tmap_wrapper: tmap_wrapper_0.0.19/tmap

annotate tmap_wrapper_0.0.19/tmap_wrapper.xml @ 0:de2efe4dda3f

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

author	nilshomer
date	Tue, 07 Jun 2011 16:46:26 -0400
parents
children

rev	line source
0 de2efe4dda3f 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">
de2efe4dda3f 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>
de2efe4dda3f 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>
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	4 <command interpreter="python">
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	5 tmap_wrapper.py
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	6
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	7 ## reference source
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	8 --fileSource=$genomeSource.refGenomeSource
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	9 #if $genomeSource.refGenomeSource == "history":
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	10 ##build index on the fly
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	11 --ref="${genomeSource.ownFile}"
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	12 --dbkey=$dbkey
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	13 #else:
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	14 ##use precomputed indexes
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	15 --ref="${ filter( lambda x: str( x[0] ) == str( $genomeSource.indices ), $__app__.tool_data_tables[ 'tmap_indexes' ].get_fields() )[0][-1] }"
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	16 --do_not_build_index
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	17 #end if
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	18
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	19 ## input fastq
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	20 --fastq=$input
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	21
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	22 ## output file
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	23 --output=$output
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	24
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	25 ## run parameters
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	26 --params=$params.source_select
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	27 #if $params.source_select != "pre_set":
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	28 --mapall=$params.mapall.source_select
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	29 #if $params.mapall.source_select == "true":
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	30 --threads=$params.mapall.threads
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	31 --matchScore=$params.mapall.matchScore
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	32 --mismatchPenalty=$params.mapall.mismatchPenalty
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	33 --gapOpenPenalty=$params.mapall.gapOpenPenalty
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	34 --gapExtensPenalty=$params.mapall.gapExtensPenalty
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	35 --flowPenalty=$params.mapall.flowPenalty
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	36 --flowOrder=$params.mappll.flowOrder
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	37 --bandWidth=$params.mapall.bandWidth
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	38 --globalMap=$params.mapall.globalMap
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	39 --duplicateWindow=$params.mapall.duplicateWindow
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	40 --scoringThreshold=$params.mapall.scoringThreshold
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	41 --queueSize=$params.mapall.queueSize
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	42 --outputFilter=$params.mapall.outputFilter
de2efe4dda3f 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
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	44 #if $params.mapall.rgTag.source_select == "true":
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	45 --rgTagID=$params.mapall.rgTag.rgTagID
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	46 --rgTagCN=$params.mapall.rgTag.rgTagCN
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	47 --rgTagDS=$params.mapall.rgTag.rgTagDS
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	48 --rgTagDT=$params.mapall.rgTag.rgTagDT
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	49 --rgTagLB=$params.mapall.rgTag.rgTagLB
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	50 --rgTagPI=$params.mapall.rgTag.rgTagPI
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	51 --rgTagPL=$params.mapall.rgTag.rgTagPL
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	52 --rgTagPU=$params.mapall.rgTag.rgTagPU
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	53 --rgTagSM=$params.mapall.rgTag.rgTagSM
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	54 #end if
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	55 --filterIndependently=$params.mapall.filterIndependently
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	56 #end if
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	57 --map1=$params.map1.source_select
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	58 #if $params.map1.source_select == "true":
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	59 --map1SeedLength=$params.map1.map1SeedLength
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	60 --map1SeedMismatches=$params.map1.map1SeedMismatches
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	61 --map1SecondarySeedLength=$params.map1.map1SecondarySeedLength
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	62 --map1NumEdits=$params.map1.map1NumEdits
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	63 --map1BaseError=$params.map1.map1BaseError
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	64 --map1Mismatches=$params.map1.map1Mismatches
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	65 --map1GapOpens=$params.map1.map1GapOpens
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	66 --map1GapExtensions=$params.map1.map1GapExtensions
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	67 --map1MaxCALsDeletion=$params.map1.map1MaxCALsDeletion
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	68 --map1EndIndels=$params.map1.map1EndIndels
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	69 --map1MaxOptimalCALs=$params.map1.map1MaxOptimalCALs
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	70 --map1MaxNodes=$params.map1.map1MaxNodes
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	71 #end if
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	72 --map2=$params.map2.source_select
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	73 #if $params.map2.source_select == "true":
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	74 --map2Coefficient=$params.map2.map2Coefficient
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	75 --map2SeedIntervalSize=$params.map2.map2SeedIntervalSize
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	76 --map2ZBest=$params.map2.map2ZBest
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	77 --map2ReverseTrigger=$params.map2.map2ReverseTrigger
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	78 #end if
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	79 --map3=$params.map3.source_select
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	80 #if $params.map3.source_select == "true":
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	81 --map3SeedLength=$params.map3.map3SeedLength
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	82 --map3SeedMaxHits=$params.map3.map3SeedMaxHits
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	83 --map3SeedWindow=$params.map3.map3SeedWindow
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	84 --map3HPEnumeration=$params.map3.map3HPEnumeration
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	85 #end if
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	86 --MAP1=$params.MAP1.source_select
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	87 #if $params.MAP1.source_select == "true":
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	88 --MAP1SeedLength=$params.MAP1.MAP1SeedLength
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	89 --MAP1SeedMismatches=$params.MAP1.MAP1SeedMismatches
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	90 --MAP1SecondarySeedLength=$params.MAP1.MAP1SecondarySeedLength
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	91 --MAP1NumEdits=$params.MAP1.MAP1NumEdits
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	92 --MAP1BaseError=$params.MAP1.MAP1BaseError
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	93 --MAP1Mismatches=$params.MAP1.MAP1Mismatches
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	94 --MAP1GapOpens=$params.MAP1.MAP1GapOpens
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	95 --MAP1GapExtensions=$params.MAP1.MAP1GapExtensions
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	96 --MAP1MaxCALsDeletion=$params.MAP1.MAP1MaxCALsDeletion
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	97 --MAP1EndIndels=$params.MAP1.MAP1EndIndels
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	98 --MAP1MaxOptimalCALs=$params.MAP1.MAP1MaxOptimalCALs
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	99 --MAP1MaxNodes=$params.MAP1.MAP1MaxNodes
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	100 #end if
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	101 --MAP2=$params.MAP2.source_select
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	102 #if $params.MAP2.source_select == "true":
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	103 --MAP2Coefficient=$params.MAP2.MAP2Coefficient
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	104 --MAP2SeedIntervalSize=$params.MAP2.MAP2SeedIntervalSize
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	105 --MAP2ZBest=$params.MAP2.MAP2ZBest
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	106 --MAP2ReverseTrigger=$params.MAP2.MAP2ReverseTrigger
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	107 #end if
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	108 --MAP3=$params.MAP3.source_select
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	109 #if $params.MAP3.source_select == "true":
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	110 --MAP3SeedLength=$params.MAP3.MAP3SeedLength
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	111 --MAP3SeedMaxHits=$params.MAP3.MAP3SeedMaxHits
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	112 --MAP3SeedWindow=$params.MAP3.MAP3SeedWindow
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	113 --MAP3HPEnumeration=$params.MAP3.MAP3HPEnumeration
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	114 #end if
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	115 #else:
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	116 --threads="4"
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	117 --map1="false"
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	118 --map2="false"
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	119 --map3="false"
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	120 --MAP1="false"
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	121 --MAP2="false"
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	122 --MAP3="false"
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	123 #end if
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	124
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	125 ## suppress output SAM header
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	126 --suppressHeader=$suppressHeader
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	127 </command>
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	128 <requirements>
de2efe4dda3f 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>
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	130 </requirements>
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	131 <inputs>
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	132 <conditional name="genomeSource">
de2efe4dda3f 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?">
de2efe4dda3f 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>
de2efe4dda3f 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>
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	136 </param>
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	137 <when value="indexed">
de2efe4dda3f 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">
de2efe4dda3f 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">
de2efe4dda3f 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" />
de2efe4dda3f 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" />
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	142 </options>
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	143 </param>
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	144 </when>
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	145 <when value="history">
de2efe4dda3f 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" />
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	147 </when>
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	148 </conditional>
de2efe4dda3f 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" />
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	150 <conditional name="params">
de2efe4dda3f 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">
de2efe4dda3f 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>
de2efe4dda3f 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>
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	154 </param>
de2efe4dda3f 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" />
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	156 <when value="full">
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	157 <conditional name="mapall">
de2efe4dda3f 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">
de2efe4dda3f 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>
de2efe4dda3f 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>
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	161 </param>
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	162 <when value="false" />
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	163 <when value="true">
de2efe4dda3f 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)" />
de2efe4dda3f 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)" />
de2efe4dda3f 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)" />
de2efe4dda3f 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)" />
de2efe4dda3f 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)" />
de2efe4dda3f 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)" />
de2efe4dda3f 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" />
de2efe4dda3f 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)" />
de2efe4dda3f 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)" />
de2efe4dda3f 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)"/>
de2efe4dda3f 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" />
de2efe4dda3f 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" />
de2efe4dda3f 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)" />
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	177 <conditional name="rgTag">
de2efe4dda3f 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">
de2efe4dda3f 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>
de2efe4dda3f 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>
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	181 </param>
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	182 <when value="false" />
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	183 <when value="true">
de2efe4dda3f 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" />
de2efe4dda3f 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" />
de2efe4dda3f 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" />
de2efe4dda3f 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" />
de2efe4dda3f 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" />
de2efe4dda3f 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" />
de2efe4dda3f 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" />
de2efe4dda3f 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" />
de2efe4dda3f 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" />
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	193 </when>
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	194 </conditional>
de2efe4dda3f 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" />
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	196 </when>
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	197 </conditional>
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	198 <conditional name="map1">
de2efe4dda3f 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">
de2efe4dda3f 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>
de2efe4dda3f 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>
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	202 </param>
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	203 <when value="true">
de2efe4dda3f 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)" />
de2efe4dda3f 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)" />
de2efe4dda3f 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)" />
de2efe4dda3f 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)" />
de2efe4dda3f 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)" />
de2efe4dda3f 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)" />
de2efe4dda3f 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)" />
de2efe4dda3f 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)" />
de2efe4dda3f 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)" />
de2efe4dda3f 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)" />
de2efe4dda3f 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)" />
de2efe4dda3f 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)" />
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	216 </when>
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	217 <when value="false" />
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	218 </conditional>
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	219 <conditional name="map2">
de2efe4dda3f 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">
de2efe4dda3f 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>
de2efe4dda3f 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>
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	223 </param>
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	224 <when value="true">
de2efe4dda3f 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)" />
de2efe4dda3f 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)" />
de2efe4dda3f 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)" />
de2efe4dda3f 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)" />
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	229 </when>
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	230 <when value="false" />
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	231 </conditional>
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	232 <conditional name="map3">
de2efe4dda3f 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">
de2efe4dda3f 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>
de2efe4dda3f 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>
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	236 </param>
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	237 <when value="true">
de2efe4dda3f 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)" />
de2efe4dda3f 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)" />
de2efe4dda3f 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)" />
de2efe4dda3f 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)" />
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	242 </when>
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	243 <when value="false" />
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	244 </conditional>
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	245 <conditional name="MAP1">
de2efe4dda3f 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">
de2efe4dda3f 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>
de2efe4dda3f 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>
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	249 </param>
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	250 <when value="true">
de2efe4dda3f 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)" />
de2efe4dda3f 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)" />
de2efe4dda3f 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)" />
de2efe4dda3f 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)" />
de2efe4dda3f 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)" />
de2efe4dda3f 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)" />
de2efe4dda3f 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)" />
de2efe4dda3f 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)" />
de2efe4dda3f 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)" />
de2efe4dda3f 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)" />
de2efe4dda3f 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)" />
de2efe4dda3f 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)" />
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	263 </when>
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	264 <when value="false" />
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	265 </conditional>
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	266 <conditional name="MAP2">
de2efe4dda3f 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">
de2efe4dda3f 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>
de2efe4dda3f 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>
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	270 </param>
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	271 <when value="true">
de2efe4dda3f 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)" />
de2efe4dda3f 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)" />
de2efe4dda3f 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)" />
de2efe4dda3f 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)" />
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	276 </when>
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	277 <when value="false" />
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	278 </conditional>
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	279 <conditional name="MAP3">
de2efe4dda3f 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">
de2efe4dda3f 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>
de2efe4dda3f 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>
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	283 </param>
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	284 <when value="true">
de2efe4dda3f 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)" />
de2efe4dda3f 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)" />
de2efe4dda3f 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)" />
de2efe4dda3f 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)" />
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	289 </when>
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	290 <when value="false" />
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	291 </conditional>
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	292 </when>
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	293 </conditional>
de2efe4dda3f 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" />
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	295 </inputs>
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	296 <outputs>
de2efe4dda3f 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">
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	298 <actions>
de2efe4dda3f 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">
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	300 <when value="indexed">
de2efe4dda3f 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">
de2efe4dda3f 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">
de2efe4dda3f 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"/>
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	304 </option>
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	305 </action>
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	306 </when>
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	307 </conditional>
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	308 </actions>
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	309 </data>
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	310 </outputs>
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	311 <help>
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	312
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	313 What it does
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	314
de2efe4dda3f 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.
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	316
de2efe4dda3f 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:
de2efe4dda3f 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.
de2efe4dda3f 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
de2efe4dda3f 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.
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	321
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	322 ------
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	323
de2efe4dda3f 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
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	325
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	326 .. class:: warningmark
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	327
de2efe4dda3f 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.
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	329
de2efe4dda3f 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/
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	331
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	332 ------
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	333
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	334 Input formats
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	335
de2efe4dda3f 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.
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	337
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	338 ------
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	339
de2efe4dda3f 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
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	341
de2efe4dda3f 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).
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	343
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	344 ------
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	345
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	346 Outputs
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	347
de2efe4dda3f 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::
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	349
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	350 Column Description
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	351 -------- --------------------------------------------------------
de2efe4dda3f 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
de2efe4dda3f 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
de2efe4dda3f 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
de2efe4dda3f 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
de2efe4dda3f 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)
de2efe4dda3f 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
de2efe4dda3f 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)
de2efe4dda3f 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
de2efe4dda3f 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
de2efe4dda3f 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
de2efe4dda3f 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)
de2efe4dda3f 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
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	364
de2efe4dda3f 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::
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	366
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	367 Flag Description
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	368 ------ -------------------------------------
de2efe4dda3f 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
de2efe4dda3f 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
de2efe4dda3f 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
de2efe4dda3f 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
de2efe4dda3f 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)
de2efe4dda3f 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
de2efe4dda3f 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
de2efe4dda3f 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
de2efe4dda3f 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
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	378
de2efe4dda3f 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)::
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	380
de2efe4dda3f 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
de2efe4dda3f 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
de2efe4dda3f 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
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	384
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	385 -------
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	386
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	387 TMAP settings
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	388
de2efe4dda3f 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.
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	390
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	391 ------
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	392
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	393 TMAP parameter list
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	394
de2efe4dda3f 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:
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	396
de2efe4dda3f 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::
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	398
de2efe4dda3f 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]
de2efe4dda3f 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]
de2efe4dda3f 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]
de2efe4dda3f 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]
de2efe4dda3f 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]
de2efe4dda3f 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]
de2efe4dda3f 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]
de2efe4dda3f 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]
de2efe4dda3f 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]
de2efe4dda3f 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]
de2efe4dda3f 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]
de2efe4dda3f 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]
de2efe4dda3f 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
de2efe4dda3f 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
de2efe4dda3f 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
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	414 3 - all alignments
de2efe4dda3f 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)]
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	416
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	417 For mapall options::
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	418
de2efe4dda3f 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]
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	420
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	421 For map1 options::
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	422
de2efe4dda3f 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]
de2efe4dda3f 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]
de2efe4dda3f 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]
de2efe4dda3f 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]
de2efe4dda3f 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]
de2efe4dda3f 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]
de2efe4dda3f 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]
de2efe4dda3f 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]
de2efe4dda3f 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]
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	432
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	433 For map2 options::
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	434
de2efe4dda3f 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]
de2efe4dda3f 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]
de2efe4dda3f 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]
de2efe4dda3f 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]
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	439
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	440 For map3 options::
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	441
de2efe4dda3f 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]
de2efe4dda3f 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]
de2efe4dda3f 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]
de2efe4dda3f 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]
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	446
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	447 </help>
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	448 </tool>
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	449
de2efe4dda3f 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:de2efe4dda3f