tmap_wrapper: tmap_wrapper_0.3.3/tmap

annotate tmap_wrapper_0.3.3/tmap_wrapper.xml @ 2:e2640d81157a default tip

* moving to TMAP 0.3.3

author	Nils Homer <nilshomer@gmail.com>
date	Sun, 26 Feb 2012 20:28:27 -0500
parents	tmap_wrapper_0.0.19/tmap_wrapper.xml@de2efe4dda3f
children

rev	line source
2 e2640d81157a * moving to TMAP 0.3.3 Nils Homer <nilshomer@gmail.com> parents: 0 diff changeset	1 <tool id="tmap_wrapper" name="Map with TMAP" version="0.3.3">
0 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 ), $__app__.tool_data_tables[ 'tmap_indexes' ].get_fields() )[0][-1] }"
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	16 --do_not_build_index
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	17 #end if
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	18
2 e2640d81157a * moving to TMAP 0.3.3 Nils Homer <nilshomer@gmail.com> parents: 0 diff changeset	19 ## input SFF/fastq
e2640d81157a * moving to TMAP 0.3.3 Nils Homer <nilshomer@gmail.com> parents: 0 diff changeset	20 --input=$inputs.input
e2640d81157a * moving to TMAP 0.3.3 Nils Homer <nilshomer@gmail.com> parents: 0 diff changeset	21 --inputtype=$inputs.inputtype
0 de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	22
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	23 ## output file
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	24 --output=$output
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	25
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	26 ## run parameters
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	27 --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	28 #if $params.source_select != "pre_set":
2 e2640d81157a * moving to TMAP 0.3.3 Nils Homer <nilshomer@gmail.com> parents: 0 diff changeset	29 --algorithm=$params.algorithm
e2640d81157a * moving to TMAP 0.3.3 Nils Homer <nilshomer@gmail.com> parents: 0 diff changeset	30 --globalOptions=$params.globalOptions
e2640d81157a * moving to TMAP 0.3.3 Nils Homer <nilshomer@gmail.com> parents: 0 diff changeset	31 --flowspaceOptions=$params.flowspaceOptions
e2640d81157a * moving to TMAP 0.3.3 Nils Homer <nilshomer@gmail.com> parents: 0 diff changeset	32 --pairingOptions=$params.pairingOptions
e2640d81157a * moving to TMAP 0.3.3 Nils Homer <nilshomer@gmail.com> parents: 0 diff changeset	33 --algorithmOptions=$params.algorithmOptions
e2640d81157a * moving to TMAP 0.3.3 Nils Homer <nilshomer@gmail.com> parents: 0 diff changeset	34 --threads=$params.threads
0 de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	35 #else:
2 e2640d81157a * moving to TMAP 0.3.3 Nils Homer <nilshomer@gmail.com> parents: 0 diff changeset	36 --algorithm=''
e2640d81157a * moving to TMAP 0.3.3 Nils Homer <nilshomer@gmail.com> parents: 0 diff changeset	37 --globalOptions=''
e2640d81157a * moving to TMAP 0.3.3 Nils Homer <nilshomer@gmail.com> parents: 0 diff changeset	38 --flowspaceOptions=''
e2640d81157a * moving to TMAP 0.3.3 Nils Homer <nilshomer@gmail.com> parents: 0 diff changeset	39 --pairingOptions=''
e2640d81157a * moving to TMAP 0.3.3 Nils Homer <nilshomer@gmail.com> parents: 0 diff changeset	40 --algorithmOptions=''
0 de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	41 --threads="4"
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	42 #end if
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	43
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	44 ## suppress output SAM header
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	45 --suppressHeader=$suppressHeader
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	46 </command>
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	47 <requirements>
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	48 <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	49 </requirements>
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	50 <inputs>
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	51 <conditional name="genomeSource">
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	52 <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	53 <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	54 <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	55 </param>
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	56 <when value="indexed">
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	57 <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	58 <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	59 <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	60 <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	61 </options>
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	62 </param>
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	63 </when>
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	64 <when value="history">
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	65 <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	66 </when>
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	67 </conditional>
2 e2640d81157a * moving to TMAP 0.3.3 Nils Homer <nilshomer@gmail.com> parents: 0 diff changeset	68 <conditional name="inputs">
e2640d81157a * moving to TMAP 0.3.3 Nils Homer <nilshomer@gmail.com> parents: 0 diff changeset	69 <param name="source_select" type="select" label="The input type" help="The input type" >
e2640d81157a * moving to TMAP 0.3.3 Nils Homer <nilshomer@gmail.com> parents: 0 diff changeset	70 <option value="fastq">FASTQ</option>
e2640d81157a * moving to TMAP 0.3.3 Nils Homer <nilshomer@gmail.com> parents: 0 diff changeset	71 <option value="sff">SFF</option>
e2640d81157a * moving to TMAP 0.3.3 Nils Homer <nilshomer@gmail.com> parents: 0 diff changeset	72 </param>
e2640d81157a * moving to TMAP 0.3.3 Nils Homer <nilshomer@gmail.com> parents: 0 diff changeset	73 <when value="fastq">
e2640d81157a * moving to TMAP 0.3.3 Nils Homer <nilshomer@gmail.com> parents: 0 diff changeset	74 <param name="input" type="data" value="" format="fastqsanger" label="FASTQ file" help="Must have Sanger-scaled quality values with ASCII offset 33" />
e2640d81157a * moving to TMAP 0.3.3 Nils Homer <nilshomer@gmail.com> parents: 0 diff changeset	75 <param name="inputtype" type="text" value="fastq" label="the input type (do not modify)"/>
e2640d81157a * moving to TMAP 0.3.3 Nils Homer <nilshomer@gmail.com> parents: 0 diff changeset	76 </when>
e2640d81157a * moving to TMAP 0.3.3 Nils Homer <nilshomer@gmail.com> parents: 0 diff changeset	77 <when value="sff">
e2640d81157a * moving to TMAP 0.3.3 Nils Homer <nilshomer@gmail.com> parents: 0 diff changeset	78 <param name="input" type="data" value="" format="sff" label="SFF file" help="Must be a SFF file" />
e2640d81157a * moving to TMAP 0.3.3 Nils Homer <nilshomer@gmail.com> parents: 0 diff changeset	79 <param name="inputtype" type="text" value="sff" label="the input type (do not modify)"/>
e2640d81157a * moving to TMAP 0.3.3 Nils Homer <nilshomer@gmail.com> parents: 0 diff changeset	80 </when>
e2640d81157a * moving to TMAP 0.3.3 Nils Homer <nilshomer@gmail.com> parents: 0 diff changeset	81 </conditional>
0 de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	82 <conditional name="params">
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	83 <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	84 <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	85 <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	86 </param>
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	87 <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	88 <when value="full">
2 e2640d81157a * moving to TMAP 0.3.3 Nils Homer <nilshomer@gmail.com> parents: 0 diff changeset	89 <param name="algorithm" type="select" label="The main algorithm to use">
e2640d81157a * moving to TMAP 0.3.3 Nils Homer <nilshomer@gmail.com> parents: 0 diff changeset	90 <option value="mapall" selected="true">mapall</option>
e2640d81157a * moving to TMAP 0.3.3 Nils Homer <nilshomer@gmail.com> parents: 0 diff changeset	91 <option value="map1" selected="false">map1</option>
e2640d81157a * moving to TMAP 0.3.3 Nils Homer <nilshomer@gmail.com> parents: 0 diff changeset	92 <option value="map2" selected="false">map2</option>
e2640d81157a * moving to TMAP 0.3.3 Nils Homer <nilshomer@gmail.com> parents: 0 diff changeset	93 <option value="map3" selected="false">map3</option>
e2640d81157a * moving to TMAP 0.3.3 Nils Homer <nilshomer@gmail.com> parents: 0 diff changeset	94 <option value="map4" selected="false">map4</option>
e2640d81157a * moving to TMAP 0.3.3 Nils Homer <nilshomer@gmail.com> parents: 0 diff changeset	95 </param>
e2640d81157a * moving to TMAP 0.3.3 Nils Homer <nilshomer@gmail.com> parents: 0 diff changeset	96 <param name="threads" type="integer" value="4" label="The number of threads (-n)" />
e2640d81157a * moving to TMAP 0.3.3 Nils Homer <nilshomer@gmail.com> parents: 0 diff changeset	97 <param name="globalOptions" type="text" value="" label="The global options" />
e2640d81157a * moving to TMAP 0.3.3 Nils Homer <nilshomer@gmail.com> parents: 0 diff changeset	98 <param name="flowspaceOptions" type="text" value="" label="The flowspace options" />
e2640d81157a * moving to TMAP 0.3.3 Nils Homer <nilshomer@gmail.com> parents: 0 diff changeset	99 <param name="pairingOptions" type="text" value="" label="The pairing options" />
e2640d81157a * moving to TMAP 0.3.3 Nils Homer <nilshomer@gmail.com> parents: 0 diff changeset	100 <param name="algorithmOptions" type="text" value="" label="The algorithm options" />
0 de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	101 </when>
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	102 </conditional>
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	103 <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	104 </inputs>
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	105 <outputs>
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	106 <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	107 <actions>
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	108 <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	109 <when value="indexed">
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	110 <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	111 <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	112 <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	113 </option>
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	114 </action>
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	115 </when>
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	116 </conditional>
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	117 </actions>
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	118 </data>
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	119 </outputs>
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	120 <help>
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	121
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	122 What it does
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	123
2 e2640d81157a * moving to TMAP 0.3.3 Nils Homer <nilshomer@gmail.com> parents: 0 diff changeset	124 See the TMAP manual for more information.
0 de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	125
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	126 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	127 - 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	128 - 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	129 - 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	130
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	131 ------
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	132
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	133 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	134
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	135 .. class:: warningmark
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	136
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	137 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	138
2 e2640d81157a * moving to TMAP 0.3.3 Nils Homer <nilshomer@gmail.com> parents: 0 diff changeset	139 .. __: http://github.com/iontorrent/TMAP
0 de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	140
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	141 ------
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	142
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	143 Input formats
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	144
2 e2640d81157a * moving to TMAP 0.3.3 Nils Homer <nilshomer@gmail.com> parents: 0 diff changeset	145 TMAP accepts files in Sanger FASTQ format. Use the FASTQ Groomer to prepare your files. TMAP also accepts SFF files.
0 de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	146
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	147 ------
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	148
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	149 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	150
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	151 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	152
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	153 ------
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	154
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	155 Outputs
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	156
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	157 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	158
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	159 Column Description
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	160 -------- --------------------------------------------------------
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	161 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	162 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	163 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	164 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	165 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	166 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	167 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	168 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	169 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	170 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	171 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	172 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	173
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	174 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	175
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	176 Flag Description
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	177 ------ -------------------------------------
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	178 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	179 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	180 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	181 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	182 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	183 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	184 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	185 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	186 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	187
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	188 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	189
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	190 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	191 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	192 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	193
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	194 -------
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	195
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	196 TMAP settings
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	197
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	198 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	199
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	200
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	201 </help>
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	202 </tool>
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	203
de2efe4dda3f Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository nilshomer parents: diff changeset	204

Mercurial > repos > nilshomer > tmap_wrapper

annotate tmap_wrapper_0.3.3/tmap_wrapper.xml @ 2:e2640d81157a default tip