events) == 'yes':
2 028fafca04fa "planemo upload commit 9e4d2776d6b3276e2849943439799b82d989bc3b" iuc parents: 1 diff changeset	140 --minqvalue $rbec.minqvalue
0 4aa531981208 Uploaded iuc parents: diff changeset	141 --minfold $rbec.minfold
4aa531981208 Uploaded iuc parents: diff changeset	142 #if str($rbec.nodifftests) == 'no':
4aa531981208 Uploaded iuc parents: diff changeset	143 --nodifftests
4aa531981208 Uploaded iuc parents: diff changeset	144 #end if
4aa531981208 Uploaded iuc parents: diff changeset	145 --edgerod $rbec.edgerod
4aa531981208 Uploaded iuc parents: diff changeset	146 --diffp $rbec.diffp
4aa531981208 Uploaded iuc parents: diff changeset	147 #end if
4aa531981208 Uploaded iuc parents: diff changeset	148 #end if
4aa531981208 Uploaded iuc parents: diff changeset	149 2>&1
4aa531981208 Uploaded iuc parents: diff changeset	150 --out '$output_html.files_path'
2 028fafca04fa "planemo upload commit 9e4d2776d6b3276e2849943439799b82d989bc3b" iuc parents: 1 diff changeset	151 #if str($save_design_file) == 'yes':
028fafca04fa "planemo upload commit 9e4d2776d6b3276e2849943439799b82d989bc3b" iuc parents: 1 diff changeset	152 && cp '$build_design_file' '$output_design_file'
028fafca04fa "planemo upload commit 9e4d2776d6b3276e2849943439799b82d989bc3b" iuc parents: 1 diff changeset	153 #end if
028fafca04fa "planemo upload commit 9e4d2776d6b3276e2849943439799b82d989bc3b" iuc parents: 1 diff changeset	154 && mv $output_dir/*.counts '$replicates_counts'
028fafca04fa "planemo upload commit 9e4d2776d6b3276e2849943439799b82d989bc3b" iuc parents: 1 diff changeset	155 && mv $output_dir/*.bed '$output_bed'
1 7e0a12282c7f Uploaded iuc parents: 0 diff changeset	156 && mv $output_dir/*.html '$output_html'
7e0a12282c7f Uploaded iuc parents: 0 diff changeset	157 && mv $output_dir/*.table.txt '$all_events_table'
0 4aa531981208 Uploaded iuc parents: diff changeset	158 ]]>
4aa531981208 Uploaded iuc parents: diff changeset	159 </command>
2 028fafca04fa "planemo upload commit 9e4d2776d6b3276e2849943439799b82d989bc3b" iuc parents: 1 diff changeset	160 <configfiles>
028fafca04fa "planemo upload commit 9e4d2776d6b3276e2849943439799b82d989bc3b" iuc parents: 1 diff changeset	161 <configfile name="build_design_file"><![CDATA[#for $condition_items in $condition_repeat:
028fafca04fa "planemo upload commit 9e4d2776d6b3276e2849943439799b82d989bc3b" iuc parents: 1 diff changeset	162 #for $signal_items in $condition_items.signal_repeat:
028fafca04fa "planemo upload commit 9e4d2776d6b3276e2849943439799b82d989bc3b" iuc parents: 1 diff changeset	163 #if str($signal_items.fixedreadcount_cond.fixedreadcount_select) == 'yes':
028fafca04fa "planemo upload commit 9e4d2776d6b3276e2849943439799b82d989bc3b" iuc parents: 1 diff changeset	164 #set $frc = $signal_items.fixedreadcount_cond.fixedreadcount
028fafca04fa "planemo upload commit 9e4d2776d6b3276e2849943439799b82d989bc3b" iuc parents: 1 diff changeset	165 #else:
028fafca04fa "planemo upload commit 9e4d2776d6b3276e2849943439799b82d989bc3b" iuc parents: 1 diff changeset	166 #set $frc = ''
028fafca04fa "planemo upload commit 9e4d2776d6b3276e2849943439799b82d989bc3b" iuc parents: 1 diff changeset	167 #end if
028fafca04fa "planemo upload commit 9e4d2776d6b3276e2849943439799b82d989bc3b" iuc parents: 1 diff changeset	168 ${signal_items.signal} Signal ${signal_items.signal.ext.upper()} ${condition_items.condition_name} ${signal_items.replicate_name} ${condition_items.experiment_type} ${frc}
028fafca04fa "planemo upload commit 9e4d2776d6b3276e2849943439799b82d989bc3b" iuc parents: 1 diff changeset	169 #end for
028fafca04fa "planemo upload commit 9e4d2776d6b3276e2849943439799b82d989bc3b" iuc parents: 1 diff changeset	170 #for $control_items in $condition_items.control_repeat:
028fafca04fa "planemo upload commit 9e4d2776d6b3276e2849943439799b82d989bc3b" iuc parents: 1 diff changeset	171 #if str($control_items.specify_replicate_name_cond.specify_replicate_name) == 'yes':
028fafca04fa "planemo upload commit 9e4d2776d6b3276e2849943439799b82d989bc3b" iuc parents: 1 diff changeset	172 #set $rn = $control_items.specify_replicate_name_cond.replicate_name
028fafca04fa "planemo upload commit 9e4d2776d6b3276e2849943439799b82d989bc3b" iuc parents: 1 diff changeset	173 #else:
028fafca04fa "planemo upload commit 9e4d2776d6b3276e2849943439799b82d989bc3b" iuc parents: 1 diff changeset	174 #set $rn = ''
028fafca04fa "planemo upload commit 9e4d2776d6b3276e2849943439799b82d989bc3b" iuc parents: 1 diff changeset	175 #end if
028fafca04fa "planemo upload commit 9e4d2776d6b3276e2849943439799b82d989bc3b" iuc parents: 1 diff changeset	176 #if str($control_items.fixedreadcount_cond.fixedreadcount_select) == 'yes':
028fafca04fa "planemo upload commit 9e4d2776d6b3276e2849943439799b82d989bc3b" iuc parents: 1 diff changeset	177 #set $frc = $control_items.fixedreadcount_cond.fixedreadcount
028fafca04fa "planemo upload commit 9e4d2776d6b3276e2849943439799b82d989bc3b" iuc parents: 1 diff changeset	178 #else:
028fafca04fa "planemo upload commit 9e4d2776d6b3276e2849943439799b82d989bc3b" iuc parents: 1 diff changeset	179 #set $frc = ''
028fafca04fa "planemo upload commit 9e4d2776d6b3276e2849943439799b82d989bc3b" iuc parents: 1 diff changeset	180 #end if
028fafca04fa "planemo upload commit 9e4d2776d6b3276e2849943439799b82d989bc3b" iuc parents: 1 diff changeset	181 ${control_items.control} Control ${control_items.control.ext.upper()} ${condition_items.condition_name} ${rn} ${condition_items.experiment_type} ${frc}
028fafca04fa "planemo upload commit 9e4d2776d6b3276e2849943439799b82d989bc3b" iuc parents: 1 diff changeset	182 #end for
028fafca04fa "planemo upload commit 9e4d2776d6b3276e2849943439799b82d989bc3b" iuc parents: 1 diff changeset	183 #end for ]]></configfile>
028fafca04fa "planemo upload commit 9e4d2776d6b3276e2849943439799b82d989bc3b" iuc parents: 1 diff changeset	184 </configfiles>
0 4aa531981208 Uploaded iuc parents: diff changeset	185 <inputs>
2 028fafca04fa "planemo upload commit 9e4d2776d6b3276e2849943439799b82d989bc3b" iuc parents: 1 diff changeset	186 <repeat name="condition_repeat" title="Condition" min="1">
028fafca04fa "planemo upload commit 9e4d2776d6b3276e2849943439799b82d989bc3b" iuc parents: 1 diff changeset	187 <param name="condition_name" type="text" value="cond" label="Condition name">
028fafca04fa "planemo upload commit 9e4d2776d6b3276e2849943439799b82d989bc3b" iuc parents: 1 diff changeset	188 <validator type="empty_field" />
028fafca04fa "planemo upload commit 9e4d2776d6b3276e2849943439799b82d989bc3b" iuc parents: 1 diff changeset	189 </param>
028fafca04fa "planemo upload commit 9e4d2776d6b3276e2849943439799b82d989bc3b" iuc parents: 1 diff changeset	190 <expand macro="param_experiment_type" />
028fafca04fa "planemo upload commit 9e4d2776d6b3276e2849943439799b82d989bc3b" iuc parents: 1 diff changeset	191 <repeat name="signal_repeat" title="Signal" min="1">
028fafca04fa "planemo upload commit 9e4d2776d6b3276e2849943439799b82d989bc3b" iuc parents: 1 diff changeset	192 <param name="signal" type="data" format="bam,bed,scidx" label="Select signal" help="Supported formats are bam, bed and scidx">
028fafca04fa "planemo upload commit 9e4d2776d6b3276e2849943439799b82d989bc3b" iuc parents: 1 diff changeset	193 <validator type="unspecified_build" />
028fafca04fa "planemo upload commit 9e4d2776d6b3276e2849943439799b82d989bc3b" iuc parents: 1 diff changeset	194 </param>
028fafca04fa "planemo upload commit 9e4d2776d6b3276e2849943439799b82d989bc3b" iuc parents: 1 diff changeset	195 <param name="replicate_name" type="text" value="1" label="Replicate name">
028fafca04fa "planemo upload commit 9e4d2776d6b3276e2849943439799b82d989bc3b" iuc parents: 1 diff changeset	196 <validator type="empty_field" />
028fafca04fa "planemo upload commit 9e4d2776d6b3276e2849943439799b82d989bc3b" iuc parents: 1 diff changeset	197 </param>
028fafca04fa "planemo upload commit 9e4d2776d6b3276e2849943439799b82d989bc3b" iuc parents: 1 diff changeset	198 <expand macro="cond_fixedreadcount" />
028fafca04fa "planemo upload commit 9e4d2776d6b3276e2849943439799b82d989bc3b" iuc parents: 1 diff changeset	199 </repeat>
028fafca04fa "planemo upload commit 9e4d2776d6b3276e2849943439799b82d989bc3b" iuc parents: 1 diff changeset	200 <repeat name="control_repeat" title="Control" min="0">
028fafca04fa "planemo upload commit 9e4d2776d6b3276e2849943439799b82d989bc3b" iuc parents: 1 diff changeset	201 <param name="control" type="data" format="bam,bed,scidx" label="Select control" help="Optional, supported formats are bam, bed and scidx">
028fafca04fa "planemo upload commit 9e4d2776d6b3276e2849943439799b82d989bc3b" iuc parents: 1 diff changeset	202 <validator type="unspecified_build" />
028fafca04fa "planemo upload commit 9e4d2776d6b3276e2849943439799b82d989bc3b" iuc parents: 1 diff changeset	203 </param>
028fafca04fa "planemo upload commit 9e4d2776d6b3276e2849943439799b82d989bc3b" iuc parents: 1 diff changeset	204 <conditional name="specify_replicate_name_cond">
028fafca04fa "planemo upload commit 9e4d2776d6b3276e2849943439799b82d989bc3b" iuc parents: 1 diff changeset	205 <param name="specify_replicate_name" type="select" label="Specify replicate name?" help="Optional for control. If used, the control will only be used for the corresponding named signal replicate">
028fafca04fa "planemo upload commit 9e4d2776d6b3276e2849943439799b82d989bc3b" iuc parents: 1 diff changeset	206 <option value="no" selected="True">No</option>
028fafca04fa "planemo upload commit 9e4d2776d6b3276e2849943439799b82d989bc3b" iuc parents: 1 diff changeset	207 <option value="yes">Yes</option>
028fafca04fa "planemo upload commit 9e4d2776d6b3276e2849943439799b82d989bc3b" iuc parents: 1 diff changeset	208 </param>
028fafca04fa "planemo upload commit 9e4d2776d6b3276e2849943439799b82d989bc3b" iuc parents: 1 diff changeset	209 <when value="yes">
028fafca04fa "planemo upload commit 9e4d2776d6b3276e2849943439799b82d989bc3b" iuc parents: 1 diff changeset	210 <param name="replicate_name" type="text" optional="true" label="Replicate name"/>
028fafca04fa "planemo upload commit 9e4d2776d6b3276e2849943439799b82d989bc3b" iuc parents: 1 diff changeset	211 </when>
028fafca04fa "planemo upload commit 9e4d2776d6b3276e2849943439799b82d989bc3b" iuc parents: 1 diff changeset	212 <when value="no" />
028fafca04fa "planemo upload commit 9e4d2776d6b3276e2849943439799b82d989bc3b" iuc parents: 1 diff changeset	213 </conditional>
028fafca04fa "planemo upload commit 9e4d2776d6b3276e2849943439799b82d989bc3b" iuc parents: 1 diff changeset	214 <expand macro="cond_fixedreadcount" />
028fafca04fa "planemo upload commit 9e4d2776d6b3276e2849943439799b82d989bc3b" iuc parents: 1 diff changeset	215 </repeat>
028fafca04fa "planemo upload commit 9e4d2776d6b3276e2849943439799b82d989bc3b" iuc parents: 1 diff changeset	216 </repeat>
028fafca04fa "planemo upload commit 9e4d2776d6b3276e2849943439799b82d989bc3b" iuc parents: 1 diff changeset	217 <param name="save_design_file" type="select" display="radio" label="Output design file?">
028fafca04fa "planemo upload commit 9e4d2776d6b3276e2849943439799b82d989bc3b" iuc parents: 1 diff changeset	218 <option value="no" selected="true">No</option>
028fafca04fa "planemo upload commit 9e4d2776d6b3276e2849943439799b82d989bc3b" iuc parents: 1 diff changeset	219 <option value="yes">Yes</option>
0 4aa531981208 Uploaded iuc parents: diff changeset	220 </param>
4aa531981208 Uploaded iuc parents: diff changeset	221 <!-- Advanced options -->
4aa531981208 Uploaded iuc parents: diff changeset	222 <conditional name="advanced_options_cond">
4aa531981208 Uploaded iuc parents: diff changeset	223 <param name="advanced_options" type="select" label="Advanced options">
4aa531981208 Uploaded iuc parents: diff changeset	224 <option value="hide" selected="true">Hide</option>
4aa531981208 Uploaded iuc parents: diff changeset	225 <option value="display">Display</option>
4aa531981208 Uploaded iuc parents: diff changeset	226 </param>
4aa531981208 Uploaded iuc parents: diff changeset	227 <when value="display">
4aa531981208 Uploaded iuc parents: diff changeset	228 <!-- Limits on how many reads -->
4aa531981208 Uploaded iuc parents: diff changeset	229 <conditional name="reads_limits_options_cond">
4aa531981208 Uploaded iuc parents: diff changeset	230 <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.">
4aa531981208 Uploaded iuc parents: diff changeset	231 <option value="no" selected="True">No</option>
4aa531981208 Uploaded iuc parents: diff changeset	232 <option value="yes">Yes</option>
4aa531981208 Uploaded iuc parents: diff changeset	233 </param>
4aa531981208 Uploaded iuc parents: diff changeset	234 <when value="no" />
4aa531981208 Uploaded iuc parents: diff changeset	235 <when value="yes">
4aa531981208 Uploaded iuc parents: diff changeset	236 <param name="fixedpb" type="integer" value="0" min="0" label="Fixed per-base limit" help="Zero value estimates from background model"/>
4aa531981208 Uploaded iuc parents: diff changeset	237 <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" />
4aa531981208 Uploaded iuc parents: diff changeset	238 <param name="nonunique" type="select" label="Use non-unique reads?">
4aa531981208 Uploaded iuc parents: diff changeset	239 <option value="no" selected="True">No</option>
4aa531981208 Uploaded iuc parents: diff changeset	240 <option value="yes">Yes</option>
4aa531981208 Uploaded iuc parents: diff changeset	241 </param>
4aa531981208 Uploaded iuc parents: diff changeset	242 <param name="mappability" type="float" value="0.0" min="0.8" label="Fraction of the genome that is mappable for these experiments" />
4aa531981208 Uploaded iuc parents: diff changeset	243 <param name="nocache" type="select" label="Turn off caching of the entire set of experiments?" help="Run slower with less memory" >
4aa531981208 Uploaded iuc parents: diff changeset	244 <option value="no" selected="True">No</option>
4aa531981208 Uploaded iuc parents: diff changeset	245 <option value="yes">Yes</option>
4aa531981208 Uploaded iuc parents: diff changeset	246 </param>
4aa531981208 Uploaded iuc parents: diff changeset	247 </when>
4aa531981208 Uploaded iuc parents: diff changeset	248 </conditional>
4aa531981208 Uploaded iuc parents: diff changeset	249 <!-- Scaling data -->
4aa531981208 Uploaded iuc parents: diff changeset	250 <conditional name="scale_data_cond">
2 028fafca04fa "planemo upload commit 9e4d2776d6b3276e2849943439799b82d989bc3b" iuc parents: 1 diff changeset	251 <param name="scale_data" type="select" label="Set data scaling parameters?" help="Default behavior is to scale signal to corresponding controls using the Normalization of ChIP-seq (NCIS) method.[2]">
0 4aa531981208 Uploaded iuc parents: diff changeset	252 <option value="no" selected="True">No</option>
4aa531981208 Uploaded iuc parents: diff changeset	253 <option value="yes">Yes</option>
4aa531981208 Uploaded iuc parents: diff changeset	254 </param>
4aa531981208 Uploaded iuc parents: diff changeset	255 <when value="yes">
4aa531981208 Uploaded iuc parents: diff changeset	256 <param name="scaling" type="select" label="Use signal vs control scaling?">
4aa531981208 Uploaded iuc parents: diff changeset	257 <option value="yes" selected="True">Yes</option>
4aa531981208 Uploaded iuc parents: diff changeset	258 <option value="no">No</option>
4aa531981208 Uploaded iuc parents: diff changeset	259 </param>
4aa531981208 Uploaded iuc parents: diff changeset	260 <param name="medianscale" type="select" label="Use the median signal/control ratio as the scaling factor?">
4aa531981208 Uploaded iuc parents: diff changeset	261 <option value="no" selected="True">No</option>
4aa531981208 Uploaded iuc parents: diff changeset	262 <option value="yes">Yes</option>
4aa531981208 Uploaded iuc parents: diff changeset	263 </param>
4aa531981208 Uploaded iuc parents: diff changeset	264 <param name="regressionscale" type="select" label="Use scaling by regression on binned tag counts?">
4aa531981208 Uploaded iuc parents: diff changeset	265 <option value="no" selected="True">No</option>
4aa531981208 Uploaded iuc parents: diff changeset	266 <option value="yes">Yes</option>
4aa531981208 Uploaded iuc parents: diff changeset	267 </param>
4aa531981208 Uploaded iuc parents: diff changeset	268 <param name="sesscale" type="select" label="Estimate scaling factor by SES?" help="SES: Diaz, et al. Stat Appl Genet Mol Biol. 2012">
4aa531981208 Uploaded iuc parents: diff changeset	269 <option value="no" selected="True">No</option>
4aa531981208 Uploaded iuc parents: diff changeset	270 <option value="yes">Yes</option>
4aa531981208 Uploaded iuc parents: diff changeset	271 </param>
4aa531981208 Uploaded iuc parents: diff changeset	272 <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" />
4aa531981208 Uploaded iuc parents: diff changeset	273 <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)." />
4aa531981208 Uploaded iuc parents: diff changeset	274 <param name="plotscaling" type="select" label="Plot diagnostic information for the chosen scaling method?">
4aa531981208 Uploaded iuc parents: diff changeset	275 <option value="no" selected="True">No</option>
4aa531981208 Uploaded iuc parents: diff changeset	276 <option value="yes">Yes</option>
4aa531981208 Uploaded iuc parents: diff changeset	277 </param>
4aa531981208 Uploaded iuc parents: diff changeset	278 </when>
4aa531981208 Uploaded iuc parents: diff changeset	279 <when value="no" />
4aa531981208 Uploaded iuc parents: diff changeset	280 </conditional>
4aa531981208 Uploaded iuc parents: diff changeset	281 <!-- Running MultiGPS -->
4aa531981208 Uploaded iuc parents: diff changeset	282 <param name="readdistributionfile" type="data" optional="True" format="tabular" label="Optional binding event read distribution file for initializing models" help="A default initial distribution appropriate for ChIP-seq data is used if this option is not specified." />
4aa531981208 Uploaded iuc parents: diff changeset	283 <param name="maxtrainingrounds" type="integer" value="3" min="0" label="Maximum number of training rounds for updating binding event read distributions" />
4aa531981208 Uploaded iuc parents: diff changeset	284 <param name="nomodelupdate" type="select" label="Perform binding model updates?">
4aa531981208 Uploaded iuc parents: diff changeset	285 <option value="yes" selected="True">Yes</option>
4aa531981208 Uploaded iuc parents: diff changeset	286 <option value="no">No</option>
4aa531981208 Uploaded iuc parents: diff changeset	287 </param>
4aa531981208 Uploaded iuc parents: diff changeset	288 <param name="minmodelupdateevents" type="integer" value="500" min="0" label="Minimum number of events to support an update of the read distribution" />
4aa531981208 Uploaded iuc parents: diff changeset	289 <conditional name="binding_model_smoothing_cond">
4aa531981208 Uploaded iuc parents: diff changeset	290 <param name="nomodelsmoothing" type="select" label="Perform binding model smoothing?" help="Smoothing performed with a cubic spline.">
4aa531981208 Uploaded iuc parents: diff changeset	291 <option value="yes" selected="True">Yes</option>
4aa531981208 Uploaded iuc parents: diff changeset	292 <option value="no">No</option>
4aa531981208 Uploaded iuc parents: diff changeset	293 </param>
4aa531981208 Uploaded iuc parents: diff changeset	294 <when value="yes">
4aa531981208 Uploaded iuc parents: diff changeset	295 <param name="splinesmoothparam" type="integer" value="30" min="0" label="Spline smoothing parameter" />
4aa531981208 Uploaded iuc parents: diff changeset	296 </when>
4aa531981208 Uploaded iuc parents: diff changeset	297 <when value="no" />
4aa531981208 Uploaded iuc parents: diff changeset	298 </conditional>
4aa531981208 Uploaded iuc parents: diff changeset	299 <conditional name="gauss_model_smoothing_cond">
4aa531981208 Uploaded iuc parents: diff changeset	300 <param name="gaussmodelsmoothing" type="select" label="Use Gaussian model smoothing?" help="Select No to smooth with a cubic spline.">
4aa531981208 Uploaded iuc parents: diff changeset	301 <option value="no" selected="True">No</option>
4aa531981208 Uploaded iuc parents: diff changeset	302 <option value="yes">Yes</option>
4aa531981208 Uploaded iuc parents: diff changeset	303 </param>
4aa531981208 Uploaded iuc parents: diff changeset	304 <when value="no" />
4aa531981208 Uploaded iuc parents: diff changeset	305 <when value="yes">
4aa531981208 Uploaded iuc parents: diff changeset	306 <param name="gausssmoothparam" type="integer" value="3" min="0" label="Smoothing factor" help="Gaussian smoothing standard deviation." />
4aa531981208 Uploaded iuc parents: diff changeset	307 </when>
4aa531981208 Uploaded iuc parents: diff changeset	308 </conditional>
4aa531981208 Uploaded iuc parents: diff changeset	309 <param name="jointinmodel" type="select" label="Allow joint events in model updates?">
4aa531981208 Uploaded iuc parents: diff changeset	310 <option value="no" selected="True">No</option>
4aa531981208 Uploaded iuc parents: diff changeset	311 <option value="yes">Yes</option>
4aa531981208 Uploaded iuc parents: diff changeset	312 </param>
4aa531981208 Uploaded iuc parents: diff changeset	313 <param name="fixedmodelrange" type="select" label="Keep binding model range fixed to inital size?" help="Select No to vary automatically">
4aa531981208 Uploaded iuc parents: diff changeset	314 <option value="no" selected="True">No</option>
4aa531981208 Uploaded iuc parents: diff changeset	315 <option value="yes">Yes</option>
4aa531981208 Uploaded iuc parents: diff changeset	316 </param>
4aa531981208 Uploaded iuc parents: diff changeset	317 <param name="prlogconf" type="integer" value="-6" label="Poisson log threshold for potential region scanning" />
4aa531981208 Uploaded iuc parents: diff changeset	318 <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." />
4aa531981208 Uploaded iuc parents: diff changeset	319 <param name="alphascale" type="float" value="1.0" min="0" label="Alpha scaling factor" />
4aa531981208 Uploaded iuc parents: diff changeset	320 <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.">
4aa531981208 Uploaded iuc parents: diff changeset	321 <option value="yes" selected="True">Yes</option>
4aa531981208 Uploaded iuc parents: diff changeset	322 <option value="no">No</option>
4aa531981208 Uploaded iuc parents: diff changeset	323 </param>
4aa531981208 Uploaded iuc parents: diff changeset	324 <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." />
4aa531981208 Uploaded iuc parents: diff changeset	325 <!-- MultiGPS priors -->
4aa531981208 Uploaded iuc parents: diff changeset	326 <conditional name="use_motif_cond">
4aa531981208 Uploaded iuc parents: diff changeset	327 <param name="use_motif" type="select" label="Perform motif-finding or use a motif-prior?">
4aa531981208 Uploaded iuc parents: diff changeset	328 <option value="no" selected="True">No</option>
4aa531981208 Uploaded iuc parents: diff changeset	329 <option value="yes">Yes</option>
4aa531981208 Uploaded iuc parents: diff changeset	330 </param>
4aa531981208 Uploaded iuc parents: diff changeset	331 <when value="yes">
4aa531981208 Uploaded iuc parents: diff changeset	332 <!-- Specifying the genome -->
4aa531981208 Uploaded iuc parents: diff changeset	333 <conditional name="reference_genome_cond">
4aa531981208 Uploaded iuc parents: diff changeset	334 <param name="reference_genome_source" type="select" label="Choose the source for the reference genome">
4aa531981208 Uploaded iuc parents: diff changeset	335 <option value="cached">locally cached</option>
4aa531981208 Uploaded iuc parents: diff changeset	336 <option value="history">from history</option>
4aa531981208 Uploaded iuc parents: diff changeset	337 </param>
4aa531981208 Uploaded iuc parents: diff changeset	338 <when value="cached">
4aa531981208 Uploaded iuc parents: diff changeset	339 <param name="reference_genome" type="select" label="Using reference genome">
4aa531981208 Uploaded iuc parents: diff changeset	340 <options from_data_table="all_fasta">
2 028fafca04fa "planemo upload commit 9e4d2776d6b3276e2849943439799b82d989bc3b" iuc parents: 1 diff changeset	341 <!-- <filter type="data_meta" key="dbkey" ref="expt" column="1"/> does not yet work in a repeat...-->
0 4aa531981208 Uploaded iuc parents: diff changeset	342 </options>
4aa531981208 Uploaded iuc parents: diff changeset	343 <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file"/>
4aa531981208 Uploaded iuc parents: diff changeset	344 </param>
4aa531981208 Uploaded iuc parents: diff changeset	345 </when>
4aa531981208 Uploaded iuc parents: diff changeset	346 <when value="history">
4aa531981208 Uploaded iuc parents: diff changeset	347 <param name="reference_genome" type="data" format="fasta" label="Using reference genome">
4aa531981208 Uploaded iuc parents: diff changeset	348 <options>
2 028fafca04fa "planemo upload commit 9e4d2776d6b3276e2849943439799b82d989bc3b" iuc parents: 1 diff changeset	349 <!-- <filter type="data_meta" key="dbkey" ref="expt"/> does not yet work in a repeat...-->
0 4aa531981208 Uploaded iuc parents: diff changeset	350 </options>
4aa531981208 Uploaded iuc parents: diff changeset	351 <validator type="no_options" message="The current history does not include a fasta dataset with the build associated with the selected input file"/>
4aa531981208 Uploaded iuc parents: diff changeset	352 </param>
4aa531981208 Uploaded iuc parents: diff changeset	353 </when>
4aa531981208 Uploaded iuc parents: diff changeset	354 </conditional>
4aa531981208 Uploaded iuc parents: diff changeset	355 <!-- MultiGPS priors options -->
4aa531981208 Uploaded iuc parents: diff changeset	356 <conditional name="multigps_priors_cond">
4aa531981208 Uploaded iuc parents: diff changeset	357 <param name="multigps_priors" type="select" label="Specify MultiGPS priors options?">
4aa531981208 Uploaded iuc parents: diff changeset	358 <option value="no" selected="True">No</option>
4aa531981208 Uploaded iuc parents: diff changeset	359 <option value="yes">Yes</option>
4aa531981208 Uploaded iuc parents: diff changeset	360 </param>
4aa531981208 Uploaded iuc parents: diff changeset	361 <when value="no" />
4aa531981208 Uploaded iuc parents: diff changeset	362 <when value="yes">
4aa531981208 Uploaded iuc parents: diff changeset	363 <param name="noposprior" type="select" label="Perform inter-experiment positional prior?">
4aa531981208 Uploaded iuc parents: diff changeset	364 <option value="yes" selected="True">Yes</option>
4aa531981208 Uploaded iuc parents: diff changeset	365 <option value="no">No</option>
4aa531981208 Uploaded iuc parents: diff changeset	366 </param>
4aa531981208 Uploaded iuc parents: diff changeset	367 <param name="probshared" type="float" value="0.9" min="0.0" label="Probability that events are shared across conditions" />
4aa531981208 Uploaded iuc parents: diff changeset	368 <conditional name="both_motifs_cond">
4aa531981208 Uploaded iuc parents: diff changeset	369 <param name="nomotifs" type="select" label="Perform both motif-finding and motif priors?">
4aa531981208 Uploaded iuc parents: diff changeset	370 <option value="yes" selected="True">Yes</option>
4aa531981208 Uploaded iuc parents: diff changeset	371 <option value="no">No</option>
4aa531981208 Uploaded iuc parents: diff changeset	372 </param>
4aa531981208 Uploaded iuc parents: diff changeset	373 <when value="yes">
4aa531981208 Uploaded iuc parents: diff changeset	374 <expand macro="motif_finding_params" />
4aa531981208 Uploaded iuc parents: diff changeset	375 </when>
4aa531981208 Uploaded iuc parents: diff changeset	376 <when value="no">
4aa531981208 Uploaded iuc parents: diff changeset	377 <conditional name="nomotifprior_cond">
4aa531981208 Uploaded iuc parents: diff changeset	378 <param name="nomotifprior" type="select" label="Perform motif-finding only?" help="Selecting Yes turns off motif priors.">
4aa531981208 Uploaded iuc parents: diff changeset	379 <option value="no" selected="True">No</option>
4aa531981208 Uploaded iuc parents: diff changeset	380 <option value="yes">Yes</option>
4aa531981208 Uploaded iuc parents: diff changeset	381 </param>
4aa531981208 Uploaded iuc parents: diff changeset	382 <when value="no" />
4aa531981208 Uploaded iuc parents: diff changeset	383 <when value="yes">
4aa531981208 Uploaded iuc parents: diff changeset	384 <expand macro="motif_finding_params" />
4aa531981208 Uploaded iuc parents: diff changeset	385 </when>
4aa531981208 Uploaded iuc parents: diff changeset	386 </conditional>
4aa531981208 Uploaded iuc parents: diff changeset	387 </when>
4aa531981208 Uploaded iuc parents: diff changeset	388 </conditional>
4aa531981208 Uploaded iuc parents: diff changeset	389 </when>
4aa531981208 Uploaded iuc parents: diff changeset	390 </conditional>
4aa531981208 Uploaded iuc parents: diff changeset	391 </when>
4aa531981208 Uploaded iuc parents: diff changeset	392 <when value="no" />
4aa531981208 Uploaded iuc parents: diff changeset	393 </conditional>
4aa531981208 Uploaded iuc parents: diff changeset	394 <!-- Reporting binding events -->
4aa531981208 Uploaded iuc parents: diff changeset	395 <conditional name="report_binding_events_cond">
4aa531981208 Uploaded iuc parents: diff changeset	396 <param name="report_binding_events" type="select" label="Report binding events?">
4aa531981208 Uploaded iuc parents: diff changeset	397 <option value="no" selected="True">No</option>
4aa531981208 Uploaded iuc parents: diff changeset	398 <option value="yes">Yes</option>
4aa531981208 Uploaded iuc parents: diff changeset	399 </param>
4aa531981208 Uploaded iuc parents: diff changeset	400 <when value="no" />
4aa531981208 Uploaded iuc parents: diff changeset	401 <when value="yes">
4aa531981208 Uploaded iuc parents: diff changeset	402 <param name="minqvalue" type="float" min="0" value="0.001" label="Minimum Q-value (corrected p-value) of reported binding events" />
4aa531981208 Uploaded iuc parents: diff changeset	403 <param name="minfold" type="float" min="0" value="1.5" label="Minimum event fold-change vs scaled control" />
4aa531981208 Uploaded iuc parents: diff changeset	404 <param name="nodifftests" type="select" label="Run differential enrichment tests?">
4aa531981208 Uploaded iuc parents: diff changeset	405 <option value="yes" selected="True">Yes</option>
4aa531981208 Uploaded iuc parents: diff changeset	406 <option value="no">No</option>
4aa531981208 Uploaded iuc parents: diff changeset	407 </param>
4aa531981208 Uploaded iuc parents: diff changeset	408 <param name="edgerod" type="float" min="0" value="0.15" label="EdgeR over-dispersion parameter value" />
4aa531981208 Uploaded iuc parents: diff changeset	409 <param name="diffp" type="float" min="0" value="0.01" label="Minimum p-value for reporting differential enrichment" />
4aa531981208 Uploaded iuc parents: diff changeset	410 </when>
4aa531981208 Uploaded iuc parents: diff changeset	411 </conditional>
4aa531981208 Uploaded iuc parents: diff changeset	412 </when>
4aa531981208 Uploaded iuc parents: diff changeset	413 <when value="hide" />
4aa531981208 Uploaded iuc parents: diff changeset	414 </conditional>
2 028fafca04fa "planemo upload commit 9e4d2776d6b3276e2849943439799b82d989bc3b" iuc parents: 1 diff changeset	415 <!-- Functional testing -->
028fafca04fa "planemo upload commit 9e4d2776d6b3276e2849943439799b82d989bc3b" iuc parents: 1 diff changeset	416 <param name="in_test_mode" type="hidden" value="no" />
0 4aa531981208 Uploaded iuc parents: diff changeset	417 </inputs>
4aa531981208 Uploaded iuc parents: diff changeset	418 <outputs>
2 028fafca04fa "planemo upload commit 9e4d2776d6b3276e2849943439799b82d989bc3b" iuc parents: 1 diff changeset	419 <data name="output_design_file" format="tabular" label="${tool.name} (design file) on ${on_string}">
028fafca04fa "planemo upload commit 9e4d2776d6b3276e2849943439799b82d989bc3b" iuc parents: 1 diff changeset	420 <filter>save_design_file == 'yes'</filter>
028fafca04fa "planemo upload commit 9e4d2776d6b3276e2849943439799b82d989bc3b" iuc parents: 1 diff changeset	421 </data>
028fafca04fa "planemo upload commit 9e4d2776d6b3276e2849943439799b82d989bc3b" iuc parents: 1 diff changeset	422 <data name="output_bed" format="bed" label="${tool.name} (bed) on ${on_string}"/>
028fafca04fa "planemo upload commit 9e4d2776d6b3276e2849943439799b82d989bc3b" iuc parents: 1 diff changeset	423 <data name="output_html" format="html" label="${tool.name} (html) on ${on_string}"/>
028fafca04fa "planemo upload commit 9e4d2776d6b3276e2849943439799b82d989bc3b" iuc parents: 1 diff changeset	424 <data name="replicates_counts" format="tabular" label="${tool.name} (replicates counts) on ${on_string}"/>
028fafca04fa "planemo upload commit 9e4d2776d6b3276e2849943439799b82d989bc3b" iuc parents: 1 diff changeset	425 <data name="all_events_table" format="tabular" label="${tool.name} (all events table) on ${on_string}"/>
0 4aa531981208 Uploaded iuc parents: diff changeset	426 </outputs>
4aa531981208 Uploaded iuc parents: diff changeset	427 <tests>
4aa531981208 Uploaded iuc parents: diff changeset	428 <test>
2 028fafca04fa "planemo upload commit 9e4d2776d6b3276e2849943439799b82d989bc3b" iuc parents: 1 diff changeset	429 <repeat name="condition_repeat">
028fafca04fa "planemo upload commit 9e4d2776d6b3276e2849943439799b82d989bc3b" iuc parents: 1 diff changeset	430 <repeat name="signal_repeat">
028fafca04fa "planemo upload commit 9e4d2776d6b3276e2849943439799b82d989bc3b" iuc parents: 1 diff changeset	431 <param name="signal" value="expt_hg19.scidx" ftype="scidx" dbkey="hg19" />
028fafca04fa "planemo upload commit 9e4d2776d6b3276e2849943439799b82d989bc3b" iuc parents: 1 diff changeset	432 </repeat>
028fafca04fa "planemo upload commit 9e4d2776d6b3276e2849943439799b82d989bc3b" iuc parents: 1 diff changeset	433 </repeat>
028fafca04fa "planemo upload commit 9e4d2776d6b3276e2849943439799b82d989bc3b" iuc parents: 1 diff changeset	434 <param name="advanced_options" value="hide" />
028fafca04fa "planemo upload commit 9e4d2776d6b3276e2849943439799b82d989bc3b" iuc parents: 1 diff changeset	435 <param name="in_test_mode" value="yes" />
0 4aa531981208 Uploaded iuc parents: diff changeset	436 <output name="output_html" file="hg19_output_html1.html" ftype="html" compare="contains"/>
2 028fafca04fa "planemo upload commit 9e4d2776d6b3276e2849943439799b82d989bc3b" iuc parents: 1 diff changeset	437 <output name="output_bed" file="hg19_output_bed1.bed" ftype="bed"/>
0 4aa531981208 Uploaded iuc parents: diff changeset	438 <output name="all_events_table" file="hg19_all_events_table1.tabular" ftype="tabular"/>
4aa531981208 Uploaded iuc parents: diff changeset	439 <output name="replicates_counts" file="hg19_replicates_counts1.tabular" ftype="tabular"/>
4aa531981208 Uploaded iuc parents: diff changeset	440 </test>
4aa531981208 Uploaded iuc parents: diff changeset	441 <test>
2 028fafca04fa "planemo upload commit 9e4d2776d6b3276e2849943439799b82d989bc3b" iuc parents: 1 diff changeset	442 <repeat name="condition_repeat">
028fafca04fa "planemo upload commit 9e4d2776d6b3276e2849943439799b82d989bc3b" iuc parents: 1 diff changeset	443 <repeat name="signal_repeat">
028fafca04fa "planemo upload commit 9e4d2776d6b3276e2849943439799b82d989bc3b" iuc parents: 1 diff changeset	444 <param name="signal" value="expt_hg19.scidx" ftype="scidx" dbkey="hg19" />
028fafca04fa "planemo upload commit 9e4d2776d6b3276e2849943439799b82d989bc3b" iuc parents: 1 diff changeset	445 </repeat>
028fafca04fa "planemo upload commit 9e4d2776d6b3276e2849943439799b82d989bc3b" iuc parents: 1 diff changeset	446 <repeat name="control_repeat">
028fafca04fa "planemo upload commit 9e4d2776d6b3276e2849943439799b82d989bc3b" iuc parents: 1 diff changeset	447 <param name="control" value="cntrl_hg19.scidx" ftype="scidx" dbkey="hg19" />
028fafca04fa "planemo upload commit 9e4d2776d6b3276e2849943439799b82d989bc3b" iuc parents: 1 diff changeset	448 </repeat>
028fafca04fa "planemo upload commit 9e4d2776d6b3276e2849943439799b82d989bc3b" iuc parents: 1 diff changeset	449 </repeat>
028fafca04fa "planemo upload commit 9e4d2776d6b3276e2849943439799b82d989bc3b" iuc parents: 1 diff changeset	450 <param name="advanced_options" value="display" />
028fafca04fa "planemo upload commit 9e4d2776d6b3276e2849943439799b82d989bc3b" iuc parents: 1 diff changeset	451 <param name="in_test_mode" value="yes" />
0 4aa531981208 Uploaded iuc parents: diff changeset	452 <output name="output_html" file="hg19_output_html2.html" ftype="html" compare="contains"/>
2 028fafca04fa "planemo upload commit 9e4d2776d6b3276e2849943439799b82d989bc3b" iuc parents: 1 diff changeset	453 <output name="output_bed" file="hg19_output_bed2.bed" ftype="bed"/>
0 4aa531981208 Uploaded iuc parents: diff changeset	454 <output name="all_events_table" file="hg19_all_events_table2.tabular" ftype="tabular"/>
4aa531981208 Uploaded iuc parents: diff changeset	455 <output name="replicates_counts" file="hg19_replicates_counts2.tabular" ftype="tabular"/>
4aa531981208 Uploaded iuc parents: diff changeset	456 </test>
4aa531981208 Uploaded iuc parents: diff changeset	457 </tests>
4aa531981208 Uploaded iuc parents: diff changeset	458 <help>
4aa531981208 Uploaded iuc parents: diff changeset	459
4aa531981208 Uploaded iuc parents: diff changeset	460 What it does
4aa531981208 Uploaded iuc parents: diff changeset	461
4aa531981208 Uploaded iuc parents: diff changeset	462 MultiGPS is a framework for analyzing collections of multi-condition ChIP-seq datasets and characterizing
4aa531981208 Uploaded iuc parents: diff changeset	463 differential binding events between conditions. MultiGPS encourages consistency in the reported binding
4aa531981208 Uploaded iuc parents: diff changeset	464 event locations across conditions and provides accurate estimation of ChIP enrichment levels at each event.
4aa531981208 Uploaded iuc parents: diff changeset	465 MultiGPS performs significant EM optimization of binding events along the genome and across experimental
4aa531981208 Uploaded iuc parents: diff changeset	466 conditions, and it integrates motif-finding via MEME. The tool loads all data into memory, so the potential
4aa531981208 Uploaded iuc parents: diff changeset	467 exists for time and memory intensive analyses if running over many conditions or large datasets.
4aa531981208 Uploaded iuc parents: diff changeset	468
4aa531981208 Uploaded iuc parents: diff changeset	469 -----
4aa531981208 Uploaded iuc parents: diff changeset	470
4aa531981208 Uploaded iuc parents: diff changeset	471 Options
4aa531981208 Uploaded iuc parents: diff changeset	472
4aa531981208 Uploaded iuc parents: diff changeset	473 * Loading data:
4aa531981208 Uploaded iuc parents: diff changeset	474
2 028fafca04fa "planemo upload commit 9e4d2776d6b3276e2849943439799b82d989bc3b" iuc parents: 1 diff changeset	475 - Optional file containing reads from a control experiment - file containing reads from a control experiment
0 4aa531981208 Uploaded iuc parents: diff changeset	476 - Fixed per-base limit - Fixed per-base limit (default: estimated from background model).
4aa531981208 Uploaded iuc parents: diff changeset	477 - Poisson threshold for filtering per base - Look at neighboring positions to decide what the per-base limit should be.
4aa531981208 Uploaded iuc parents: diff changeset	478 - Use non-unique reads - Use non-unique reads.
4aa531981208 Uploaded iuc parents: diff changeset	479 - Fraction of the genome that is mappable for these experiments - Fraction of the genome that is mappable for these experiments
4aa531981208 Uploaded iuc parents: diff changeset	480 - Turn off caching of the entire set of experiments? - Flag to turn off caching of the entire set of experiments (i.e. run slower with less memory).
4aa531981208 Uploaded iuc parents: diff changeset	481
4aa531981208 Uploaded iuc parents: diff changeset	482 * Scaling control vs signal counts:
4aa531981208 Uploaded iuc parents: diff changeset	483
4aa531981208 Uploaded iuc parents: diff changeset	484 - Use signal vs control scaling? - Flag to turn off auto estimation of signal vs control scaling factor
4aa531981208 Uploaded iuc parents: diff changeset	485 - Use the median signal/control ratio as the scaling factor? - Flag to use scaling by median ratio (default = scaling by NCIS).
4aa531981208 Uploaded iuc parents: diff changeset	486 - Use scaling by regression on binned tag counts? - Flag to use scaling by regression (default = scaling by NCIS).
4aa531981208 Uploaded iuc parents: diff changeset	487 - Estimate scaling factor by SES? - Specify whether to estimate scaling factor by SES.
4aa531981208 Uploaded iuc parents: diff changeset	488 - Multiply control counts by total tag count ratio and then by this factor - Multiply control counts by total tag count ratio and then by this factor (default: NCIS).
4aa531981208 Uploaded iuc parents: diff changeset	489 - Window size for estimating scaling ratios - Window size in base pairs for estimating scaling ratios
4aa531981208 Uploaded iuc parents: diff changeset	490 - Plot diagnostic information for the chosen scaling method? - Flag to plot diagnostic information for the chosen scaling method.
4aa531981208 Uploaded iuc parents: diff changeset	491
4aa531981208 Uploaded iuc parents: diff changeset	492 * Running MultiGPS:
4aa531981208 Uploaded iuc parents: diff changeset	493
4aa531981208 Uploaded iuc parents: diff changeset	494 - Optional binding event read distribution file - Binding event read distribution file for initializing models. The true distribution of reads around binding events is estimated during MultiGPS training. A default initial distribution appropriate for ChIP-seq data is used if this option is not specified.
4aa531981208 Uploaded iuc parents: diff changeset	495 - Maximum number of training rounds for updating binding event read distributions - Maximum number of training rounds for updating binding event read distributions.
4aa531981208 Uploaded iuc parents: diff changeset	496 - Perform binding model updates? - Perform binding model updates?
4aa531981208 Uploaded iuc parents: diff changeset	497 - Minimum number of events to support an update of the read distribution - Minimum number of events to support an update of the read distribution
4aa531981208 Uploaded iuc parents: diff changeset	498 - Perform binding model smoothing? - Smooth with a cubic spline using a specified smoothing factor.
4aa531981208 Uploaded iuc parents: diff changeset	499 - Spline smoothing parameter - Smoothing parameter for smoothing cubic spline.
4aa531981208 Uploaded iuc parents: diff changeset	500 - Perform Gaussian model smoothing? - Select "Yes" to use Gaussian model smoothing using a specified smoothing factor if binding model smoothing is not performed.
4aa531981208 Uploaded iuc parents: diff changeset	501 - Allow joint events in model updates? - Specify whether to allow joint events in model updates.
4aa531981208 Uploaded iuc parents: diff changeset	502 - Keep binding model range fixed to inital size? - Flag to keep binding model range fixed to inital size (default: vary automatically)
4aa531981208 Uploaded iuc parents: diff changeset	503 - Poisson log threshold for potential region scanning - Poisson log threshold for potential region scanning.
4aa531981208 Uploaded iuc parents: diff changeset	504 - Alpha scaling factor - Alpha scaling factor. Increasing this parameter results in stricter binding event calls.
4aa531981208 Uploaded iuc parents: diff changeset	505 - Impose this alpha - The alpha parameter 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. Default: estimate alpha automatically.
4aa531981208 Uploaded iuc parents: diff changeset	506 - Share component configs in the ML step? - Flag to not share component configs in the ML step
4aa531981208 Uploaded iuc parents: diff changeset	507 - Optional file containing a set of regions to ignore during MultiGPS training - File containing a set of regions to ignore during MultiGPS training. It’s a good idea to exclude the mitochondrial genome and other ‘blacklisted’ regions that contain artifactual accumulations of reads in both ChIP-seq and control experiments. MultiGPS will waste time trying to model binding events in these regions, even though they will not typically appear significantly enriched over the control (and thus will not be reported to the user).
4aa531981208 Uploaded iuc parents: diff changeset	508
4aa531981208 Uploaded iuc parents: diff changeset	509 * MultiGPS priors:
4aa531981208 Uploaded iuc parents: diff changeset	510
4aa531981208 Uploaded iuc parents: diff changeset	511 - Perform inter-experiment positional prior? - Flag to turn off inter-experiment positional prior (default=on).
4aa531981208 Uploaded iuc parents: diff changeset	512 - Probability that events are shared across conditions - Probability that events are shared across conditions.
4aa531981208 Uploaded iuc parents: diff changeset	513 - Perform both motif-finding and motif priors? - Flag to turn off motif-finding and motif priors.
4aa531981208 Uploaded iuc parents: diff changeset	514 - Perform motif-finding only? - Flag to turn off motif priors only.
4aa531981208 Uploaded iuc parents: diff changeset	515 - Number of motifs MEME should find for each condition - Number of motifs MEME should find for each condition.
4aa531981208 Uploaded iuc parents: diff changeset	516 - Minimum motif width for MEME - minw arg for MEME.
4aa531981208 Uploaded iuc parents: diff changeset	517 - Maximum motif width for MEME - maxw arg for MEME.
4aa531981208 Uploaded iuc parents: diff changeset	518
4aa531981208 Uploaded iuc parents: diff changeset	519 * Reporting binding events:
4aa531981208 Uploaded iuc parents: diff changeset	520
4aa531981208 Uploaded iuc parents: diff changeset	521 - Minimum Q-value (corrected p-value) of reported binding events - Minimum Q-value (corrected p-value) of reported binding events.
4aa531981208 Uploaded iuc parents: diff changeset	522 - Minimum event fold-change vs scaled control - Minimum event fold-change vs scaled control.
4aa531981208 Uploaded iuc parents: diff changeset	523 - Run differential enrichment tests? - Choose whether to run differential enrichment tests.
4aa531981208 Uploaded iuc parents: diff changeset	524 - EdgeR over-dispersion parameter value - EdgeR over-dispersion parameter value.
4aa531981208 Uploaded iuc parents: diff changeset	525 - Minimum p-value for reporting differential enrichment - Minimum p-value for reporting differential enrichment.
4aa531981208 Uploaded iuc parents: diff changeset	526
4aa531981208 Uploaded iuc parents: diff changeset	527 </help>
4aa531981208 Uploaded iuc parents: diff changeset	528 <citations>
4aa531981208 Uploaded iuc parents: diff changeset	529 <citation type="doi">10.1371/journal.pcbi.1003501</citation>
4aa531981208 Uploaded iuc parents: diff changeset	530 </citations>
4aa531981208 Uploaded iuc parents: diff changeset	531 </tool>
2 028fafca04fa "planemo upload commit 9e4d2776d6b3276e2849943439799b82d989bc3b" iuc parents: 1 diff changeset	532

Mercurial > repos > iuc > multigps

annotate multigps.xml @ 2:028fafca04fa draft default tip