tophat2_aurora: tophat2_aurora.xml annotate

author	Makoto Nasuno <nasuno@ascade.co.jp>
date	Fri, 26 Feb 2016 14:23:22 +0900
parents
children

rev	line source
0 589de4bdaca4 for Apache Aurora jobrunner Makoto Nasuno <nasuno@ascade.co.jp> parents: diff changeset	1 <tool id="tophat2_parallel" name="Tophat parallel for aurora" version="0.7">
589de4bdaca4 for Apache Aurora jobrunner Makoto Nasuno <nasuno@ascade.co.jp> parents: diff changeset	2 <!-- Wrapper compatible with Tophat version 2.0.0+ -->
589de4bdaca4 for Apache Aurora jobrunner Makoto Nasuno <nasuno@ascade.co.jp> parents: diff changeset	3 <description>Gapped-read mapper for RNA-seq data</description>
589de4bdaca4 for Apache Aurora jobrunner Makoto Nasuno <nasuno@ascade.co.jp> parents: diff changeset	4 <!-- <version_command>tophat2 --version</version_command> -->
589de4bdaca4 for Apache Aurora jobrunner Makoto Nasuno <nasuno@ascade.co.jp> parents: diff changeset	5 <requirements>
589de4bdaca4 for Apache Aurora jobrunner Makoto Nasuno <nasuno@ascade.co.jp> parents: diff changeset	6 <container type="docker">nasuno/tophat2:2.0.9</container>
589de4bdaca4 for Apache Aurora jobrunner Makoto Nasuno <nasuno@ascade.co.jp> parents: diff changeset	7 </requirements>
589de4bdaca4 for Apache Aurora jobrunner Makoto Nasuno <nasuno@ascade.co.jp> parents: diff changeset	8
589de4bdaca4 for Apache Aurora jobrunner Makoto Nasuno <nasuno@ascade.co.jp> parents: diff changeset	9 <command>
589de4bdaca4 for Apache Aurora jobrunner Makoto Nasuno <nasuno@ascade.co.jp> parents: diff changeset	10 ##
589de4bdaca4 for Apache Aurora jobrunner Makoto Nasuno <nasuno@ascade.co.jp> parents: diff changeset	11 ## Set path to index, building the reference if necessary.
589de4bdaca4 for Apache Aurora jobrunner Makoto Nasuno <nasuno@ascade.co.jp> parents: diff changeset	12 ##
589de4bdaca4 for Apache Aurora jobrunner Makoto Nasuno <nasuno@ascade.co.jp> parents: diff changeset	13
589de4bdaca4 for Apache Aurora jobrunner Makoto Nasuno <nasuno@ascade.co.jp> parents: diff changeset	14 #set index_path = ''
589de4bdaca4 for Apache Aurora jobrunner Makoto Nasuno <nasuno@ascade.co.jp> parents: diff changeset	15 #if $refGenomeSource.genomeSource == "history":
589de4bdaca4 for Apache Aurora jobrunner Makoto Nasuno <nasuno@ascade.co.jp> parents: diff changeset	16 bowtie2-build "$refGenomeSource.ownFile" genome ; ln -s "$refGenomeSource.ownFile" genome.fa ;
589de4bdaca4 for Apache Aurora jobrunner Makoto Nasuno <nasuno@ascade.co.jp> parents: diff changeset	17 #set index_path = 'genome'
589de4bdaca4 for Apache Aurora jobrunner Makoto Nasuno <nasuno@ascade.co.jp> parents: diff changeset	18 #else:
589de4bdaca4 for Apache Aurora jobrunner Makoto Nasuno <nasuno@ascade.co.jp> parents: diff changeset	19 #set index_path = $refGenomeSource.index.fields.path
589de4bdaca4 for Apache Aurora jobrunner Makoto Nasuno <nasuno@ascade.co.jp> parents: diff changeset	20 #end if
589de4bdaca4 for Apache Aurora jobrunner Makoto Nasuno <nasuno@ascade.co.jp> parents: diff changeset	21
589de4bdaca4 for Apache Aurora jobrunner Makoto Nasuno <nasuno@ascade.co.jp> parents: diff changeset	22 ##
589de4bdaca4 for Apache Aurora jobrunner Makoto Nasuno <nasuno@ascade.co.jp> parents: diff changeset	23 ## Run tophat.
589de4bdaca4 for Apache Aurora jobrunner Makoto Nasuno <nasuno@ascade.co.jp> parents: diff changeset	24 ##
589de4bdaca4 for Apache Aurora jobrunner Makoto Nasuno <nasuno@ascade.co.jp> parents: diff changeset	25
589de4bdaca4 for Apache Aurora jobrunner Makoto Nasuno <nasuno@ascade.co.jp> parents: diff changeset	26 tophat2
589de4bdaca4 for Apache Aurora jobrunner Makoto Nasuno <nasuno@ascade.co.jp> parents: diff changeset	27
589de4bdaca4 for Apache Aurora jobrunner Makoto Nasuno <nasuno@ascade.co.jp> parents: diff changeset	28 ## Change this to accommodate the number of threads you have available.
589de4bdaca4 for Apache Aurora jobrunner Makoto Nasuno <nasuno@ascade.co.jp> parents: diff changeset	29 --num-threads \${GALAXY_SLOTS:-4}
589de4bdaca4 for Apache Aurora jobrunner Makoto Nasuno <nasuno@ascade.co.jp> parents: diff changeset	30
589de4bdaca4 for Apache Aurora jobrunner Makoto Nasuno <nasuno@ascade.co.jp> parents: diff changeset	31 --output-dir ./tophat_out
589de4bdaca4 for Apache Aurora jobrunner Makoto Nasuno <nasuno@ascade.co.jp> parents: diff changeset	32
589de4bdaca4 for Apache Aurora jobrunner Makoto Nasuno <nasuno@ascade.co.jp> parents: diff changeset	33 ## Set params.
589de4bdaca4 for Apache Aurora jobrunner Makoto Nasuno <nasuno@ascade.co.jp> parents: diff changeset	34 #if $params.settingsType == "full":
589de4bdaca4 for Apache Aurora jobrunner Makoto Nasuno <nasuno@ascade.co.jp> parents: diff changeset	35 --read-mismatches $params.read_mismatches
589de4bdaca4 for Apache Aurora jobrunner Makoto Nasuno <nasuno@ascade.co.jp> parents: diff changeset	36 #if str($params.bowtie_n) == "Yes":
589de4bdaca4 for Apache Aurora jobrunner Makoto Nasuno <nasuno@ascade.co.jp> parents: diff changeset	37 --bowtie-n
589de4bdaca4 for Apache Aurora jobrunner Makoto Nasuno <nasuno@ascade.co.jp> parents: diff changeset	38 #end if
589de4bdaca4 for Apache Aurora jobrunner Makoto Nasuno <nasuno@ascade.co.jp> parents: diff changeset	39
589de4bdaca4 for Apache Aurora jobrunner Makoto Nasuno <nasuno@ascade.co.jp> parents: diff changeset	40 --read-edit-dist $params.read_edit_dist
589de4bdaca4 for Apache Aurora jobrunner Makoto Nasuno <nasuno@ascade.co.jp> parents: diff changeset	41 --read-realign-edit-dist $params.read_realign_edit_dist
589de4bdaca4 for Apache Aurora jobrunner Makoto Nasuno <nasuno@ascade.co.jp> parents: diff changeset	42 -a $params.anchor_length
589de4bdaca4 for Apache Aurora jobrunner Makoto Nasuno <nasuno@ascade.co.jp> parents: diff changeset	43 -m $params.splice_mismatches
589de4bdaca4 for Apache Aurora jobrunner Makoto Nasuno <nasuno@ascade.co.jp> parents: diff changeset	44 -i $params.min_intron_length
589de4bdaca4 for Apache Aurora jobrunner Makoto Nasuno <nasuno@ascade.co.jp> parents: diff changeset	45 -I $params.max_intron_length
589de4bdaca4 for Apache Aurora jobrunner Makoto Nasuno <nasuno@ascade.co.jp> parents: diff changeset	46 -g $params.max_multihits
589de4bdaca4 for Apache Aurora jobrunner Makoto Nasuno <nasuno@ascade.co.jp> parents: diff changeset	47 --min-segment-intron $params.min_segment_intron
589de4bdaca4 for Apache Aurora jobrunner Makoto Nasuno <nasuno@ascade.co.jp> parents: diff changeset	48 --max-segment-intron $params.max_segment_intron
589de4bdaca4 for Apache Aurora jobrunner Makoto Nasuno <nasuno@ascade.co.jp> parents: diff changeset	49 --segment-mismatches $params.seg_mismatches
589de4bdaca4 for Apache Aurora jobrunner Makoto Nasuno <nasuno@ascade.co.jp> parents: diff changeset	50 --segment-length $params.seg_length
589de4bdaca4 for Apache Aurora jobrunner Makoto Nasuno <nasuno@ascade.co.jp> parents: diff changeset	51 --library-type $params.library_type
589de4bdaca4 for Apache Aurora jobrunner Makoto Nasuno <nasuno@ascade.co.jp> parents: diff changeset	52
589de4bdaca4 for Apache Aurora jobrunner Makoto Nasuno <nasuno@ascade.co.jp> parents: diff changeset	53 ## Indel search.
589de4bdaca4 for Apache Aurora jobrunner Makoto Nasuno <nasuno@ascade.co.jp> parents: diff changeset	54 #if $params.indel_search.allow_indel_search == "Yes":
589de4bdaca4 for Apache Aurora jobrunner Makoto Nasuno <nasuno@ascade.co.jp> parents: diff changeset	55 ## --allow-indels
589de4bdaca4 for Apache Aurora jobrunner Makoto Nasuno <nasuno@ascade.co.jp> parents: diff changeset	56 --max-insertion-length $params.indel_search.max_insertion_length
589de4bdaca4 for Apache Aurora jobrunner Makoto Nasuno <nasuno@ascade.co.jp> parents: diff changeset	57 --max-deletion-length $params.indel_search.max_deletion_length
589de4bdaca4 for Apache Aurora jobrunner Makoto Nasuno <nasuno@ascade.co.jp> parents: diff changeset	58 #else:
589de4bdaca4 for Apache Aurora jobrunner Makoto Nasuno <nasuno@ascade.co.jp> parents: diff changeset	59 --no-novel-indels
589de4bdaca4 for Apache Aurora jobrunner Makoto Nasuno <nasuno@ascade.co.jp> parents: diff changeset	60 #end if
589de4bdaca4 for Apache Aurora jobrunner Makoto Nasuno <nasuno@ascade.co.jp> parents: diff changeset	61
589de4bdaca4 for Apache Aurora jobrunner Makoto Nasuno <nasuno@ascade.co.jp> parents: diff changeset	62 ## Supplying junctions parameters.
589de4bdaca4 for Apache Aurora jobrunner Makoto Nasuno <nasuno@ascade.co.jp> parents: diff changeset	63 #if $params.own_junctions.use_junctions == "Yes":
589de4bdaca4 for Apache Aurora jobrunner Makoto Nasuno <nasuno@ascade.co.jp> parents: diff changeset	64 #if $params.own_junctions.gene_model_ann.use_annotations == "Yes":
589de4bdaca4 for Apache Aurora jobrunner Makoto Nasuno <nasuno@ascade.co.jp> parents: diff changeset	65 -G $params.own_junctions.gene_model_ann.gene_annotation_model
589de4bdaca4 for Apache Aurora jobrunner Makoto Nasuno <nasuno@ascade.co.jp> parents: diff changeset	66 #end if
589de4bdaca4 for Apache Aurora jobrunner Makoto Nasuno <nasuno@ascade.co.jp> parents: diff changeset	67 #if $params.own_junctions.raw_juncs.use_juncs == "Yes":
589de4bdaca4 for Apache Aurora jobrunner Makoto Nasuno <nasuno@ascade.co.jp> parents: diff changeset	68 -j $params.own_junctions.raw_juncs.raw_juncs
589de4bdaca4 for Apache Aurora jobrunner Makoto Nasuno <nasuno@ascade.co.jp> parents: diff changeset	69 #end if
589de4bdaca4 for Apache Aurora jobrunner Makoto Nasuno <nasuno@ascade.co.jp> parents: diff changeset	70 #if str($params.own_junctions.no_novel_juncs) == "Yes":
589de4bdaca4 for Apache Aurora jobrunner Makoto Nasuno <nasuno@ascade.co.jp> parents: diff changeset	71 --no-novel-juncs
589de4bdaca4 for Apache Aurora jobrunner Makoto Nasuno <nasuno@ascade.co.jp> parents: diff changeset	72 #end if
589de4bdaca4 for Apache Aurora jobrunner Makoto Nasuno <nasuno@ascade.co.jp> parents: diff changeset	73 #end if
589de4bdaca4 for Apache Aurora jobrunner Makoto Nasuno <nasuno@ascade.co.jp> parents: diff changeset	74
589de4bdaca4 for Apache Aurora jobrunner Makoto Nasuno <nasuno@ascade.co.jp> parents: diff changeset	75 #if $params.coverage_search.use_search == "Yes":
589de4bdaca4 for Apache Aurora jobrunner Makoto Nasuno <nasuno@ascade.co.jp> parents: diff changeset	76 --coverage-search
589de4bdaca4 for Apache Aurora jobrunner Makoto Nasuno <nasuno@ascade.co.jp> parents: diff changeset	77 --min-coverage-intron $params.coverage_search.min_coverage_intron
589de4bdaca4 for Apache Aurora jobrunner Makoto Nasuno <nasuno@ascade.co.jp> parents: diff changeset	78 --max-coverage-intron $params.coverage_search.max_coverage_intron
589de4bdaca4 for Apache Aurora jobrunner Makoto Nasuno <nasuno@ascade.co.jp> parents: diff changeset	79 #else:
589de4bdaca4 for Apache Aurora jobrunner Makoto Nasuno <nasuno@ascade.co.jp> parents: diff changeset	80 --no-coverage-search
589de4bdaca4 for Apache Aurora jobrunner Makoto Nasuno <nasuno@ascade.co.jp> parents: diff changeset	81 #end if
589de4bdaca4 for Apache Aurora jobrunner Makoto Nasuno <nasuno@ascade.co.jp> parents: diff changeset	82
589de4bdaca4 for Apache Aurora jobrunner Makoto Nasuno <nasuno@ascade.co.jp> parents: diff changeset	83 #if str($params.microexon_search) == "Yes":
589de4bdaca4 for Apache Aurora jobrunner Makoto Nasuno <nasuno@ascade.co.jp> parents: diff changeset	84 --microexon-search
589de4bdaca4 for Apache Aurora jobrunner Makoto Nasuno <nasuno@ascade.co.jp> parents: diff changeset	85 #end if
589de4bdaca4 for Apache Aurora jobrunner Makoto Nasuno <nasuno@ascade.co.jp> parents: diff changeset	86
589de4bdaca4 for Apache Aurora jobrunner Makoto Nasuno <nasuno@ascade.co.jp> parents: diff changeset	87 #if $params.fusion_search.do_search == "Yes":
589de4bdaca4 for Apache Aurora jobrunner Makoto Nasuno <nasuno@ascade.co.jp> parents: diff changeset	88 --fusion-search
589de4bdaca4 for Apache Aurora jobrunner Makoto Nasuno <nasuno@ascade.co.jp> parents: diff changeset	89 --fusion-anchor-length $params.fusion_search.anchor_len
589de4bdaca4 for Apache Aurora jobrunner Makoto Nasuno <nasuno@ascade.co.jp> parents: diff changeset	90 --fusion-min-dist $params.fusion_search.min_dist
589de4bdaca4 for Apache Aurora jobrunner Makoto Nasuno <nasuno@ascade.co.jp> parents: diff changeset	91 --fusion-read-mismatches $params.fusion_search.read_mismatches
589de4bdaca4 for Apache Aurora jobrunner Makoto Nasuno <nasuno@ascade.co.jp> parents: diff changeset	92 --fusion-multireads $params.fusion_search.multireads
589de4bdaca4 for Apache Aurora jobrunner Makoto Nasuno <nasuno@ascade.co.jp> parents: diff changeset	93 --fusion-multipairs $params.fusion_search.multipairs
589de4bdaca4 for Apache Aurora jobrunner Makoto Nasuno <nasuno@ascade.co.jp> parents: diff changeset	94 --fusion-ignore-chromosomes "$params.fusion_search.ignore_chromosomes"
589de4bdaca4 for Apache Aurora jobrunner Makoto Nasuno <nasuno@ascade.co.jp> parents: diff changeset	95 #end if
589de4bdaca4 for Apache Aurora jobrunner Makoto Nasuno <nasuno@ascade.co.jp> parents: diff changeset	96
589de4bdaca4 for Apache Aurora jobrunner Makoto Nasuno <nasuno@ascade.co.jp> parents: diff changeset	97 #if $params.bowtie2_settings.b2_settings == "Yes":
589de4bdaca4 for Apache Aurora jobrunner Makoto Nasuno <nasuno@ascade.co.jp> parents: diff changeset	98 #if $params.bowtie2_settings.preset.b2_preset == "Yes":
589de4bdaca4 for Apache Aurora jobrunner Makoto Nasuno <nasuno@ascade.co.jp> parents: diff changeset	99 --b2-$params.bowtie2_settings.preset.b2_preset_select
589de4bdaca4 for Apache Aurora jobrunner Makoto Nasuno <nasuno@ascade.co.jp> parents: diff changeset	100 #end if
589de4bdaca4 for Apache Aurora jobrunner Makoto Nasuno <nasuno@ascade.co.jp> parents: diff changeset	101 #end if
589de4bdaca4 for Apache Aurora jobrunner Makoto Nasuno <nasuno@ascade.co.jp> parents: diff changeset	102
589de4bdaca4 for Apache Aurora jobrunner Makoto Nasuno <nasuno@ascade.co.jp> parents: diff changeset	103 #end if
589de4bdaca4 for Apache Aurora jobrunner Makoto Nasuno <nasuno@ascade.co.jp> parents: diff changeset	104
589de4bdaca4 for Apache Aurora jobrunner Makoto Nasuno <nasuno@ascade.co.jp> parents: diff changeset	105 ## Read group information.
589de4bdaca4 for Apache Aurora jobrunner Makoto Nasuno <nasuno@ascade.co.jp> parents: diff changeset	106 #if $readGroup.specReadGroup == "yes"
589de4bdaca4 for Apache Aurora jobrunner Makoto Nasuno <nasuno@ascade.co.jp> parents: diff changeset	107 --rg-id "$readGroup.rgid"
589de4bdaca4 for Apache Aurora jobrunner Makoto Nasuno <nasuno@ascade.co.jp> parents: diff changeset	108 --rg-library "$readGroup.rglb"
589de4bdaca4 for Apache Aurora jobrunner Makoto Nasuno <nasuno@ascade.co.jp> parents: diff changeset	109 --rg-platform "$readGroup.rgpl"
589de4bdaca4 for Apache Aurora jobrunner Makoto Nasuno <nasuno@ascade.co.jp> parents: diff changeset	110 --rg-sample "$readGroup.rgsm"
589de4bdaca4 for Apache Aurora jobrunner Makoto Nasuno <nasuno@ascade.co.jp> parents: diff changeset	111 #end if
589de4bdaca4 for Apache Aurora jobrunner Makoto Nasuno <nasuno@ascade.co.jp> parents: diff changeset	112
589de4bdaca4 for Apache Aurora jobrunner Makoto Nasuno <nasuno@ascade.co.jp> parents: diff changeset	113 ## Set index path, inputs and parameters specific to paired data.
589de4bdaca4 for Apache Aurora jobrunner Makoto Nasuno <nasuno@ascade.co.jp> parents: diff changeset	114 #if $singlePaired.sPaired != "single"
589de4bdaca4 for Apache Aurora jobrunner Makoto Nasuno <nasuno@ascade.co.jp> parents: diff changeset	115 -r $singlePaired.mate_inner_distance
589de4bdaca4 for Apache Aurora jobrunner Makoto Nasuno <nasuno@ascade.co.jp> parents: diff changeset	116 --mate-std-dev=$singlePaired.mate_std_dev
589de4bdaca4 for Apache Aurora jobrunner Makoto Nasuno <nasuno@ascade.co.jp> parents: diff changeset	117
589de4bdaca4 for Apache Aurora jobrunner Makoto Nasuno <nasuno@ascade.co.jp> parents: diff changeset	118 #if str($singlePaired.report_discordant_pairs) == "No":
589de4bdaca4 for Apache Aurora jobrunner Makoto Nasuno <nasuno@ascade.co.jp> parents: diff changeset	119 --no-discordant
589de4bdaca4 for Apache Aurora jobrunner Makoto Nasuno <nasuno@ascade.co.jp> parents: diff changeset	120 #end if
589de4bdaca4 for Apache Aurora jobrunner Makoto Nasuno <nasuno@ascade.co.jp> parents: diff changeset	121
589de4bdaca4 for Apache Aurora jobrunner Makoto Nasuno <nasuno@ascade.co.jp> parents: diff changeset	122 #if $singlePaired.sPaired == "paired"
589de4bdaca4 for Apache Aurora jobrunner Makoto Nasuno <nasuno@ascade.co.jp> parents: diff changeset	123 ${index_path} "$singlePaired.input1" "$singlePaired.input2"
589de4bdaca4 for Apache Aurora jobrunner Makoto Nasuno <nasuno@ascade.co.jp> parents: diff changeset	124 #else
589de4bdaca4 for Apache Aurora jobrunner Makoto Nasuno <nasuno@ascade.co.jp> parents: diff changeset	125 ${index_path} "$singlePaired.input.forward" "$singlePaired.input.reverse"
589de4bdaca4 for Apache Aurora jobrunner Makoto Nasuno <nasuno@ascade.co.jp> parents: diff changeset	126 #end if
589de4bdaca4 for Apache Aurora jobrunner Makoto Nasuno <nasuno@ascade.co.jp> parents: diff changeset	127 #else
589de4bdaca4 for Apache Aurora jobrunner Makoto Nasuno <nasuno@ascade.co.jp> parents: diff changeset	128 ${index_path} "$singlePaired.input1"
589de4bdaca4 for Apache Aurora jobrunner Makoto Nasuno <nasuno@ascade.co.jp> parents: diff changeset	129 #end if
589de4bdaca4 for Apache Aurora jobrunner Makoto Nasuno <nasuno@ascade.co.jp> parents: diff changeset	130 </command>
589de4bdaca4 for Apache Aurora jobrunner Makoto Nasuno <nasuno@ascade.co.jp> parents: diff changeset	131
589de4bdaca4 for Apache Aurora jobrunner Makoto Nasuno <nasuno@ascade.co.jp> parents: diff changeset	132 <inputs>
589de4bdaca4 for Apache Aurora jobrunner Makoto Nasuno <nasuno@ascade.co.jp> parents: diff changeset	133 <param name="job_annotation" type="text" value="tophat.parallel" label="Job Annotation" />
589de4bdaca4 for Apache Aurora jobrunner Makoto Nasuno <nasuno@ascade.co.jp> parents: diff changeset	134 <conditional name="singlePaired">
589de4bdaca4 for Apache Aurora jobrunner Makoto Nasuno <nasuno@ascade.co.jp> parents: diff changeset	135 <param name="sPaired" type="select" label="Is this library mate-paired?">
589de4bdaca4 for Apache Aurora jobrunner Makoto Nasuno <nasuno@ascade.co.jp> parents: diff changeset	136 <option value="single">Single-end</option>
589de4bdaca4 for Apache Aurora jobrunner Makoto Nasuno <nasuno@ascade.co.jp> parents: diff changeset	137 <option value="paired">Paired-end (as individual datasets)</option>
589de4bdaca4 for Apache Aurora jobrunner Makoto Nasuno <nasuno@ascade.co.jp> parents: diff changeset	138 <option value="paired_collection">Paired-end (as collection)</option>
589de4bdaca4 for Apache Aurora jobrunner Makoto Nasuno <nasuno@ascade.co.jp> parents: diff changeset	139 </param>
589de4bdaca4 for Apache Aurora jobrunner Makoto Nasuno <nasuno@ascade.co.jp> parents: diff changeset	140 <when value="single">
589de4bdaca4 for Apache Aurora jobrunner Makoto Nasuno <nasuno@ascade.co.jp> parents: diff changeset	141 <param format="fastqsanger" name="input1" type="data" label="RNA-Seq FASTQ file" help="Nucleotide-space: Must have Sanger-scaled quality values with ASCII offset 33"/>
589de4bdaca4 for Apache Aurora jobrunner Makoto Nasuno <nasuno@ascade.co.jp> parents: diff changeset	142 </when>
589de4bdaca4 for Apache Aurora jobrunner Makoto Nasuno <nasuno@ascade.co.jp> parents: diff changeset	143 <when value="paired">
589de4bdaca4 for Apache Aurora jobrunner Makoto Nasuno <nasuno@ascade.co.jp> parents: diff changeset	144 <param format="fastqsanger" name="input1" type="data" label="RNA-Seq FASTQ file, forward reads" help="Nucleotide-space: Must have Sanger-scaled quality values with ASCII offset 33" />
589de4bdaca4 for Apache Aurora jobrunner Makoto Nasuno <nasuno@ascade.co.jp> parents: diff changeset	145 <param format="fastqsanger" name="input2" type="data" label="RNA-Seq FASTQ file, reverse reads" help="Nucleotide-space: Must have Sanger-scaled quality values with ASCII offset 33" />
589de4bdaca4 for Apache Aurora jobrunner Makoto Nasuno <nasuno@ascade.co.jp> parents: diff changeset	146 <expand macro="paired_parameters" />
589de4bdaca4 for Apache Aurora jobrunner Makoto Nasuno <nasuno@ascade.co.jp> parents: diff changeset	147 </when>
589de4bdaca4 for Apache Aurora jobrunner Makoto Nasuno <nasuno@ascade.co.jp> parents: diff changeset	148 <when value="paired_collection">
589de4bdaca4 for Apache Aurora jobrunner Makoto Nasuno <nasuno@ascade.co.jp> parents: diff changeset	149 <param format="fastqsanger" name="input" type="data_collection" collection_type="paired" label="RNA-Seq FASTQ paired reads" help="Nucleotide-space: Must have Sanger-scaled quality values with ASCII offset 33" />
589de4bdaca4 for Apache Aurora jobrunner Makoto Nasuno <nasuno@ascade.co.jp> parents: diff changeset	150 <expand macro="paired_parameters" />
589de4bdaca4 for Apache Aurora jobrunner Makoto Nasuno <nasuno@ascade.co.jp> parents: diff changeset	151 </when>
589de4bdaca4 for Apache Aurora jobrunner Makoto Nasuno <nasuno@ascade.co.jp> parents: diff changeset	152 </conditional>
589de4bdaca4 for Apache Aurora jobrunner Makoto Nasuno <nasuno@ascade.co.jp> parents: diff changeset	153 <expand macro="refGenomeSourceConditional">
589de4bdaca4 for Apache Aurora jobrunner Makoto Nasuno <nasuno@ascade.co.jp> parents: diff changeset	154 <options from_data_table="tophat2_indexes">
589de4bdaca4 for Apache Aurora jobrunner Makoto Nasuno <nasuno@ascade.co.jp> parents: diff changeset	155 <filter type="sort_by" column="2"/>
589de4bdaca4 for Apache Aurora jobrunner Makoto Nasuno <nasuno@ascade.co.jp> parents: diff changeset	156 <validator type="no_options" message="No genomes are available for the selected input dataset"/>
589de4bdaca4 for Apache Aurora jobrunner Makoto Nasuno <nasuno@ascade.co.jp> parents: diff changeset	157 </options>
589de4bdaca4 for Apache Aurora jobrunner Makoto Nasuno <nasuno@ascade.co.jp> parents: diff changeset	158 </expand>
589de4bdaca4 for Apache Aurora jobrunner Makoto Nasuno <nasuno@ascade.co.jp> parents: diff changeset	159 <conditional name="params">
589de4bdaca4 for Apache Aurora jobrunner Makoto Nasuno <nasuno@ascade.co.jp> parents: diff changeset	160 <param name="settingsType" type="select" label="TopHat settings to use" help="You can use the default settings or set custom values for any of Tophat's parameters.">
589de4bdaca4 for Apache Aurora jobrunner Makoto Nasuno <nasuno@ascade.co.jp> parents: diff changeset	161 <option value="preSet">Use Defaults</option>
589de4bdaca4 for Apache Aurora jobrunner Makoto Nasuno <nasuno@ascade.co.jp> parents: diff changeset	162 <option value="full">Full parameter list</option>
589de4bdaca4 for Apache Aurora jobrunner Makoto Nasuno <nasuno@ascade.co.jp> parents: diff changeset	163 </param>
589de4bdaca4 for Apache Aurora jobrunner Makoto Nasuno <nasuno@ascade.co.jp> parents: diff changeset	164 <when value="preSet" />
589de4bdaca4 for Apache Aurora jobrunner Makoto Nasuno <nasuno@ascade.co.jp> parents: diff changeset	165 <!-- Full/advanced params. -->
589de4bdaca4 for Apache Aurora jobrunner Makoto Nasuno <nasuno@ascade.co.jp> parents: diff changeset	166 <when value="full">
589de4bdaca4 for Apache Aurora jobrunner Makoto Nasuno <nasuno@ascade.co.jp> parents: diff changeset	167 <param name="read_realign_edit_dist" type="integer" value="1000" label="Max realign edit distance" help="Some of the reads spanning multiple exons may be mapped incorrectly as a contiguous alignment to the genome even though the correct alignment should be a spliced one - this can happen in the presence of processed pseudogenes that are rarely (if at all) transcribed or expressed. This option can direct TopHat to re-align reads for which the edit distance of an alignment obtained in a previous mapping step is above or equal to this option value. If you set this option to 0, TopHat will map every read in all the mapping steps (transcriptome if you provided gene annotations, genome, and finally splice variants detected by TopHat), reporting the best possible alignment found in any of these mapping steps. This may greatly increase the mapping accuracy at the expense of an increase in running time. The default value for this option is set such that TopHat will not try to realign reads already mapped in earlier steps." />
589de4bdaca4 for Apache Aurora jobrunner Makoto Nasuno <nasuno@ascade.co.jp> parents: diff changeset	168
589de4bdaca4 for Apache Aurora jobrunner Makoto Nasuno <nasuno@ascade.co.jp> parents: diff changeset	169 <param name="read_edit_dist" type="integer" value="2" label="Max edit distance" help="Final read alignments having more than these many edit distance are discarded." />
589de4bdaca4 for Apache Aurora jobrunner Makoto Nasuno <nasuno@ascade.co.jp> parents: diff changeset	170
589de4bdaca4 for Apache Aurora jobrunner Makoto Nasuno <nasuno@ascade.co.jp> parents: diff changeset	171 <param name="library_type" type="select" label="Library Type" help="TopHat will treat the reads as strand specific. Every read alignment will have an XS attribute tag. Consider supplying library type options below to select the correct RNA-seq protocol.">
589de4bdaca4 for Apache Aurora jobrunner Makoto Nasuno <nasuno@ascade.co.jp> parents: diff changeset	172 <option value="fr-unstranded">FR Unstranded</option>
589de4bdaca4 for Apache Aurora jobrunner Makoto Nasuno <nasuno@ascade.co.jp> parents: diff changeset	173 <option value="fr-firststrand">FR First Strand</option>
589de4bdaca4 for Apache Aurora jobrunner Makoto Nasuno <nasuno@ascade.co.jp> parents: diff changeset	174 <option value="fr-secondstrand">FR Second Strand</option>
589de4bdaca4 for Apache Aurora jobrunner Makoto Nasuno <nasuno@ascade.co.jp> parents: diff changeset	175 </param>
589de4bdaca4 for Apache Aurora jobrunner Makoto Nasuno <nasuno@ascade.co.jp> parents: diff changeset	176 <param name="read_mismatches" type="integer" value="2" label="Final read mismatches" help="Final read alignments having more than these many mismatches are discarded." />
589de4bdaca4 for Apache Aurora jobrunner Makoto Nasuno <nasuno@ascade.co.jp> parents: diff changeset	177 <param name="bowtie_n" type="select" label="Use bowtie -n mode">
589de4bdaca4 for Apache Aurora jobrunner Makoto Nasuno <nasuno@ascade.co.jp> parents: diff changeset	178 <option selected="true" value="No">No</option>
589de4bdaca4 for Apache Aurora jobrunner Makoto Nasuno <nasuno@ascade.co.jp> parents: diff changeset	179 <option value="Yes">Yes</option>
589de4bdaca4 for Apache Aurora jobrunner Makoto Nasuno <nasuno@ascade.co.jp> parents: diff changeset	180 </param>
589de4bdaca4 for Apache Aurora jobrunner Makoto Nasuno <nasuno@ascade.co.jp> parents: diff changeset	181 <param name="anchor_length" type="integer" value="8" label="Anchor length (at least 3)" help="Report junctions spanned by reads with at least this many bases on each side of the junction." />
589de4bdaca4 for Apache Aurora jobrunner Makoto Nasuno <nasuno@ascade.co.jp> parents: diff changeset	182 <param name="splice_mismatches" type="integer" value="0" label="Maximum number of mismatches that can appear in the anchor region of spliced alignment" />
589de4bdaca4 for Apache Aurora jobrunner Makoto Nasuno <nasuno@ascade.co.jp> parents: diff changeset	183 <param name="min_intron_length" type="integer" value="70" label="The minimum intron length" help="TopHat will ignore donor/acceptor pairs closer than this many bases apart." />
589de4bdaca4 for Apache Aurora jobrunner Makoto Nasuno <nasuno@ascade.co.jp> parents: diff changeset	184 <param name="max_intron_length" type="integer" value="500000" label="The maximum intron length" help="When searching for junctions ab initio, TopHat will ignore donor/acceptor pairs farther than this many bases apart, except when such a pair is supported by a split segment alignment of a long read." />
589de4bdaca4 for Apache Aurora jobrunner Makoto Nasuno <nasuno@ascade.co.jp> parents: diff changeset	185 <expand macro="indel_searchConditional" />
589de4bdaca4 for Apache Aurora jobrunner Makoto Nasuno <nasuno@ascade.co.jp> parents: diff changeset	186 alignments (number of reads divided by average depth of coverage)" help="0.0 to 1.0 (0 to turn off)" />
589de4bdaca4 for Apache Aurora jobrunner Makoto Nasuno <nasuno@ascade.co.jp> parents: diff changeset	187 <param name="max_multihits" type="integer" value="20" label="Maximum number of alignments to be allowed" />
589de4bdaca4 for Apache Aurora jobrunner Makoto Nasuno <nasuno@ascade.co.jp> parents: diff changeset	188 <param name="min_segment_intron" type="integer" value="50" label="Minimum intron length that may be found during split-segment (default) search" />
589de4bdaca4 for Apache Aurora jobrunner Makoto Nasuno <nasuno@ascade.co.jp> parents: diff changeset	189 <param name="max_segment_intron" type="integer" value="500000" label="Maximum intron length that may be found during split-segment (default) search" />
589de4bdaca4 for Apache Aurora jobrunner Makoto Nasuno <nasuno@ascade.co.jp> parents: diff changeset	190 <param name="seg_mismatches" type="integer" min="0" max="3" value="2" label="Number of mismatches allowed in each segment alignment for reads mapped independently" />
589de4bdaca4 for Apache Aurora jobrunner Makoto Nasuno <nasuno@ascade.co.jp> parents: diff changeset	191 <param name="seg_length" type="integer" value="25" label="Minimum length of read segments" />
589de4bdaca4 for Apache Aurora jobrunner Makoto Nasuno <nasuno@ascade.co.jp> parents: diff changeset	192
589de4bdaca4 for Apache Aurora jobrunner Makoto Nasuno <nasuno@ascade.co.jp> parents: diff changeset	193 <!-- Options for supplying own junctions. -->
589de4bdaca4 for Apache Aurora jobrunner Makoto Nasuno <nasuno@ascade.co.jp> parents: diff changeset	194 <expand macro="own_junctionsConditional" />
589de4bdaca4 for Apache Aurora jobrunner Makoto Nasuno <nasuno@ascade.co.jp> parents: diff changeset	195 <!-- Coverage search. -->
589de4bdaca4 for Apache Aurora jobrunner Makoto Nasuno <nasuno@ascade.co.jp> parents: diff changeset	196 <conditional name="coverage_search">
589de4bdaca4 for Apache Aurora jobrunner Makoto Nasuno <nasuno@ascade.co.jp> parents: diff changeset	197 <param name="use_search" type="select" label="Use Coverage Search" help="Enables the coverage based search for junctions. Use when coverage search is disabled by default (such as for reads 75bp or longer), for maximum sensitivity.">
589de4bdaca4 for Apache Aurora jobrunner Makoto Nasuno <nasuno@ascade.co.jp> parents: diff changeset	198 <option selected="true" value="No">No</option>
589de4bdaca4 for Apache Aurora jobrunner Makoto Nasuno <nasuno@ascade.co.jp> parents: diff changeset	199 <option value="Yes">Yes</option>
589de4bdaca4 for Apache Aurora jobrunner Makoto Nasuno <nasuno@ascade.co.jp> parents: diff changeset	200 </param>
589de4bdaca4 for Apache Aurora jobrunner Makoto Nasuno <nasuno@ascade.co.jp> parents: diff changeset	201 <when value="Yes">
589de4bdaca4 for Apache Aurora jobrunner Makoto Nasuno <nasuno@ascade.co.jp> parents: diff changeset	202 <param name="min_coverage_intron" type="integer" value="50" label="Minimum intron length that may be found during coverage search" />
589de4bdaca4 for Apache Aurora jobrunner Makoto Nasuno <nasuno@ascade.co.jp> parents: diff changeset	203 <param name="max_coverage_intron" type="integer" value="20000" label="Maximum intron length that may be found during coverage search" />
589de4bdaca4 for Apache Aurora jobrunner Makoto Nasuno <nasuno@ascade.co.jp> parents: diff changeset	204 </when>
589de4bdaca4 for Apache Aurora jobrunner Makoto Nasuno <nasuno@ascade.co.jp> parents: diff changeset	205 <when value="No" />
589de4bdaca4 for Apache Aurora jobrunner Makoto Nasuno <nasuno@ascade.co.jp> parents: diff changeset	206 </conditional>
589de4bdaca4 for Apache Aurora jobrunner Makoto Nasuno <nasuno@ascade.co.jp> parents: diff changeset	207
589de4bdaca4 for Apache Aurora jobrunner Makoto Nasuno <nasuno@ascade.co.jp> parents: diff changeset	208 <!-- Microexon search params -->
589de4bdaca4 for Apache Aurora jobrunner Makoto Nasuno <nasuno@ascade.co.jp> parents: diff changeset	209 <param name="microexon_search" type="select" label="Use Microexon Search" help="With this option, the pipeline will attempt to find alignments incident to microexons. Works only for reads 50bp or longer.">
589de4bdaca4 for Apache Aurora jobrunner Makoto Nasuno <nasuno@ascade.co.jp> parents: diff changeset	210 <option value="No">No</option>
589de4bdaca4 for Apache Aurora jobrunner Makoto Nasuno <nasuno@ascade.co.jp> parents: diff changeset	211 <option value="Yes">Yes</option>
589de4bdaca4 for Apache Aurora jobrunner Makoto Nasuno <nasuno@ascade.co.jp> parents: diff changeset	212 </param>
589de4bdaca4 for Apache Aurora jobrunner Makoto Nasuno <nasuno@ascade.co.jp> parents: diff changeset	213
589de4bdaca4 for Apache Aurora jobrunner Makoto Nasuno <nasuno@ascade.co.jp> parents: diff changeset	214 <!-- Fusion mapping. -->
589de4bdaca4 for Apache Aurora jobrunner Makoto Nasuno <nasuno@ascade.co.jp> parents: diff changeset	215 <conditional name="fusion_search">
589de4bdaca4 for Apache Aurora jobrunner Makoto Nasuno <nasuno@ascade.co.jp> parents: diff changeset	216 <param name="do_search" type="select" label="Do Fusion Search">
589de4bdaca4 for Apache Aurora jobrunner Makoto Nasuno <nasuno@ascade.co.jp> parents: diff changeset	217 <option selected="true" value="No">No</option>
589de4bdaca4 for Apache Aurora jobrunner Makoto Nasuno <nasuno@ascade.co.jp> parents: diff changeset	218 <option value="Yes">Yes</option>
589de4bdaca4 for Apache Aurora jobrunner Makoto Nasuno <nasuno@ascade.co.jp> parents: diff changeset	219 </param>
589de4bdaca4 for Apache Aurora jobrunner Makoto Nasuno <nasuno@ascade.co.jp> parents: diff changeset	220 <when value="No" />
589de4bdaca4 for Apache Aurora jobrunner Makoto Nasuno <nasuno@ascade.co.jp> parents: diff changeset	221 <when value="Yes">
589de4bdaca4 for Apache Aurora jobrunner Makoto Nasuno <nasuno@ascade.co.jp> parents: diff changeset	222 <param name="anchor_len" type="integer" value="20" label="Anchor Length" help="A 'supporting' read must map to both sides of a fusion by at least this many bases."/>
589de4bdaca4 for Apache Aurora jobrunner Makoto Nasuno <nasuno@ascade.co.jp> parents: diff changeset	223 <param name="min_dist" type="integer" value="10000000" label="Minimum Distance" help="For intra-chromosomal fusions, TopHat-Fusion tries to find fusions separated by at least this distance."/>
589de4bdaca4 for Apache Aurora jobrunner Makoto Nasuno <nasuno@ascade.co.jp> parents: diff changeset	224 <param name="read_mismatches" type="integer" value="2" label="Read Mismatches" help="Reads support fusions if they map across fusion with at most this many mismatches."/>
589de4bdaca4 for Apache Aurora jobrunner Makoto Nasuno <nasuno@ascade.co.jp> parents: diff changeset	225 <param name="multireads" type="integer" value="2" label="Multireads" help="Reads that map to more than this many places will be ignored. It may be possible that a fusion is supported by reads (or pairs) that map to multiple places."/>
589de4bdaca4 for Apache Aurora jobrunner Makoto Nasuno <nasuno@ascade.co.jp> parents: diff changeset	226 <param name="multipairs" type="integer" value="2" label="Multipairs" help="Pairs that map to more than this many places will be ignored."/>
589de4bdaca4 for Apache Aurora jobrunner Makoto Nasuno <nasuno@ascade.co.jp> parents: diff changeset	227 <param name="ignore_chromosomes" type="text" value='' label="Ignore some chromosomes such as chrM when detecting fusion break points"/>
589de4bdaca4 for Apache Aurora jobrunner Makoto Nasuno <nasuno@ascade.co.jp> parents: diff changeset	228 </when>
589de4bdaca4 for Apache Aurora jobrunner Makoto Nasuno <nasuno@ascade.co.jp> parents: diff changeset	229 </conditional>
589de4bdaca4 for Apache Aurora jobrunner Makoto Nasuno <nasuno@ascade.co.jp> parents: diff changeset	230
589de4bdaca4 for Apache Aurora jobrunner Makoto Nasuno <nasuno@ascade.co.jp> parents: diff changeset	231 <!-- Bowtie2 settings. -->
589de4bdaca4 for Apache Aurora jobrunner Makoto Nasuno <nasuno@ascade.co.jp> parents: diff changeset	232 <conditional name="bowtie2_settings">
589de4bdaca4 for Apache Aurora jobrunner Makoto Nasuno <nasuno@ascade.co.jp> parents: diff changeset	233 <param name="b2_settings" type="select" label="Set Bowtie2 settings">
589de4bdaca4 for Apache Aurora jobrunner Makoto Nasuno <nasuno@ascade.co.jp> parents: diff changeset	234 <option selected="true" value="No">No</option>
589de4bdaca4 for Apache Aurora jobrunner Makoto Nasuno <nasuno@ascade.co.jp> parents: diff changeset	235 <option value="Yes">Yes</option>
589de4bdaca4 for Apache Aurora jobrunner Makoto Nasuno <nasuno@ascade.co.jp> parents: diff changeset	236 </param>
589de4bdaca4 for Apache Aurora jobrunner Makoto Nasuno <nasuno@ascade.co.jp> parents: diff changeset	237 <when value="No" />
589de4bdaca4 for Apache Aurora jobrunner Makoto Nasuno <nasuno@ascade.co.jp> parents: diff changeset	238 <when value="Yes">
589de4bdaca4 for Apache Aurora jobrunner Makoto Nasuno <nasuno@ascade.co.jp> parents: diff changeset	239 <conditional name="preset">
589de4bdaca4 for Apache Aurora jobrunner Makoto Nasuno <nasuno@ascade.co.jp> parents: diff changeset	240 <param name="b2_preset" type="select" label="Use Preset options">
589de4bdaca4 for Apache Aurora jobrunner Makoto Nasuno <nasuno@ascade.co.jp> parents: diff changeset	241 <option selected="true" value="Yes">Yes</option>
589de4bdaca4 for Apache Aurora jobrunner Makoto Nasuno <nasuno@ascade.co.jp> parents: diff changeset	242 <option value="No">No</option>
589de4bdaca4 for Apache Aurora jobrunner Makoto Nasuno <nasuno@ascade.co.jp> parents: diff changeset	243 </param>
589de4bdaca4 for Apache Aurora jobrunner Makoto Nasuno <nasuno@ascade.co.jp> parents: diff changeset	244 <when value="Yes">
589de4bdaca4 for Apache Aurora jobrunner Makoto Nasuno <nasuno@ascade.co.jp> parents: diff changeset	245 <param name="b2_preset_select" type="select" label="Preset option">
589de4bdaca4 for Apache Aurora jobrunner Makoto Nasuno <nasuno@ascade.co.jp> parents: diff changeset	246 <option value="very-fast">Very fast</option>
589de4bdaca4 for Apache Aurora jobrunner Makoto Nasuno <nasuno@ascade.co.jp> parents: diff changeset	247 <option value="fast">Fast</option>
589de4bdaca4 for Apache Aurora jobrunner Makoto Nasuno <nasuno@ascade.co.jp> parents: diff changeset	248 <option selected="true" value="sensitive">Sensitive</option>
589de4bdaca4 for Apache Aurora jobrunner Makoto Nasuno <nasuno@ascade.co.jp> parents: diff changeset	249 <option value="very-sensitive">Very sensitive</option>
589de4bdaca4 for Apache Aurora jobrunner Makoto Nasuno <nasuno@ascade.co.jp> parents: diff changeset	250 </param>
589de4bdaca4 for Apache Aurora jobrunner Makoto Nasuno <nasuno@ascade.co.jp> parents: diff changeset	251 </when>
589de4bdaca4 for Apache Aurora jobrunner Makoto Nasuno <nasuno@ascade.co.jp> parents: diff changeset	252 <!-- TODO: -->
589de4bdaca4 for Apache Aurora jobrunner Makoto Nasuno <nasuno@ascade.co.jp> parents: diff changeset	253 <when value="No" />
589de4bdaca4 for Apache Aurora jobrunner Makoto Nasuno <nasuno@ascade.co.jp> parents: diff changeset	254 </conditional>
589de4bdaca4 for Apache Aurora jobrunner Makoto Nasuno <nasuno@ascade.co.jp> parents: diff changeset	255 </when>
589de4bdaca4 for Apache Aurora jobrunner Makoto Nasuno <nasuno@ascade.co.jp> parents: diff changeset	256 </conditional>
589de4bdaca4 for Apache Aurora jobrunner Makoto Nasuno <nasuno@ascade.co.jp> parents: diff changeset	257 </when> <!-- full -->
589de4bdaca4 for Apache Aurora jobrunner Makoto Nasuno <nasuno@ascade.co.jp> parents: diff changeset	258 </conditional> <!-- params -->
589de4bdaca4 for Apache Aurora jobrunner Makoto Nasuno <nasuno@ascade.co.jp> parents: diff changeset	259 <conditional name="readGroup">
589de4bdaca4 for Apache Aurora jobrunner Makoto Nasuno <nasuno@ascade.co.jp> parents: diff changeset	260 <param name="specReadGroup" type="select" label="Specify read group?">
589de4bdaca4 for Apache Aurora jobrunner Makoto Nasuno <nasuno@ascade.co.jp> parents: diff changeset	261 <option value="yes">Yes</option>
589de4bdaca4 for Apache Aurora jobrunner Makoto Nasuno <nasuno@ascade.co.jp> parents: diff changeset	262 <option value="no" selected="True">No</option>
589de4bdaca4 for Apache Aurora jobrunner Makoto Nasuno <nasuno@ascade.co.jp> parents: diff changeset	263 </param>
589de4bdaca4 for Apache Aurora jobrunner Makoto Nasuno <nasuno@ascade.co.jp> parents: diff changeset	264 <when value="yes">
589de4bdaca4 for Apache Aurora jobrunner Makoto Nasuno <nasuno@ascade.co.jp> parents: diff changeset	265 <param name="rgid" type="text" size="25" label="Read group identiﬁer (ID). Each @RG line must have a unique ID. The value of ID is used in the RG tags of alignment records. Must be unique among all read groups in header section." help="Required if RG specified. Read group IDs may be modiﬁed when merging SAM ﬁles in order to handle collisions." />
589de4bdaca4 for Apache Aurora jobrunner Makoto Nasuno <nasuno@ascade.co.jp> parents: diff changeset	266 <param name="rglb" type="text" size="25" label="Library name (LB)" help="Required if RG specified" />
589de4bdaca4 for Apache Aurora jobrunner Makoto Nasuno <nasuno@ascade.co.jp> parents: diff changeset	267 <param name="rgpl" type="text" size="25" label="Platform/technology used to produce the reads (PL)" help="Required if RG specified. Valid values : CAPILLARY, LS454, ILLUMINA, SOLID, HELICOS, IONTORRENT and PACBIO" />
589de4bdaca4 for Apache Aurora jobrunner Makoto Nasuno <nasuno@ascade.co.jp> parents: diff changeset	268 <param name="rgsm" type="text" size="25" label="Sample (SM)" help="Required if RG specified. Use pool name where a pool is being sequenced" />
589de4bdaca4 for Apache Aurora jobrunner Makoto Nasuno <nasuno@ascade.co.jp> parents: diff changeset	269 </when>
589de4bdaca4 for Apache Aurora jobrunner Makoto Nasuno <nasuno@ascade.co.jp> parents: diff changeset	270 <when value="no" />
589de4bdaca4 for Apache Aurora jobrunner Makoto Nasuno <nasuno@ascade.co.jp> parents: diff changeset	271 </conditional> <!-- readGroup -->
589de4bdaca4 for Apache Aurora jobrunner Makoto Nasuno <nasuno@ascade.co.jp> parents: diff changeset	272 </inputs>
589de4bdaca4 for Apache Aurora jobrunner Makoto Nasuno <nasuno@ascade.co.jp> parents: diff changeset	273
589de4bdaca4 for Apache Aurora jobrunner Makoto Nasuno <nasuno@ascade.co.jp> parents: diff changeset	274 <stdio>
589de4bdaca4 for Apache Aurora jobrunner Makoto Nasuno <nasuno@ascade.co.jp> parents: diff changeset	275 <regex match="Exception\|Error" source="both" level="fatal" description="Tool execution failed"/>
589de4bdaca4 for Apache Aurora jobrunner Makoto Nasuno <nasuno@ascade.co.jp> parents: diff changeset	276 <regex match=".*" source="both" level="log" description="tool progress"/>
589de4bdaca4 for Apache Aurora jobrunner Makoto Nasuno <nasuno@ascade.co.jp> parents: diff changeset	277 </stdio>
589de4bdaca4 for Apache Aurora jobrunner Makoto Nasuno <nasuno@ascade.co.jp> parents: diff changeset	278
589de4bdaca4 for Apache Aurora jobrunner Makoto Nasuno <nasuno@ascade.co.jp> parents: diff changeset	279 <outputs>
589de4bdaca4 for Apache Aurora jobrunner Makoto Nasuno <nasuno@ascade.co.jp> parents: diff changeset	280 <!--
589de4bdaca4 for Apache Aurora jobrunner Makoto Nasuno <nasuno@ascade.co.jp> parents: diff changeset	281 <data format="txt" name="align_summary" label="${tool.name} on ${on_string}: align_summary" from_work_dir="tophat_out/align_summary.txt"/>
589de4bdaca4 for Apache Aurora jobrunner Makoto Nasuno <nasuno@ascade.co.jp> parents: diff changeset	282 <data format="tabular" name="fusions" label="${tool.name} on ${on_string}: fusions" from_work_dir="tophat_out/fusions.out">
589de4bdaca4 for Apache Aurora jobrunner Makoto Nasuno <nasuno@ascade.co.jp> parents: diff changeset	283 <filter>(params['settingsType'] == 'full' and params['fusion_search']['do_search'] == 'Yes')</filter>
589de4bdaca4 for Apache Aurora jobrunner Makoto Nasuno <nasuno@ascade.co.jp> parents: diff changeset	284 </data>
589de4bdaca4 for Apache Aurora jobrunner Makoto Nasuno <nasuno@ascade.co.jp> parents: diff changeset	285 <data format="bed" name="insertions" label="${tool.name} on ${on_string}: insertions" from_work_dir="tophat_out/insertions.bed">
589de4bdaca4 for Apache Aurora jobrunner Makoto Nasuno <nasuno@ascade.co.jp> parents: diff changeset	286 <expand macro="dbKeyActions" />
589de4bdaca4 for Apache Aurora jobrunner Makoto Nasuno <nasuno@ascade.co.jp> parents: diff changeset	287 </data>
589de4bdaca4 for Apache Aurora jobrunner Makoto Nasuno <nasuno@ascade.co.jp> parents: diff changeset	288 <data format="bed" name="deletions" label="${tool.name} on ${on_string}: deletions" from_work_dir="tophat_out/deletions.bed">
589de4bdaca4 for Apache Aurora jobrunner Makoto Nasuno <nasuno@ascade.co.jp> parents: diff changeset	289 <expand macro="dbKeyActions" />
589de4bdaca4 for Apache Aurora jobrunner Makoto Nasuno <nasuno@ascade.co.jp> parents: diff changeset	290 </data>
589de4bdaca4 for Apache Aurora jobrunner Makoto Nasuno <nasuno@ascade.co.jp> parents: diff changeset	291 <data format="bed" name="junctions" label="${tool.name} on ${on_string}: splice junctions" from_work_dir="tophat_out/junctions.bed">
589de4bdaca4 for Apache Aurora jobrunner Makoto Nasuno <nasuno@ascade.co.jp> parents: diff changeset	292 <expand macro="dbKeyActions" />
589de4bdaca4 for Apache Aurora jobrunner Makoto Nasuno <nasuno@ascade.co.jp> parents: diff changeset	293 </data>
589de4bdaca4 for Apache Aurora jobrunner Makoto Nasuno <nasuno@ascade.co.jp> parents: diff changeset	294 -->
589de4bdaca4 for Apache Aurora jobrunner Makoto Nasuno <nasuno@ascade.co.jp> parents: diff changeset	295 <data format="bam" name="accepted_hits" label="${tool.name} on ${on_string}: accepted_hits" from_work_dir="tophat_out/accepted_hits.bam">
589de4bdaca4 for Apache Aurora jobrunner Makoto Nasuno <nasuno@ascade.co.jp> parents: diff changeset	296 <expand macro="dbKeyActions" />
589de4bdaca4 for Apache Aurora jobrunner Makoto Nasuno <nasuno@ascade.co.jp> parents: diff changeset	297 </data>
589de4bdaca4 for Apache Aurora jobrunner Makoto Nasuno <nasuno@ascade.co.jp> parents: diff changeset	298 </outputs>
589de4bdaca4 for Apache Aurora jobrunner Makoto Nasuno <nasuno@ascade.co.jp> parents: diff changeset	299
589de4bdaca4 for Apache Aurora jobrunner Makoto Nasuno <nasuno@ascade.co.jp> parents: diff changeset	300 <macros>
589de4bdaca4 for Apache Aurora jobrunner Makoto Nasuno <nasuno@ascade.co.jp> parents: diff changeset	301 <import>tophat_macros.xml</import>
589de4bdaca4 for Apache Aurora jobrunner Makoto Nasuno <nasuno@ascade.co.jp> parents: diff changeset	302 <xml name="paired_parameters">
589de4bdaca4 for Apache Aurora jobrunner Makoto Nasuno <nasuno@ascade.co.jp> parents: diff changeset	303 <param name="mate_inner_distance" type="integer" value="300" label="Mean Inner Distance between Mate Pairs" />
589de4bdaca4 for Apache Aurora jobrunner Makoto Nasuno <nasuno@ascade.co.jp> parents: diff changeset	304 <param name="mate_std_dev" type="integer" value="20" label="Std. Dev for Distance between Mate Pairs" help="The standard deviation for the distribution on inner distances between mate pairs."/>
589de4bdaca4 for Apache Aurora jobrunner Makoto Nasuno <nasuno@ascade.co.jp> parents: diff changeset	305 <!-- Discordant pairs. -->
589de4bdaca4 for Apache Aurora jobrunner Makoto Nasuno <nasuno@ascade.co.jp> parents: diff changeset	306 <param name="report_discordant_pairs" type="select" label="Report discordant pair alignments?">
589de4bdaca4 for Apache Aurora jobrunner Makoto Nasuno <nasuno@ascade.co.jp> parents: diff changeset	307 <option value="No">No</option>
589de4bdaca4 for Apache Aurora jobrunner Makoto Nasuno <nasuno@ascade.co.jp> parents: diff changeset	308 <option selected="True" value="Yes">Yes</option>
589de4bdaca4 for Apache Aurora jobrunner Makoto Nasuno <nasuno@ascade.co.jp> parents: diff changeset	309 </param>
589de4bdaca4 for Apache Aurora jobrunner Makoto Nasuno <nasuno@ascade.co.jp> parents: diff changeset	310 </xml>
589de4bdaca4 for Apache Aurora jobrunner Makoto Nasuno <nasuno@ascade.co.jp> parents: diff changeset	311 <macro name="dbKeyActions">
589de4bdaca4 for Apache Aurora jobrunner Makoto Nasuno <nasuno@ascade.co.jp> parents: diff changeset	312 <actions>
589de4bdaca4 for Apache Aurora jobrunner Makoto Nasuno <nasuno@ascade.co.jp> parents: diff changeset	313 <conditional name="refGenomeSource.genomeSource">
589de4bdaca4 for Apache Aurora jobrunner Makoto Nasuno <nasuno@ascade.co.jp> parents: diff changeset	314 <when value="indexed">
589de4bdaca4 for Apache Aurora jobrunner Makoto Nasuno <nasuno@ascade.co.jp> parents: diff changeset	315 <action type="metadata" name="dbkey">
589de4bdaca4 for Apache Aurora jobrunner Makoto Nasuno <nasuno@ascade.co.jp> parents: diff changeset	316 <option type="from_data_table" name="tophat2_indexes" column="1" offset="0">
589de4bdaca4 for Apache Aurora jobrunner Makoto Nasuno <nasuno@ascade.co.jp> parents: diff changeset	317 <filter type="param_value" column="0" value="#" compare="startswith" keep="False"/>
589de4bdaca4 for Apache Aurora jobrunner Makoto Nasuno <nasuno@ascade.co.jp> parents: diff changeset	318 <filter type="param_value" ref="refGenomeSource.index" column="0"/>
589de4bdaca4 for Apache Aurora jobrunner Makoto Nasuno <nasuno@ascade.co.jp> parents: diff changeset	319 </option>
589de4bdaca4 for Apache Aurora jobrunner Makoto Nasuno <nasuno@ascade.co.jp> parents: diff changeset	320 </action>
589de4bdaca4 for Apache Aurora jobrunner Makoto Nasuno <nasuno@ascade.co.jp> parents: diff changeset	321 </when>
589de4bdaca4 for Apache Aurora jobrunner Makoto Nasuno <nasuno@ascade.co.jp> parents: diff changeset	322 <when value="history">
589de4bdaca4 for Apache Aurora jobrunner Makoto Nasuno <nasuno@ascade.co.jp> parents: diff changeset	323 <action type="metadata" name="dbkey">
589de4bdaca4 for Apache Aurora jobrunner Makoto Nasuno <nasuno@ascade.co.jp> parents: diff changeset	324 <option type="from_param" name="refGenomeSource.ownFile" param_attribute="dbkey" />
589de4bdaca4 for Apache Aurora jobrunner Makoto Nasuno <nasuno@ascade.co.jp> parents: diff changeset	325 </action>
589de4bdaca4 for Apache Aurora jobrunner Makoto Nasuno <nasuno@ascade.co.jp> parents: diff changeset	326 </when>
589de4bdaca4 for Apache Aurora jobrunner Makoto Nasuno <nasuno@ascade.co.jp> parents: diff changeset	327 </conditional>
589de4bdaca4 for Apache Aurora jobrunner Makoto Nasuno <nasuno@ascade.co.jp> parents: diff changeset	328 </actions>
589de4bdaca4 for Apache Aurora jobrunner Makoto Nasuno <nasuno@ascade.co.jp> parents: diff changeset	329 </macro>
589de4bdaca4 for Apache Aurora jobrunner Makoto Nasuno <nasuno@ascade.co.jp> parents: diff changeset	330 </macros>
589de4bdaca4 for Apache Aurora jobrunner Makoto Nasuno <nasuno@ascade.co.jp> parents: diff changeset	331
589de4bdaca4 for Apache Aurora jobrunner Makoto Nasuno <nasuno@ascade.co.jp> parents: diff changeset	332 <help>
589de4bdaca4 for Apache Aurora jobrunner Makoto Nasuno <nasuno@ascade.co.jp> parents: diff changeset	333 Tophat Overview
589de4bdaca4 for Apache Aurora jobrunner Makoto Nasuno <nasuno@ascade.co.jp> parents: diff changeset	334
589de4bdaca4 for Apache Aurora jobrunner Makoto Nasuno <nasuno@ascade.co.jp> parents: diff changeset	335 TopHat_ is a fast splice junction mapper for RNA-Seq reads. It aligns RNA-Seq reads to mammalian-sized genomes using the ultra high-throughput short read aligner Bowtie(2), and then analyzes the mapping results to identify splice junctions between exons. Please cite: Kim D, Pertea G, Trapnell C, Pimentel H, Kelley R, and Salzberg SL. TopHat2: accurate alignment
589de4bdaca4 for Apache Aurora jobrunner Makoto Nasuno <nasuno@ascade.co.jp> parents: diff changeset	336 of transcriptomes in the presence of insertions, deletions and gene fusions. Genome Biol 14:R36, 2013.
589de4bdaca4 for Apache Aurora jobrunner Makoto Nasuno <nasuno@ascade.co.jp> parents: diff changeset	337
589de4bdaca4 for Apache Aurora jobrunner Makoto Nasuno <nasuno@ascade.co.jp> parents: diff changeset	338 .. _Tophat: http://ccb.jhu.edu/software/tophat/
589de4bdaca4 for Apache Aurora jobrunner Makoto Nasuno <nasuno@ascade.co.jp> parents: diff changeset	339
589de4bdaca4 for Apache Aurora jobrunner Makoto Nasuno <nasuno@ascade.co.jp> parents: diff changeset	340 ------
589de4bdaca4 for Apache Aurora jobrunner Makoto Nasuno <nasuno@ascade.co.jp> parents: diff changeset	341
589de4bdaca4 for Apache Aurora jobrunner Makoto Nasuno <nasuno@ascade.co.jp> parents: diff changeset	342 Know what you are doing
589de4bdaca4 for Apache Aurora jobrunner Makoto Nasuno <nasuno@ascade.co.jp> parents: diff changeset	343
589de4bdaca4 for Apache Aurora jobrunner Makoto Nasuno <nasuno@ascade.co.jp> parents: diff changeset	344 .. class:: warningmark
589de4bdaca4 for Apache Aurora jobrunner Makoto Nasuno <nasuno@ascade.co.jp> parents: diff changeset	345
589de4bdaca4 for Apache Aurora jobrunner Makoto Nasuno <nasuno@ascade.co.jp> parents: diff changeset	346 There is no such thing (yet) as an automated gearshift in splice junction identification. It is all like stick-shift driving in San Francisco. In other words, running this tool with default parameters will probably not give you meaningful results. A way to deal with this is to understand the parameters by carefully reading the `documentation`__ and experimenting. Fortunately, Galaxy makes experimenting easy.
589de4bdaca4 for Apache Aurora jobrunner Makoto Nasuno <nasuno@ascade.co.jp> parents: diff changeset	347
589de4bdaca4 for Apache Aurora jobrunner Makoto Nasuno <nasuno@ascade.co.jp> parents: diff changeset	348 .. __: http://ccb.jhu.edu/software/tophat/manual.shtml
589de4bdaca4 for Apache Aurora jobrunner Makoto Nasuno <nasuno@ascade.co.jp> parents: diff changeset	349
589de4bdaca4 for Apache Aurora jobrunner Makoto Nasuno <nasuno@ascade.co.jp> parents: diff changeset	350 ------
589de4bdaca4 for Apache Aurora jobrunner Makoto Nasuno <nasuno@ascade.co.jp> parents: diff changeset	351
589de4bdaca4 for Apache Aurora jobrunner Makoto Nasuno <nasuno@ascade.co.jp> parents: diff changeset	352 Input formats
589de4bdaca4 for Apache Aurora jobrunner Makoto Nasuno <nasuno@ascade.co.jp> parents: diff changeset	353
589de4bdaca4 for Apache Aurora jobrunner Makoto Nasuno <nasuno@ascade.co.jp> parents: diff changeset	354 Tophat accepts files in Sanger FASTQ format. Use the FASTQ Groomer to prepare your files.
589de4bdaca4 for Apache Aurora jobrunner Makoto Nasuno <nasuno@ascade.co.jp> parents: diff changeset	355
589de4bdaca4 for Apache Aurora jobrunner Makoto Nasuno <nasuno@ascade.co.jp> parents: diff changeset	356 ------
589de4bdaca4 for Apache Aurora jobrunner Makoto Nasuno <nasuno@ascade.co.jp> parents: diff changeset	357
589de4bdaca4 for Apache Aurora jobrunner Makoto Nasuno <nasuno@ascade.co.jp> parents: diff changeset	358 Outputs
589de4bdaca4 for Apache Aurora jobrunner Makoto Nasuno <nasuno@ascade.co.jp> parents: diff changeset	359
589de4bdaca4 for Apache Aurora jobrunner Makoto Nasuno <nasuno@ascade.co.jp> parents: diff changeset	360 Tophat produces two output files:
589de4bdaca4 for Apache Aurora jobrunner Makoto Nasuno <nasuno@ascade.co.jp> parents: diff changeset	361
589de4bdaca4 for Apache Aurora jobrunner Makoto Nasuno <nasuno@ascade.co.jp> parents: diff changeset	362 - junctions -- A UCSC BED_ track of junctions reported by TopHat. Each junction consists of two connected BED blocks, where each block is as long as the maximal overhang of any read spanning the junction. The score is the number of alignments spanning the junction.
589de4bdaca4 for Apache Aurora jobrunner Makoto Nasuno <nasuno@ascade.co.jp> parents: diff changeset	363 - accepted_hits -- A list of read alignments in BAM_ format.
589de4bdaca4 for Apache Aurora jobrunner Makoto Nasuno <nasuno@ascade.co.jp> parents: diff changeset	364
589de4bdaca4 for Apache Aurora jobrunner Makoto Nasuno <nasuno@ascade.co.jp> parents: diff changeset	365 .. _BED: http://genome.ucsc.edu/FAQ/FAQformat.html#format1
589de4bdaca4 for Apache Aurora jobrunner Makoto Nasuno <nasuno@ascade.co.jp> parents: diff changeset	366 .. _BAM: http://samtools.sourceforge.net/
589de4bdaca4 for Apache Aurora jobrunner Makoto Nasuno <nasuno@ascade.co.jp> parents: diff changeset	367
589de4bdaca4 for Apache Aurora jobrunner Makoto Nasuno <nasuno@ascade.co.jp> parents: diff changeset	368 Two other possible outputs, depending on the options you choose, are insertions and deletions, both of which are in BED format.
589de4bdaca4 for Apache Aurora jobrunner Makoto Nasuno <nasuno@ascade.co.jp> parents: diff changeset	369
589de4bdaca4 for Apache Aurora jobrunner Makoto Nasuno <nasuno@ascade.co.jp> parents: diff changeset	370 -------
589de4bdaca4 for Apache Aurora jobrunner Makoto Nasuno <nasuno@ascade.co.jp> parents: diff changeset	371
589de4bdaca4 for Apache Aurora jobrunner Makoto Nasuno <nasuno@ascade.co.jp> parents: diff changeset	372 Tophat settings
589de4bdaca4 for Apache Aurora jobrunner Makoto Nasuno <nasuno@ascade.co.jp> parents: diff changeset	373
589de4bdaca4 for Apache Aurora jobrunner Makoto Nasuno <nasuno@ascade.co.jp> parents: diff changeset	374 All of the options have a default value. You can change any of them. Some of the options in Tophat have been implemented here.
589de4bdaca4 for Apache Aurora jobrunner Makoto Nasuno <nasuno@ascade.co.jp> parents: diff changeset	375
589de4bdaca4 for Apache Aurora jobrunner Makoto Nasuno <nasuno@ascade.co.jp> parents: diff changeset	376 ------
589de4bdaca4 for Apache Aurora jobrunner Makoto Nasuno <nasuno@ascade.co.jp> parents: diff changeset	377
589de4bdaca4 for Apache Aurora jobrunner Makoto Nasuno <nasuno@ascade.co.jp> parents: diff changeset	378 Tophat parameter list
589de4bdaca4 for Apache Aurora jobrunner Makoto Nasuno <nasuno@ascade.co.jp> parents: diff changeset	379
589de4bdaca4 for Apache Aurora jobrunner Makoto Nasuno <nasuno@ascade.co.jp> parents: diff changeset	380 This is a list of implemented Tophat options::
589de4bdaca4 for Apache Aurora jobrunner Makoto Nasuno <nasuno@ascade.co.jp> parents: diff changeset	381
589de4bdaca4 for Apache Aurora jobrunner Makoto Nasuno <nasuno@ascade.co.jp> parents: diff changeset	382 -r This is the expected (mean) inner distance between mate pairs. For, example, for paired end runs with fragments
589de4bdaca4 for Apache Aurora jobrunner Makoto Nasuno <nasuno@ascade.co.jp> parents: diff changeset	383 selected at 300bp, where each end is 50bp, you should set -r to be 200. There is no default, and this parameter
589de4bdaca4 for Apache Aurora jobrunner Makoto Nasuno <nasuno@ascade.co.jp> parents: diff changeset	384 is required for paired end runs.
589de4bdaca4 for Apache Aurora jobrunner Makoto Nasuno <nasuno@ascade.co.jp> parents: diff changeset	385 --mate-std-dev INT The standard deviation for the distribution on inner distances between mate pairs. The default is 20bp.
589de4bdaca4 for Apache Aurora jobrunner Makoto Nasuno <nasuno@ascade.co.jp> parents: diff changeset	386 -a/--min-anchor-length INT The "anchor length". TopHat will report junctions spanned by reads with at least this many bases on each side of the junction. Note that individual spliced
589de4bdaca4 for Apache Aurora jobrunner Makoto Nasuno <nasuno@ascade.co.jp> parents: diff changeset	387 alignments may span a junction with fewer than this many bases on one side. However, every junction involved in spliced alignments is supported by at least one
589de4bdaca4 for Apache Aurora jobrunner Makoto Nasuno <nasuno@ascade.co.jp> parents: diff changeset	388 read with this many bases on each side. This must be at least 3 and the default is 8.
589de4bdaca4 for Apache Aurora jobrunner Makoto Nasuno <nasuno@ascade.co.jp> parents: diff changeset	389 -m/--splice-mismatches INT The maximum number of mismatches that may appear in the "anchor" region of a spliced alignment. The default is 0.
589de4bdaca4 for Apache Aurora jobrunner Makoto Nasuno <nasuno@ascade.co.jp> parents: diff changeset	390 -i/--min-intron-length INT The minimum intron length. TopHat will ignore donor/acceptor pairs closer than this many bases apart. The default is 70.
589de4bdaca4 for Apache Aurora jobrunner Makoto Nasuno <nasuno@ascade.co.jp> parents: diff changeset	391 -I/--max-intron-length INT The maximum intron length. When searching for junctions ab initio, TopHat will ignore donor/acceptor pairs farther than this many bases apart, except when such a pair is supported by a split segment alignment of a long read. The default is 500000.
589de4bdaca4 for Apache Aurora jobrunner Makoto Nasuno <nasuno@ascade.co.jp> parents: diff changeset	392 -g/--max-multihits INT Instructs TopHat to allow up to this many alignments to the reference for a given read, and suppresses all alignments for reads with more than this many
589de4bdaca4 for Apache Aurora jobrunner Makoto Nasuno <nasuno@ascade.co.jp> parents: diff changeset	393 alignments. The default is 40.
589de4bdaca4 for Apache Aurora jobrunner Makoto Nasuno <nasuno@ascade.co.jp> parents: diff changeset	394 -G/--GTF [GTF 2.2 file] Supply TopHat with a list of gene model annotations. TopHat will use the exon records in this file to build a set of known splice junctions for each gene, and will attempt to align reads to these junctions even if they would not normally be covered by the initial mapping.
589de4bdaca4 for Apache Aurora jobrunner Makoto Nasuno <nasuno@ascade.co.jp> parents: diff changeset	395 -j/--raw-juncs [juncs file] Supply TopHat with a list of raw junctions. Junctions are specified one per line, in a tab-delimited format. Records look like: [chrom] [left] [right] [+/-], left and right are zero-based coordinates, and specify the last character of the left sequenced to be spliced to the first character of the right sequence, inclusive.
589de4bdaca4 for Apache Aurora jobrunner Makoto Nasuno <nasuno@ascade.co.jp> parents: diff changeset	396 -no-novel-juncs Only look for junctions indicated in the supplied GFF file. (ignored without -G)
589de4bdaca4 for Apache Aurora jobrunner Makoto Nasuno <nasuno@ascade.co.jp> parents: diff changeset	397 --no-coverage-search Disables the coverage based search for junctions.
589de4bdaca4 for Apache Aurora jobrunner Makoto Nasuno <nasuno@ascade.co.jp> parents: diff changeset	398 --coverage-search Enables the coverage based search for junctions. Use when coverage search is disabled by default (such as for reads 75bp or longer), for maximum sensitivity.
589de4bdaca4 for Apache Aurora jobrunner Makoto Nasuno <nasuno@ascade.co.jp> parents: diff changeset	399 --microexon-search With this option, the pipeline will attempt to find alignments incident to microexons. Works only for reads 50bp or longer.
589de4bdaca4 for Apache Aurora jobrunner Makoto Nasuno <nasuno@ascade.co.jp> parents: diff changeset	400 --segment-mismatches Read segments are mapped independently, allowing up to this many mismatches in each segment alignment. The default is 2.
589de4bdaca4 for Apache Aurora jobrunner Makoto Nasuno <nasuno@ascade.co.jp> parents: diff changeset	401 --segment-length Each read is cut up into segments, each at least this long. These segments are mapped independently. The default is 25.
589de4bdaca4 for Apache Aurora jobrunner Makoto Nasuno <nasuno@ascade.co.jp> parents: diff changeset	402 --min-coverage-intron The minimum intron length that may be found during coverage search. The default is 50.
589de4bdaca4 for Apache Aurora jobrunner Makoto Nasuno <nasuno@ascade.co.jp> parents: diff changeset	403 --max-coverage-intron The maximum intron length that may be found during coverage search. The default is 20000.
589de4bdaca4 for Apache Aurora jobrunner Makoto Nasuno <nasuno@ascade.co.jp> parents: diff changeset	404 --min-segment-intron The minimum intron length that may be found during split-segment search. The default is 50.
589de4bdaca4 for Apache Aurora jobrunner Makoto Nasuno <nasuno@ascade.co.jp> parents: diff changeset	405 --max-segment-intron The maximum intron length that may be found during split-segment search. The default is 500000.
589de4bdaca4 for Apache Aurora jobrunner Makoto Nasuno <nasuno@ascade.co.jp> parents: diff changeset	406 </help>
589de4bdaca4 for Apache Aurora jobrunner Makoto Nasuno <nasuno@ascade.co.jp> parents: diff changeset	407 <citations>
589de4bdaca4 for Apache Aurora jobrunner Makoto Nasuno <nasuno@ascade.co.jp> parents: diff changeset	408 <citation type="doi">10.1186/gb-2013-14-4-r36</citation>
589de4bdaca4 for Apache Aurora jobrunner Makoto Nasuno <nasuno@ascade.co.jp> parents: diff changeset	409 </citations>
589de4bdaca4 for Apache Aurora jobrunner Makoto Nasuno <nasuno@ascade.co.jp> parents: diff changeset	410 </tool>

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589de4bdaca4 for Apache Aurora jobrunner