tmap_wrapper: tmap_wrapper_0.0.19/tmap

annotate tmap_wrapper_0.0.19/tmap_wrapper.xml @ 0:7cbfd271d207

Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository

author	nilshomer
date	Tue, 07 Jun 2011 17:28:45 -0400
parents
children

rev	line source
0 7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	1 <tool id="tmap_wrapper" name="Map with TMAP" version="0.0.19">
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	2 <description>for Ion Torrent</description>
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	3 <parallelism method="basic"></parallelism>
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	4 <command interpreter="python">
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	5 tmap_wrapper.py
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	6
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	7 ## reference source
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	8 --fileSource=$genomeSource.refGenomeSource
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	9 #if $genomeSource.refGenomeSource == "history":
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	10 ##build index on the fly
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	11 --ref="${genomeSource.ownFile}"
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	12 --dbkey=$dbkey
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	13 #else:
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	14 ##use precomputed indexes
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	15 --ref="${ filter( lambda x: str( x[0] ) == str( $genomeSource.indices ), $__app__.tool_data_tables[ 'tmap_indexes' ].get_fields() )[0][-1] }"
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	16 --do_not_build_index
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	17 #end if
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	18
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	19 ## input fastq
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	20 --fastq=$input
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	21
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	22 ## output file
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	23 --output=$output
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	24
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	25 ## run parameters
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	26 --params=$params.source_select
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	27 #if $params.source_select != "pre_set":
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	28 --mapall=$params.mapall.source_select
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	29 #if $params.mapall.source_select == "true":
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	30 --threads=$params.mapall.threads
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	31 --matchScore=$params.mapall.matchScore
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	32 --mismatchPenalty=$params.mapall.mismatchPenalty
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	33 --gapOpenPenalty=$params.mapall.gapOpenPenalty
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	34 --gapExtensPenalty=$params.mapall.gapExtensPenalty
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	35 --flowPenalty=$params.mapall.flowPenalty
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	36 --flowOrder=$params.mappll.flowOrder
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	37 --bandWidth=$params.mapall.bandWidth
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	38 --globalMap=$params.mapall.globalMap
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	39 --duplicateWindow=$params.mapall.duplicateWindow
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	40 --scoringThreshold=$params.mapall.scoringThreshold
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	41 --queueSize=$params.mapall.queueSize
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	42 --outputFilter=$params.mapall.outputFilter
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	43 --rgTag=$params.mapall.rgTag.source_select
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	44 #if $params.mapall.rgTag.source_select == "true":
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	45 --rgTagID=$params.mapall.rgTag.rgTagID
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	46 --rgTagCN=$params.mapall.rgTag.rgTagCN
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	47 --rgTagDS=$params.mapall.rgTag.rgTagDS
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	48 --rgTagDT=$params.mapall.rgTag.rgTagDT
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	49 --rgTagLB=$params.mapall.rgTag.rgTagLB
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	50 --rgTagPI=$params.mapall.rgTag.rgTagPI
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	51 --rgTagPL=$params.mapall.rgTag.rgTagPL
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	52 --rgTagPU=$params.mapall.rgTag.rgTagPU
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	53 --rgTagSM=$params.mapall.rgTag.rgTagSM
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	54 #end if
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	55 --filterIndependently=$params.mapall.filterIndependently
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	56 #end if
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	57 --map1=$params.map1.source_select
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	58 #if $params.map1.source_select == "true":
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	59 --map1SeedLength=$params.map1.map1SeedLength
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	60 --map1SeedMismatches=$params.map1.map1SeedMismatches
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	61 --map1SecondarySeedLength=$params.map1.map1SecondarySeedLength
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	62 --map1NumEdits=$params.map1.map1NumEdits
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	63 --map1BaseError=$params.map1.map1BaseError
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	64 --map1Mismatches=$params.map1.map1Mismatches
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	65 --map1GapOpens=$params.map1.map1GapOpens
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	66 --map1GapExtensions=$params.map1.map1GapExtensions
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	67 --map1MaxCALsDeletion=$params.map1.map1MaxCALsDeletion
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	68 --map1EndIndels=$params.map1.map1EndIndels
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	69 --map1MaxOptimalCALs=$params.map1.map1MaxOptimalCALs
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	70 --map1MaxNodes=$params.map1.map1MaxNodes
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	71 #end if
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	72 --map2=$params.map2.source_select
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	73 #if $params.map2.source_select == "true":
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	74 --map2Coefficient=$params.map2.map2Coefficient
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	75 --map2SeedIntervalSize=$params.map2.map2SeedIntervalSize
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	76 --map2ZBest=$params.map2.map2ZBest
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	77 --map2ReverseTrigger=$params.map2.map2ReverseTrigger
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	78 #end if
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	79 --map3=$params.map3.source_select
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	80 #if $params.map3.source_select == "true":
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	81 --map3SeedLength=$params.map3.map3SeedLength
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	82 --map3SeedMaxHits=$params.map3.map3SeedMaxHits
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	83 --map3SeedWindow=$params.map3.map3SeedWindow
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	84 --map3HPEnumeration=$params.map3.map3HPEnumeration
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	85 #end if
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	86 --MAP1=$params.MAP1.source_select
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	87 #if $params.MAP1.source_select == "true":
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	88 --MAP1SeedLength=$params.MAP1.MAP1SeedLength
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	89 --MAP1SeedMismatches=$params.MAP1.MAP1SeedMismatches
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	90 --MAP1SecondarySeedLength=$params.MAP1.MAP1SecondarySeedLength
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	91 --MAP1NumEdits=$params.MAP1.MAP1NumEdits
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	92 --MAP1BaseError=$params.MAP1.MAP1BaseError
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	93 --MAP1Mismatches=$params.MAP1.MAP1Mismatches
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	94 --MAP1GapOpens=$params.MAP1.MAP1GapOpens
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	95 --MAP1GapExtensions=$params.MAP1.MAP1GapExtensions
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	96 --MAP1MaxCALsDeletion=$params.MAP1.MAP1MaxCALsDeletion
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	97 --MAP1EndIndels=$params.MAP1.MAP1EndIndels
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	98 --MAP1MaxOptimalCALs=$params.MAP1.MAP1MaxOptimalCALs
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	99 --MAP1MaxNodes=$params.MAP1.MAP1MaxNodes
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	100 #end if
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	101 --MAP2=$params.MAP2.source_select
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	102 #if $params.MAP2.source_select == "true":
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	103 --MAP2Coefficient=$params.MAP2.MAP2Coefficient
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	104 --MAP2SeedIntervalSize=$params.MAP2.MAP2SeedIntervalSize
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	105 --MAP2ZBest=$params.MAP2.MAP2ZBest
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	106 --MAP2ReverseTrigger=$params.MAP2.MAP2ReverseTrigger
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	107 #end if
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	108 --MAP3=$params.MAP3.source_select
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	109 #if $params.MAP3.source_select == "true":
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	110 --MAP3SeedLength=$params.MAP3.MAP3SeedLength
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	111 --MAP3SeedMaxHits=$params.MAP3.MAP3SeedMaxHits
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	112 --MAP3SeedWindow=$params.MAP3.MAP3SeedWindow
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	113 --MAP3HPEnumeration=$params.MAP3.MAP3HPEnumeration
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	114 #end if
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	115 #else:
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	116 --threads="4"
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	117 --map1="false"
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	118 --map2="false"
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	119 --map3="false"
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	120 --MAP1="false"
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	121 --MAP2="false"
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	122 --MAP3="false"
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	123 #end if
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	124
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	125 ## suppress output SAM header
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	126 --suppressHeader=$suppressHeader
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	127 </command>
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	128 <requirements>
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	129 <requirement type='package'>tmap</requirement>
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	130 </requirements>
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	131 <inputs>
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	132 <conditional name="genomeSource">
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	133 <param name="refGenomeSource" type="select" label="Will you select a reference genome from your history or use a built-in index?">
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	134 <option value="indexed">Use a built-in index</option>
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	135 <option value="history">Use one from the history</option>
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	136 </param>
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	137 <when value="indexed">
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	138 <param name="indices" type="select" label="Select a reference genome">
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	139 <options from_data_table="tmap_indexes">
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	140 <filter type="sort_by" column="3" />
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	141 <validator type="no_options" message="No indexes are available for the selected input dataset" />
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	142 </options>
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	143 </param>
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	144 </when>
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	145 <when value="history">
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	146 <param name="ownFile" type="data" format="fasta" metadata_name="dbkey" label="Select a reference from history" />
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	147 </when>
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	148 </conditional>
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	149 <param name="input" type="data" format="fastqsanger" label="FASTQ file" help="Must have Sanger-scaled quality values with ASCII offset 33" />
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	150 <conditional name="params">
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	151 <param name="source_select" type="select" label="TMAP settings to use" help="For most mapping needs use Commonly Used settings. If you want full control use Full Parameter List">
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	152 <option value="pre_set">Commonly Used</option>
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	153 <option value="full">Full Parameter List</option>
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	154 </param>
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	155 <when value="pre_set" />
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	156 <when value="full">
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	157 <conditional name="mapall">
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	158 <param name="source_select" type="select" label="Global options to use">
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	159 <option value="false" selected="true">Commonly Used</option>
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	160 <option value="true">Full Parameter List</option>
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	161 </param>
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	162 <when value="false" />
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	163 <when value="true">
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	164 <param name="threads" type="integer" value="4" label="The number of threads (-n)" />
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	165 <param name="matchScore" type="integer" value="3" label="Match score (-A)" />
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	166 <param name="mismatchPenalty" type="integer" value="5" label="Mismatch penalty (-M)" />
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	167 <param name="gapOpenPenalty" type="integer" value="2" label="Gap open penalty (-O)" />
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	168 <param name="gapExtensPenalty" type="integer" value="2" label="Gap extension penalty (-E)" />
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	169 <param name="flowPenalty" type="integer" value="2" label="The score penalty (-X)" />
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	170 <param name="flowOrder" type="text" value="" label="The flow order ([ACGT]{4+} or sff" />
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	171 <param name="bandWidth" type="integer" value="50" label="The band width (-w)" />
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	172 <param name="globalMap" type="integer" value="2" label="The soft clipping type (-g)" help="The soft-clipping type (0 - allow on the right and left, 1 - allow on the left, 2 - allow on the right, 3 - do not allow soft-clipping)" />
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	173 <param name="duplicateWindow" type="integer" value="128" label="The duplicate window (-W)" help="Remove duplicate alignments from different algorithms within this bp window (-1 to disable)"/>
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	174 <param name="scoringThreshold" type="integer" value="1" label="The scoring threshold (-T)" help="The score threshold divided by the match score" />
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	175 <param name="queueSize" type="integer" value="262144" label="The queue size (-q)" help="The queue size for the reads" />
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	176 <param name="outputFilter" type="integer" value="1" label="The output filter (-a)" help="The output filter (0 - unique best hits, 1 - random best hit, 2 - all best htis, 3 - all alignments)" />
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	177 <conditional name="rgTag">
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	178 <param name="source_select" type="select" label="Include Custom Read Group Tags">
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	179 <option value="false" selected="true">Default</option>
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	180 <option value="true">Custom</option>
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	181 </param>
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	182 <when value="false" />
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	183 <when value="true">
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	184 <param name="rgTagID" type="text" value="" label="The Read Group ID (-R)" help="The RG ID used in the RG record in the SAM header" />
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	185 <param name="rgTagCN" type="text" value="" label="The Read Group CN (-R)" help="The RG CN used in the RG record in the SAM header" />
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	186 <param name="rgTagDS" type="text" value="" label="The Read Group DS (-R)" help="The RG DS used in the RG record in the SAM header" />
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	187 <param name="rgTagDT" type="text" value="" label="The Read Group DT (-R)" help="The RG DT used in the RG record in the SAM header" />
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	188 <param name="rgTagLB" type="text" value="" label="The Read Group LB (-R)" help="The RG LB used in the RG record in the SAM header" />
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	189 <param name="rgTagPI" type="text" value="" label="The Read Group PI (-R)" help="The RG PI used in the RG record in the SAM header" />
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	190 <param name="rgTagPL" type="text" value="" label="The Read Group PL (-R)" help="The RG PL used in the RG record in the SAM header" />
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	191 <param name="rgTagPU" type="text" value="" label="The Read Group PU (-R)" help="The RG PU used in the RG record in the SAM header" />
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	192 <param name="rgTagSM" type="text" value="" label="The Read Group SM (-R)" help="The RG SM used in the RG record in the SAM header" />
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	193 </when>
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	194 </conditional>
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	195 <param name="filterIndependently" type="boolean" truevalue="true" falsevalue="false" checked="no" label="Filter algorithm independently (-I)" help="apply the output filter for each algorithm separately" />
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	196 </when>
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	197 </conditional>
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	198 <conditional name="map1">
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	199 <param name="source_select" type="select" label="Map1 Stage One" help="Turn on mapping algorithm #1 in the first stage">
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	200 <option value="true">Turn On</option>
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	201 <option value="false" selected="true">Turn Off</option>
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	202 </param>
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	203 <when value="true">
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	204 <param name="map1SeedLength" type="integer" value="32" label="The k-mer length to seed CALs (-1 to disable) (-l)" />
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	205 <param name="map1SeedMismatches" type="integer" value="2" label="The maximum number of mismatches in the seed (-s)" />
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	206 <param name="map1SecondarySeedLength" type="integer" value="64" label="The secondary seed length (-1 to disable) (-L)" />
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	207 <param name="map1NumEdits" type="float" value="-1" label="The maximum number of edits or false-negative probability assuming the maximum error rate (-1 to auto-tune) (-p)" />
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	208 <param name="map1BaseError" type="float" value="0.02" label="The the assumed per-base maximum error rate (-P)" />
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	209 <param name="map1Mismatches" type="float" value="3" label="The maximum number of or (read length) fraction of mismatches (-m)" />
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	210 <param name="map1GapOpens" type="float" value="1" label="The maximum number of or (read length) fraction of indel starts (-o)" />
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	211 <param name="map1GapExtensions" type="float" value="6" label="The maximum number of or (read length) fraction of indel extensions (-e)" />
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	212 <param name="map1MaxCALsDeletion" type="integer" value="10" label="The maximum number of CALs to extend a deletion (-d)" />
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	213 <param name="map1EndIndels" type="integer" value="5" label="Indels are not allowed within this number of bps from the end of the read (-i)" />
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	214 <param name="map1MaxOptimalCALs" type="integer" value="32" label="Stop searching when INT optimal CALs have been found (-b)" />
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	215 <param name="map1MaxNodes" type="integer" value="2000000" label="The maximum number of alignment nodes (-Q)" />
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	216 </when>
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	217 <when value="false" />
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	218 </conditional>
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	219 <conditional name="map2">
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	220 <param name="source_select" type="select" label="Map2 Stage One" help="Turn on mapping algorithm #2 in the first stage">
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	221 <option value="true">Turn On</option>
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	222 <option value="false" selected="true">Turn Off</option>
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	223 </param>
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	224 <when value="true">
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	225 <param name="map2Coefficient" type="float" value="5.5" label="The coefficient of length-threshold adjustment (-c)" />
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	226 <param name="map2SeedIntervalSize" type="integer" value="3" label="The maximum seeding interval size (-S)" />
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	227 <param name="map2ZBest" type="integer" value="1" label="Keep the z-best nodes during prefix trie traversal (-b)" />
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	228 <param name="map2ReverseTrigger" type="integer" value="5" label="The # seeds to trigger reverse alignment (-N)" />
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	229 </when>
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	230 <when value="false" />
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	231 </conditional>
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	232 <conditional name="map3">
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	233 <param name="source_select" type="select" label="Map3 Stage One" help="Turn on mapping algorithm #3 in the first stage">
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	234 <option value="true">Turn On</option>
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	235 <option value="false" selected="true">Turn Off</option>
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	236 </param>
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	237 <when value="true">
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	238 <param name="map3SeedLength" type="integer" value="-1" label="The k-mer length to seed CALs (-1 tunes to the genome size) (-l)" />
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	239 <param name="map3SeedMaxHits" type="integer" value="12" label="The maximum number of hits returned by a seed (-S)" />
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	240 <param name="map3SeedWindow" type="integer" value="25" label="The window of bases in which to group seeds (-b)" />
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	241 <param name="map3HPEnumeration" type="integer" value="0" label="The single homopolymer error difference for enumeration (-H)" />
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	242 </when>
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	243 <when value="false" />
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	244 </conditional>
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	245 <conditional name="MAP1">
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	246 <param name="source_select" type="select" label="Map1 Stage Two" help="Turn on mapping algorithm #1 in the second stage">
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	247 <option value="true">Turn On</option>
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	248 <option value="false" selected="true">Turn Off</option>
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	249 </param>
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	250 <when value="true">
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	251 <param name="MAP1SeedLength" type="integer" value="32" label="The k-mer length to seed CALs (-1 to disable) (-l)" />
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	252 <param name="MAP1SeedMismatches" type="integer" value="2" label="The maximum number of mismatches in the seed (-s)" />
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	253 <param name="MAP1SecondarySeedLength" type="integer" value="64" label="The secondary seed length (-1 to disable) (-L)" />
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	254 <param name="MAP1NumEdits" type="float" value="-1" label="The maximum number of edits or false-negative probability assuming the maximum error rate (-1 to auto-tune) (-p)" />
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	255 <param name="MAP1BaseError" type="float" value="0.02" label="The the assumed per-base maximum error rate (-P)" />
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	256 <param name="MAP1Mismatches" type="float" value="3" label="The maximum number of or (read length) fraction of mismatches (-m)" />
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	257 <param name="MAP1GapOpens" type="float" value="1" label="The maximum number of or (read length) fraction of indel starts (-o)" />
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	258 <param name="MAP1GapExtensions" type="float" value="6" label="The maximum number of or (read length) fraction of indel extensions (-e)" />
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	259 <param name="MAP1MaxCALsDeletion" type="integer" value="10" label="The maximum number of CALs to extend a deletion (-d)" />
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	260 <param name="MAP1EndIndels" type="integer" value="5" label="Indels are not allowed within this number of bps from the end of the read (-i)" />
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	261 <param name="MAP1MaxOptimalCALs" type="integer" value="32" label="Stop searching when INT optimal CALs have been found (-b)" />
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	262 <param name="MAP1MaxNodes" type="integer" value="2000000" label="The maximum number of alignment nodes (-Q)" />
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	263 </when>
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	264 <when value="false" />
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	265 </conditional>
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	266 <conditional name="MAP2">
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	267 <param name="source_select" type="select" label="Map2 Stage Two" help="Turn on mapping algorithm #2 in the second stage">
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	268 <option value="true">Turn On</option>
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	269 <option value="false" selected="true">Turn Off</option>
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	270 </param>
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	271 <when value="true">
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	272 <param name="MAP2Coefficient" type="float" value="5.5" label="The coefficient of length-threshold adjustment (-c)" />
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	273 <param name="MAP2SeedIntervalSize" type="integer" value="3" label="The maximum seeding interval size (-S)" />
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	274 <param name="MAP2ZBest" type="integer" value="1" label="Keep the z-best nodes during prefix trie traversal (-b)" />
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	275 <param name="MAP2ReverseTrigger" type="integer" value="5" label="The # seeds to trigger reverse alignment (-N)" />
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	276 </when>
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	277 <when value="false" />
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	278 </conditional>
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	279 <conditional name="MAP3">
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	280 <param name="source_select" type="select" label="Map3 Stage Two" help="Turn on mapping algorithm #3 in the second stage">
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	281 <option value="true">Turn On</option>
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	282 <option value="false" selected="true">Turn Off</option>
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	283 </param>
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	284 <when value="true">
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	285 <param name="MAP3SeedLength" type="integer" value="-1" label="The k-mer length to seed CALs (-1 tunes to the genome size) (-l)" />
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	286 <param name="MAP3SeedMaxHits" type="integer" value="12" label="The maximum number of hits returned by a seed (-S)" />
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	287 <param name="MAP3SeedWindow" type="integer" value="25" label="The window of bases in which to group seeds (-b)" />
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	288 <param name="MAP3HPEnumeration" type="integer" value="0" label="The single homopolymer error difference for enumeration (-H)" />
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	289 </when>
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	290 <when value="false" />
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	291 </conditional>
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	292 </when>
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	293 </conditional>
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	294 <param name="suppressHeader" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Suppress the header in the output SAM file" help="TMAP produces SAM with several lines of header information" />
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	295 </inputs>
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	296 <outputs>
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	297 <data format="sam" name="output" label="${tool.name} on ${on_string}: mapped reads">
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	298 <actions>
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	299 <conditional name="genomeSource.refGenomeSource">
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	300 <when value="indexed">
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	301 <action type="metadata" name="dbkey">
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	302 <option type="from_data_table" name="tmap_indexes" column="0">
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	303 <filter type="param_value" ref="genomeSource.indices" column="1"/>
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	304 </option>
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	305 </action>
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	306 </when>
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	307 </conditional>
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	308 </actions>
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	309 </data>
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	310 </outputs>
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	311 <help>
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	312
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	313 What it does
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	314
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	315 TMAP is a fast light-weight tool that aligns DNA sequences (small queries) to a sequence database (large sequences), such as the human reference genome. TMAP follows a two-stage approach, with a set of algorithms and associated settings for each stage. If there are no mappings for a read by applying the algorithms in the first stage, then the algorithms in the second stage are applied. For example, a set of algorithms to quickly align near-perfect reads may be used in the first stage, while a set of sensitive algorithms may be used to map difficult reads in the second stage.
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	316
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	317 It combines multiple mapping algorithms to give sensitive and accurate alignments quickly. It uses three core algorithms, BWA-short, BWA-long, and a variant of the SSAHA algorithm. These algorithms are described in the following publications:
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	318 - Li, H. and Durbin, R. (2009). Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics, 25, 1754–1760.
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	319 - Li, H. and Durbin, R. (2010). Fast and accurate long-read alignment with Burrows-Wheeler
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	320 - Ning, Z., Cox, A., and Mullikin, J. (2001). SSAHA: a fast search method for large DNA databases. Genome Res., 11, 1725–1729.
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	321
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	322 ------
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	323
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	324 Know what you are doing
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	325
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	326 .. class:: warningmark
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	327
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	328 There is no such thing (yet) as an automated gearshift in short read mapping. 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.
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	329
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	330 .. __: http://www.iontorrent.com/
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	331
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	332 ------
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	333
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	334 Input formats
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	335
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	336 TMAP accepts files in Sanger FASTQ format. Use the FASTQ Groomer to prepare your files.
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	337
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	338 ------
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	339
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	340 A Note on Built-in Reference Genomes
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	341
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	342 Some genomes have multiple variants. If only one "type" of genome is listed, it is the Full version, which means that everything that came in the original genome data download (possibly with mitochondrial and plasmid DNA added if it wasn't already included). The Full version is available for every genome. Some genomes also come in the Canonical variant, which contains only the "canonical" (well-defined) chromosomes or segments, such as chr1-chr22, chrX, chrY, and chrM for human. Other variations include gender. These will come in the canonical form only, so the general Canonical variant is actually Canonical Female and the other is Canonical Male (identical to female excluding chrX).
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	343
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	344 ------
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	345
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	346 Outputs
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	347
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	348 The output is in SAM format, and has the following columns::
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	349
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	350 Column Description
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	351 -------- --------------------------------------------------------
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	352 1 QNAME Query (pair) NAME
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	353 2 FLAG bitwise FLAG
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	354 3 RNAME Reference sequence NAME
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	355 4 POS 1-based leftmost POSition/coordinate of clipped sequence
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	356 5 MAPQ MAPping Quality (Phred-scaled)
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	357 6 CIGAR extended CIGAR string
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	358 7 MRNM Mate Reference sequence NaMe ('=' if same as RNAME)
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	359 8 MPOS 1-based Mate POSition
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	360 9 ISIZE Inferred insert SIZE
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	361 10 SEQ query SEQuence on the same strand as the reference
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	362 11 QUAL query QUALity (ASCII-33 gives the Phred base quality)
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	363 12 OPT variable OPTional fields in the format TAG:VTYPE:VALU
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	364
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	365 The flags are as follows::
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	366
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	367 Flag Description
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	368 ------ -------------------------------------
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	369 0x0001 the read is paired in sequencing
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	370 0x0002 the read is mapped in a proper pair
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	371 0x0004 the query sequence itself is unmapped
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	372 0x0008 the mate is unmapped
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	373 0x0010 strand of the query (1 for reverse)
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	374 0x0020 strand of the mate
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	375 0x0040 the read is the first read in a pair
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	376 0x0080 the read is the second read in a pair
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	377 0x0100 the alignment is not primary
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	378
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	379 It looks like this (scroll sideways to see the entire example)::
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	380
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	381 QNAME FLAG RNAME POS MAPQ CIAGR MRNM MPOS ISIZE SEQ QUAL OPT
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	382 HWI-EAS91_1_30788AAXX:1:1:1761:343 4 * 0 0 * * 0 0 AAAAAAANNAAAAAAAAAAAAAAAAAAAAAAAAAAACNNANNGAGTNGNNNNNNNGCTTCCCACAGNNCTGG hhhhhhh;;hhhhhhhhhhh^hOhhhhghhhfhhhgh;;h;;hhhh;h;;;;;;;hhhhhhghhhh;;Phhh
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	383 HWI-EAS91_1_30788AAXX:1:1:1578:331 4 * 0 0 * * 0 0 GTATAGANNAATAAGAAAAAAAAAAATGAAGACTTTCNNANNTCTGNANNNNNNNTCTTTTTTCAGNNGTAG hhhhhhh;;hhhhhhhhhhhhhhhhhhhhhhhhhhhh;;h;;hhhh;h;;;;;;;hhhhhhhhhhh;;hhVh
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	384
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	385 -------
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	386
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	387 TMAP settings
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	388
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	389 All of the options have a default value. You can change most of them. Most of the options in TMAP have been implemented here.
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	390
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	391 ------
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	392
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	393 TMAP parameter list
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	394
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	395 This is an exhaustive list of TMAP options implemented here:
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	396
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	397 For the global options::
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	398
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	399 -A INT score for a match [5]
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	400 -M INT the mismatch penalty [3]
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	401 -O INT the indel start penalty [3]
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	402 -E INT the indel extend penalty [1]
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	403 -X INT the flow score penalty [7]
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	404 -w INT the band width [50]
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	405 -g map the full read [false]
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	406 -W INT remove duplicate alignments from different algorithms within this bp window (-1 to disable) [128]
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	407 -T INT score threshold divided by the match score [30]
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	408 -q INT the queue size for the reads (-1 disables) [65536]
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	409 -n INT the number of threads [1]
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	410 -a INT output filter [1]
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	411 0 - unique best hits
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	412 1 - random best hit
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	413 2 - all best hits
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	414 3 - all alignments
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	415 -R STRING the RG tags to add to the SAM header [(null)]
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	416
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	417 For mapall options::
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	418
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	419 -I apply the output filter for each algorithm separately [false]
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	420
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	421 For map1 options::
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	422
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	423 -l INT the k-mer length to seed CALs (-1 to disable) [32]
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	424 -s INT maximum number of mismatches in the seed [3]
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	425 -m NUM maximum number of or (read length) fraction of mismatches [number: 2]
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	426 -o NUM maximum number of or (read length) fraction of indel starts [number: 1]
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	427 -e NUM maximum number of or (read length) fraction of indel extensions [number: 6]
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	428 -d INT the maximum number of CALs to extend a deletion [10]
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	429 -i INT indels are not allowed within INT number of bps from the end of the read [5]
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	430 -b INT stop searching when INT optimal CALs have been found [32]
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	431 -Q INT maximum number of alignment nodes [2000000]
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	432
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	433 For map2 options::
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	434
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	435 -c FLOAT coefficient of length-threshold adjustment [5.5]
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	436 -S INT maximum seeding interval size [3]
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	437 -b INT Z-best [1]
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	438 -N INT # seeds to trigger reverse alignment [5]
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	439
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	440 For map3 options::
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	441
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	442 -l INT the k-mer length to seed CALs (-1 tunes to the genome size) [-1]
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	443 -S INT the maximum number of hits returned by a seed [8]
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	444 -b INT the window of bases in which to group seeds [50]
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	445 -H INT single homopolymer error difference for enumeration [0]
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	446
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	447 </help>
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	448 </tool>
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	449
7cbfd271d207 Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	450

Mercurial > repos > nilshomer > tmap_wrapper

annotate tmap_wrapper_0.0.19/tmap_wrapper.xml @ 0:7cbfd271d207