lastz: lastz_wrapper.xml annotate

author	devteam
date	Tue, 13 Oct 2015 12:23:37 -0400
parents
children

rev	line source
1 3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	1 <tool id="lastz_wrapper_2" name="Lastz" version="1.2.2">
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	2 <requirements>
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	3 <requirement type="package" version="1.02.00">lastz</requirement>
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	4 </requirements>
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	5 <description> map short reads against reference sequence</description>
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	6 <command interpreter="python">lastz_wrapper.py
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	7 #if $seq_name.how_to_name=="yes":
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	8 --ref_name="${seq_name.ref_name}"
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	9 #end if
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	10 --ref_source="${source.ref_source}"
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	11 --source_select="${params.source_select}"
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	12 --out_format="${out_format}"
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	13 --input2="${input2}"
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	14 #if $source.ref_source=="history":
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	15 --input1="${source.input1}"
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	16 --ref_sequences="${input1.metadata.sequences}"
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	17 #else:
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	18 --input1="${source.input1_2bit.fields.path}"
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	19 --ref_sequences="None"
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	20 #end if
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	21 #if $params.source_select=="pre_set":
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	22 --pre_set_options="${params.pre_set_options}"
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	23 #else:
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	24 --strand="${params.strand}"
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	25 --seed="${params.seed}"
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	26 --gfextend="${params.gfextend}"
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	27 --chain="${params.chain}"
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	28 --transition="${params.transition}"
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	29 --O="${params.O}"
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	30 --E="${params.E}"
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	31 --X="${params.X}"
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	32 --Y="${params.Y}"
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	33 --K="${params.K}"
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	34 --L="${params.L}"
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	35 --entropy="${params.entropy}"
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	36 #end if
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	37 --identity_min="${min_ident}"
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	38 --identity_max="${max_ident}"
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	39 --coverage="${min_cvrg}"
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	40 --output="${output1}"
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	41 --unmask="${unmask}"
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	42 --lastzSeqsFileDir="${GALAXY_DATA_INDEX_DIR}"
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	43 </command>
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	44 <inputs>
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	45 <param name="input2" format="fasta" type="data" label="Align sequencing reads in" />
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	46 <conditional name="source">
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	47 <param name="ref_source" type="select" label="Against reference sequences that are">
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	48 <option value="cached">locally cached</option>
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	49 <option value="history">in your history</option>
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	50 </param>
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	51 <when value="cached">
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	52 <param name="input1_2bit" type="select" label="Using reference genome" help="If your genome of interest is not listed, contact the Galaxy team">
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	53 <options from_data_table="lastz_seqs" />
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	54 </param>
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	55 </when>
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	56 <when value="history">
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	57 <param name="input1" type="data" format="fasta" label="Select a reference dataset" />
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	58 </when>
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	59 </conditional>
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	60 <param name="out_format" type="select" label="Output format">
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	61 <option value="sam">SAM</option>
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	62 <option value="diffs">Polymorphisms</option>
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	63 <option value="tabular">Tabular</option>
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	64 </param>
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	65 <conditional name="params">
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	66 <param name="source_select" type="select" label="Lastz settings to use" help="For most mapping needs use Commonly used settings. If you want full control use Full List">
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	67 <option value="pre_set">Commonly used</option>
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	68 <option value="full">Full Parameter List</option>
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	69 </param>
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	70 <when value="pre_set">
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	71 <param name="pre_set_options" type="select" label="Select mapping mode">
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	72 <option value="yasra98">Roche-454 98% identity</option>
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	73 <option value="yasra95">Roche-454 95% identity</option>
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	74 <option value="yasra90">Roche-454 90% identity</option>
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	75 <option value="yasra85">Roche-454 85% identity</option>
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	76 <option value="yasra75">Roche-454 75% identity</option>
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	77 <option value="yasra95short">Illumina 95% identity</option>
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	78 <option value="yasra85short">Illumina 85% identity</option>
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	79 </param>
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	80 </when>
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	81 <when value="full">
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	82 <param name="strand" type="select" label="Which strand to search?">
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	83 <option value="both">Both</option>
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	84 <option value="plus">Search forward strand only (the one in the reference)</option>
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	85 <option value="minus">Search the reverse complement strand only (opposite of the reference)</option>
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	86 </param>
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	87 <param name="seed" type="select" label="Select seeding settings" help="allows you set word size and number of mismatches">
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	88 <option value="12of19">Seed hits require a 19 bp word with matches in 12 specific positions</option>
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	89 <option value="14of22">Seed hits require a 22 bp word with matches in 14 specific positions</option>
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	90 </param>
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	91 <param name="transition" type="select" label="Select transition settings" help="affects the number of allowed transition substitutions">
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	92 <option value="transition">Allow one transition in each seed hit</option>
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	93 <option value="transition=2">Allow two transitions in a seed hit </option>
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	94 <option value="notransition">Don't allow any transitions in seed hits</option>
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	95 </param>
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	96 <param name="gfextend" type="select" label="Perform gap-free extension of seed hits to HSPs (high scoring segment pairs)?">
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	97 <option value="nogfextend">No</option>
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	98 <option value="gfextend">Yes</option>
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	99 </param>
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	100 <param name="chain" type="select" label="Perform chaining of HSPs?">
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	101 <option value="nochain">No</option>
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	102 <option value="chain">Yes</option>
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	103 </param>
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	104 <param name="O" type="integer" value="400" label="Gap opening penalty"/>
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	105 <param name="E" type="integer" value="30" label="Gap extension penalty"/>
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	106 <param name="X" type="integer" value="910" label="X-drop threshold"/>
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	107 <param name="Y" type="integer" value="9370" label="Y-drop threshold"/>
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	108 <param name="K" type="integer" value="3000" label="Set the threshold for HSPs (ungapped extensions scoring lower are discarded)"/>
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	109 <param name="L" type="integer" value="3000" label="Set the threshold for gapped alignments (gapped extensions scoring lower are discarded)"/>
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	110 <param name="entropy" type="select" label="Involve entropy when filtering HSPs?">
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	111 <option value="noentropy">No</option>
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	112 <option value="entropy">Yes</option>
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	113 </param>
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	114 </when>
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	115 </conditional>
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	116 <conditional name="seq_name">
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	117 <param name="how_to_name" type="select" label="Do you want to modify the reference name?">
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	118 <option value="no">No</option>
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	119 <option value="yes">Yes</option>
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	120 </param>
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	121 <when value="yes">
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	122 <param name="ref_name" type="text" value="Type sequence name here" label="Enter name for the Reference sequence"/>
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	123 </when>
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	124 <when value="no" />
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	125 </conditional>
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	126 <param name="min_ident" type="integer" value="0" label="Do not report matches below this identity (%)"/>
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	127 <param name="max_ident" type="integer" value="100" label="Do not report matches above this identity (%)"/>
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	128 <param name="min_cvrg" type="integer" value="0" label="Do not report matches that cover less than this percentage of each read"/>
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	129 <param name="unmask" type="select" label="Convert lowercase bases to uppercase">
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	130 <option value="yes">Yes</option>
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	131 <option value="no">No</option>
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	132 </param>
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	133 </inputs>
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	134 <outputs>
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	135 <data format="tabular" name="output1" label="${tool.name} on ${on_string}: mapped reads">
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	136 <change_format>
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	137 <when input="out_format" value="sam" format="sam" />
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	138 </change_format>
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	139 </data>
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	140 </outputs>
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	141 <tests>
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	142 <test>
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	143 <!--
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	144 Lastz command:
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	145 lastz phiX.2bit/phiX174[nickname=Ref] test-data/b1.fasta +nogfextend +nochain +gapped +strand=both +seed=12of19 +transition O=400 E=30 X=910 Y=9370 K=3000 L=3000 +noentropy +ambiguousn +nolaj +identity=0..100 +coverage=0 +format=sam- > lastz_wrapper_out2.sam
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	146 You need to point to phiX.2bit somewhere on your system. b1.fasta is located in galaxy's test-data. You will have to replace all the pluses before the
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	147 commands with 2 dashes, as double-dash can't appear in an XML comment.
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	148 -->
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	149 <param name="input2" value="b1.fasta" ftype="fasta" />
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	150 <param name="ref_source" value="cached" />
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	151 <param name="input1_2bit" value="phiX174" />
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	152 <param name="out_format" value="sam" />
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	153 <param name="source_select" value="full" />
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	154 <param name="strand" value="both" />
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	155 <param name="seed" value="12of19" />
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	156 <param name="transition" value="transition" />
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	157 <param name="gfextend" value="nogfextend" />
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	158 <param name="chain" value="nochain" />
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	159 <param name="O" value="400" />
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	160 <param name="E" value="30" />
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	161 <param name="X" value="910" />
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	162 <param name="Y" value="9370" />
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	163 <param name="K" value="3000" />
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	164 <param name="L" value="3000" />
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	165 <param name="entropy" value="noentropy" />
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	166 <!--
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	167 how_to_name is not the default. It is changed to modify
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	168 input1_2bit by adding the ref_name as a nickname
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	169 -->
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	170 <param name="how_to_name" value="yes" />
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	171 <param name="ref_name" value="Ref" />
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	172 <param name="min_ident" value="0" />
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	173 <param name="max_ident" value="100" />
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	174 <param name="min_cvrg" value="0" />
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	175 <param name="unmask" value="yes" />
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	176 <output name="output1" file="lastz_wrapper_out2.sam" />
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	177 </test>
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	178 <test>
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	179 <!--
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	180 Lastz command:
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	181 lastz test-data/phiX.fasta test-data/b1.fasta[fullnames] +yasra95short +ambiguousn +nolaj +identity=0..100 +coverage=0 +format=diffs > lastz_wrapper_out3.tabular
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	182 phiX.fasta and b1.fasta are located in galaxy's test-data. You will have to replace all the pluses before the commands with 2 dashes,
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	183 as double-dash can't appear in an XML comment.
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	184 -->
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	185 <param name="input2" value="b1.fasta" ftype="fasta" />
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	186 <param name="ref_source" value="history" />
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	187 <param name="input1" value="phiX.fasta" ftype="fasta" />
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	188 <param name="out_format" value="diffs" />
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	189 <param name="source_select" value="pre_set" />
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	190 <param name="pre_set_options" value="yasra95short" />
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	191 <param name="how_to_name" value="no" />
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	192 <param name="min_ident" value="0" />
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	193 <param name="max_ident" value="100" />
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	194 <param name="min_cvrg" value="0" />
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	195 <param name="unmask" value="yes" />
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	196 <output name="output1" file="lastz_wrapper_out3.tabular" />
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	197 </test>
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	198 <test>
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	199 <!--
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	200 Lastz command: first you will need to split the file phiX_split.fasta into two files,
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	201 phiX1.fasta and phiX2.fasta, each with 1 sequence (phiX1 and phiX2, respectively). Then:
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	202 lastz phiX1.fasta test-data/b1.fasta yasra95short ambiguousn nolaj identity=0..100 coverage=0 format=general-:score,name1,strand1,size1,start1,zstart1,end1,length1,text1,name2,strand2,size2,start2,zstart2,end2,start2+,zstart2+,end2+,length2,text2,diff,cigar,identity,coverage,gaprate,diagonal,shingle > lastz_wrapper_out4.tabular
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	203 lastz phiX2.fasta test-data/b1.fasta yasra95short ambiguousn nolaj identity=0..100 coverage=0 format=general-:score,name1,strand1,size1,start1,zstart1,end1,length1,text1,name2,strand2,size2,start2,zstart2,end2,start2+,zstart2+,end2+,length2,text2,diff,cigar,identity,coverage,gaprate,diagonal,shingle >> lastz_wrapper_out4.tabular
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	204 You need to point to phiX1.fasta and phiX2.fasta somewhere on your system.
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	205 phiX_split.fasta and b1.fasta are located in galaxy's test-data
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	206 You will have to replace all the asterisks before the commands with 2 dashes,
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	207 as double-dash can't appear in an XML comment
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	208
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	209 NOTE: since the input file include more than 1 sequence, the output must be sorted in
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	210 order for functional test to pass. This is done using the sort="True" attribute on the output.
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	211 -->
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	212 <param name="input2" value="b1.fasta" ftype="fasta" />
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	213 <param name="ref_source" value="history" />
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	214 <param name="input1" value="phiX_split.fasta" ftype="fasta" />
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	215 <param name="out_format" value="tabular" />
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	216 <param name="source_select" value="pre_set" />
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	217 <param name="pre_set_options" value="yasra95short" />
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	218 <param name="how_to_name" value="no" />
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	219 <param name="min_ident" value="0" />
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	220 <param name="max_ident" value="100" />
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	221 <param name="min_cvrg" value="0" />
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	222 <param name="unmask" value="yes" />
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	223 <output name="output1" file="lastz_wrapper_out4.tabular" sort="True" />
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	224 </test>
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	225 </tests>
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	226 <help>
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	227
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	228 What it does
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	229
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	230 LASTZ is a high performance pairwise sequence aligner derived from BLASTZ. It is written by Bob Harris in Webb Miller's laboratory at Penn State University. Special scoring sets were derived to improve runtime performance and quality. This Galaxy version of LASTZ is geared towards aligning short (Illumina/Solexa, AB/SOLiD) and medium (Roche/454) reads against a reference sequence. There is excellent, extensive documentation on LASTZ available here_.
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	231
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	232 .. _here: http://www.bx.psu.edu/miller_lab/dist/README.lastz-1.02.00/README.lastz-1.02.00.html
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	233
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	234 ------
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	235
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	236 Input formats
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	237
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	238 LASTZ accepts reference and reads in FASTA format. However, because Galaxy supports implicit format conversion the tool will recognize fastq and other method specific formats.
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	239
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	240 ------
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	241
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	242 Outputs
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	243
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	244 LASTZ generates one output. Depending on the choice you make in the Select output format drop-down, LASTZ will produce a SAM file showing sequence alignments, a list of differences between the reads and reference (Polymorphisms), or a general table with one line per alignment block (Tabular). Examples of these outputs are shown below.
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	245
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	246 SAM output
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	247
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	248 SAM has 12 columns::
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	249
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	250 1 2 3 4 5 6 7 8 9 10 11 12
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	251 ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	252 HWI-EAS91_1_30788AAXX:1:2:1670:915 99 chr9 58119878 60 36M = 58120234 392 GACCCCTACCCCACCGTGCTCTGGATCTCAGTGTTT IIIIIIIIIIIIIIIIEIIIIIII7IIIIIIIIIII XT:A:U NM:i:0 SM:i:37 AM:i:37 X0:i:1 X1:i:0 XM:i:0 XO:i:0 XG:i:0 MD:Z:36
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	253 HWI-EAS91_1_30788AAXX:1:2:1670:915 147 chr9 58120234 60 36M = 58119878 -392 ATGAGTCGAATTCTATTTTCCAAACTGTTAACAAAA IFIIDI;IIICIIIIIIIIIIIIIIIIIIIIIIIII XT:A:U NM:i:0 SM:i:37 AM:i:37 X0:i:1 X1:i:0 XM:i:0 XO:i:0 XG:i:0 MD:Z:36
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	254
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	255
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	256 where::
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	257
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	258 Column Description
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	259 --------- ---------------------------------------------------------------------
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	260 1. QNAME Query (pair) NAME
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	261 2. FLAG bitwise FLAG
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	262 3. RNAME Reference sequence NAME
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	263 4. POS 1-based leftmost POSition/coordinate of clipped sequence
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	264 5. MAPQ MAPping Quality (Phred-scaled)
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	265 6. CIGAR extended CIGAR string
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	266 7. MRNM Mate Reference sequence NaMe ('=' if same as RNAME)
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	267 8. MPOS 1-based Mate POSition
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	268 9. ISIZE Inferred insert SIZE
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	269 10. SEQ query SEQuence on the same strand as the reference
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	270 11. QUAL query QUALity (ASCII-33 gives the Phred base quality)
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	271 12. OPT variable OPTional fields in the format TAG:VTYPE:VALUE, tab-separated
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	272
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	273 The flags are as follows::
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	274
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	275 Flag Description
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	276 ------ -------------------------------------
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	277 0x0001 the read is paired in sequencing
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	278 0x0002 the read is mapped in a proper pair
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	279 0x0004 the query sequence itself is unmapped
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	280 0x0008 the mate is unmapped
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	281 0x0010 strand of the query (1 for reverse)
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	282 0x0020 strand of the mate
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	283 0x0040 the read is the first read in a pair
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	284 0x0080 the read is the second read in a pair
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	285 0x0100 the alignment is not primary
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	286
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	287 Polymorphism (SNP or differences) output
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	288
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	289 Polymorphism output contains 14 columns::
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	290
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	291 1 2 3 4 5 6 7 8 9 10 11 12 13 14
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	292 --------------------------------------------------------------------------------------------------------------------------------------------------------------
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	293 chrM 2490 2491 + 5386 HWI-EAS91_1_306UPAAXX:6:1:486:822 10 11 - 36 C A ACCTGTTTTACAGACACCTAAAGCTACATCGTCAAC ACCTGTTTTAAAGACACCTAAAGCTACATCGTCAAC
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	294 chrM 2173 2174 + 5386 HWI-EAS91_1_306UPAAXX:6:1:259:1389 26 27 + 36 G T GCGTACTTATTCGCCACCATGATTATGACCAGTGTT GCGTACTTATTCGCCACCATGATTATTACCAGTGTT
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	295
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	296 where::
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	297
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	298 1. (chrM) - Reference sequence id
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	299 2. (2490) - Start position of the difference in the reference
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	300 3. (2491) - End position of the difference in the reference
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	301 4. (+) - Strand of the reference (always plus)
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	302 5. (5386) - Length of the reference sequence
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	303 6. (HWI...) - read id
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	304 7. (10) - Start position of the difference in the read
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	305 8. (11) - End position of the difference in the read
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	306 9. (+) - Strand of the read
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	307 10. (36) - Length of the read
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	308 11. (C) - Nucleotide in the reference
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	309 12. (A) - Nucleotide in the read
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	310 13. (ACC...) - Reference side os the alignment
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	311 14. (ACC...) - Read side of the alignment
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	312
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	313 Tabular output
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	314
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	315 Tabular output is a tab-separated format with 30 columns::
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	316
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	317 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	318 -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	319 14 PHIX174 + 5386 4648 4647 4661 14 ATTTTCGTGATATT EYKX4VC01BV8HS + 204 154 153 167 154 153 167 14 ATTTTCGTGATATT .............. 14M 14/14 100.0% 14/204 6.9% 0/14 0.0% 4494 NA
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	320 16 PHIX174 + 5386 3363 3362 3378 16 GACGCCGGATTTGAGA EYKX4VC01AWJ88 - 259 36 35 51 209 208 224 16 GACGCCGGATTTGAGA ................ 16M 16/16 100.0% 16/259 6.2% 0/16 0.0% 3327 NA
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	321
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	322 The following columns are present::
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	323
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	324 Field Meaning
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	325 ---------------- -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	326 1. score Score of the alignment block. The scale and meaning of this number will vary, depending on the final stage performed and other command-line options.
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	327 2. name1 Name of the target sequence.
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	328 3. strand1 Target sequence strand, either "+" or "−".
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	329 4. size1 Size of the entire target sequence.
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	330 5. start1 Starting position of the alignment block in the target, origin-one.
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	331 6. zstart1 Starting position of the alignment block in the target, origin-zero.
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	332 7. end1 Ending position of the alignment block in the target, expressed either as origin-one closed or origin-zero half-open (the ending value is the same in both systems).
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	333 8. length1 Length of the alignment block in the target (excluding gaps).
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	334 9. text1 Aligned characters in the target, including gap characters.
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	335 10. name2 Name of the query sequence.
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	336 11. strand2 Query sequence strand, either "+" or "−".
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	337 12. size2 Size of the entire query sequence.
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	338 13. start2 Starting position of the alignment block in the query, origin-one.
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	339 14. zstart2 Starting position of the alignment block in the query, origin-zero.
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	340 15. end2 Ending position of the alignment block in the query, expressed either as origin-one closed or origin-zero half-open (the ending value is the same in both systems).
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	341 16. start2+ Starting position of the alignment block in the query, counting along the query sequence's positive strand (regardless of which query strand was aligned), origin-one. Note that if strand2 is "−", then this is the other end of the block from start2.
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	342 17. zstart2+ Starting position of the alignment block in the query, counting along the query sequence's positive strand (regardless of which query strand was aligned), origin-zero. Note that if strand2 is "−", then this is the other end of the block from zstart2.
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	343 18. end2+ Ending position of the alignment block in the query, counting along the query sequence's positive strand (regardless of which query strand was aligned), expressed either as origin-one closed or origin-zero half-open (the ending value is the same in both systems). Note that if strand2 is "−", then this is the other end of the block from end2.
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	344 19. length2 Length of the alignment block in the query (excluding gaps).
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	345 20. text2 Aligned characters in the query, including gap characters.
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	346 21. diff Differences between what would be written for text1 and text2. Matches are written as . (period), transitions as : (colon), transversions as X, and gaps as - (hyphen).
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	347 22. cigar A CIGAR-like representation of the alignment's path through the Dynamic Programming matrix. This is the short representation, without spaces, described in the Ensembl CIGAR specification.
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	348 23./24. identity Fraction of aligned bases in the block that are matches (see Identity). This is written as two fields. The first field is a fraction, written as <n>/<d>. The second field contains the same value, computed as a percentage.
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	349 25./26. coverage Fraction of the entire input sequence (target or query, whichever is shorter) that is covered by the alignment block (see Coverage). This is written as two fields. The first field is a fraction, written as <n>/<d>. The second field contains the same value, computed as a percentage.
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	350 27./28. gaprate Rate of gaps (also called indels) in the alignment block. This is written as two fields. The first field is a fraction, written as <n>/<d>, with the numerator being the number of alignment columns containing gaps and the denominator being the number without gaps. The second field contains the same value, computed as a percentage.
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	351 29. diagonal The diagonal of the start of the alignment block in the dynamic programming matrix, expressed as an identifying number start1-start2.
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	352 30. shingle A measurement of the shingle overlap between the target and the query. This is intended for the case where both the target and query are relatively short, and their ends are expected to overlap.
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	353
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	354 -------
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	355
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	356 LASTZ Settings
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	357
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	358 There are two setting modes: (1) Commonly used settings and (2) Full Parameter List.
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	359
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	360 Commonly used settings
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	361
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	362 There are seven modes::
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	363
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	364 Illumina-Solexa/AB-SOLiD 95% identity
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	365 Illumina-Solexa/AB-SOLiD 85% identity
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	366 Roche-454 98% identity
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	367 Roche-454 95% identity
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	368 Roche-454 90% identity
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	369 Roche-454 85% identity
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	370 Roche-454 75% identity
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	371
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	372 When deciding which one to use, consider the following: a 36 bp read with two differences will be 34/36 = 94% identical to the reference.
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	373
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	374 Full Parameter List
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	375
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	376 This mode gives you fuller control over lastz. The description of these and other parameters is found at the end of this page. Note that not all parameters are included in this interface. If you would like to make additional options available through Galaxy, e-mail us at galaxy-bugs@bx.psu.edu.
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	377
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	378 ------
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	379
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	380 Do you want to modify the reference name?
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	381
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	382 This option allows you to set the name of the reference sequence manually. This is helpful when, for example, you would like to make the reference name compatible with the UCSC naming conventions to be able to display your lastz results as a custom track at the UCSC Genome Browser.
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	383
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	384 ------
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	385
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	386 LASTZ parameter list
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	387
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	388 This is an exhaustive list of LASTZ options. Once again, please note that not all options are included in this interface. If you would like to make additional options available through Galaxy, e-mail us at galaxy-bugs@bx.psu.edu::
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	389
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	390 target[[s..e]][-] spec/file containing target sequence (fasta or nib)
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	391 [s..e] defines a subrange of the file
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	392 - indicates reverse-complement
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	393 (use --help=files for more details)
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	394 query[[s..e]][-] spec/file containing query sequences (fasta or nib)
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	395 if absent, queries come from stdin (unless they
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	396 aren't needed, as for --self or --tableonly)
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	397 (use --help=files for more details)
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	398 --self the target sequence is also the query
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	399 --quantum the query sequence contains quantum DNA
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	400 --seed=match<length> use a word with no gaps instead of a seed pattern
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	401 --seed=half<length> use space-free half-weight word instead of seed pattern
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	402 --match=<reward>[,<penalty>] set the score values for a match (+<reward>)
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	403 and mismatch (-<penalty>)
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	404 --[no]trans[ition][=2] allow one or two transitions in a seed hit
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	405 (by default a transition is allowed)
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	406 --word=<bits> set max bits for word hash; use this to trade time for
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	407 memory, eliminating thrashing for heavy seeds
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	408 (default is 28 bits)
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	409 --[no]filter=[<T>:]<M> filter half-weight seed hits, requiring at least M
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	410 matches and allowing no more than T transversions
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	411 (default is no filtering)
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	412 --notwins require just one seed hit
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	413 --twins=[<min>:]<maxgap> require two nearby seed hits on the same diagonal
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	414 (default is twins aren't required)
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	415 --notwins allow single, isolated seeds
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	416 --[no]recoverseeds avoid losing seeds in hash collisions. Cannot be used with --twins
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	417 --seedqueue=<entries> set number of entries in seed hit queue
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	418 (default is 262144)
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	419 --anchors=<file> read anchors from a file, instead of discovering anchors
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	420 via seeding
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	421 --recoverhits recover hash-collision seed hits
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	422 (default is not to recover seed hits)
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	423 --step=<length> set step length (default is 1)
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	424 --maxwordcount=<limit> words occurring more often than <limit> in the target
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	425 are not eligible for seeds
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	426 --strand=both search both strands
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	427 --strand=plus search + strand only (matching strand of query spec)
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	428 --strand=minus search - strand only (opposite strand of query spec)
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	429 (by default both strands are searched)
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	430 --ambiguousn treat N as an ambiguous nucleotide
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	431 (by default N is treated as a sequence splicing character)
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	432 --[no]gfextend perform gap-free extension of seed hits to HSPs
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	433 (by default no extension is performed)
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	434 --[no]chain perform chaining
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	435 --chain=<diag,anti> perform chaining with given penalties for diagonal and
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	436 anti-diagonal
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	437 (by default no chaining is performed)
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	438 --[no]gapped perform gapped alignment (instead of gap-free)
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	439 (by default gapped alignment is performed)
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	440 --score[s]=<file> read substitution scores from a file
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	441 (default is HOXD70)
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	442 --unitscore[s] scores are +1/-1 for match/mismatch
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	443 --gap=<[open,]extend> set gap open and extend penalties (default is 400,30)
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	444 --xdrop=<score> set x-drop threshold (default is 10*sub[A][A])
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	445 --ydrop=<score> set y-drop threshold (default is open+300extend)
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	446 --infer[=<control>] infer scores from the sequences, then use them
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	447 --inferonly[=<control>] infer scores, but don't use them (requires --infscores)
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	448 all inference options are read from the control file
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	449 --infscores[=<file>] write inferred scores to a file
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	450 --hspthresh=<score> set threshold for high scoring pairs (default is 3000)
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	451 ungapped extensions scoring lower are discarded
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	452 <score> can also be a percentage or base count
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	453 --entropy adjust for entropy when qualifying HSPs in the x-drop extension
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	454 method
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	455 --noentropy don't adjust for entropy when qualifying HSPs
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	456 --exact=<length> set threshold for exact matches
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	457 if specified, exact matches are found rather than high
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	458 scoring pairs (replaces --hspthresh)
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	459 --inner=<score> set threshold for HSPs during interpolation
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	460 (default is no interpolation)
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	461 --gappedthresh=<score> set threshold for gapped alignments
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	462 gapped extensions scoring lower are discarded
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	463 <score> can also be a percentage or base count
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	464 (default is to use same value as --hspthresh)
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	465 --ball=<score> set minimum score required of words 'in' a quantum ball
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	466 --[no]entropy involve entropy in filtering high scoring pairs
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	467 (default is "entropy")
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	468 --[no]mirror report/use mirror image of all gap-free alignments
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	469 (default is "mirror" for self-alignments only)
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	470 --traceback=<bytes> space for trace-back information
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	471 (default is 80.0M)
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	472 --masking=<count> mask any position in target hit this many times
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	473 zero indicates no masking
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	474 (default is no masking)
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	475 --targetcapsule=<capsule_file> the target seed word position table and seed
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	476 (as well as the target sequence)are read from specified file
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	477 --segments=<segment_file> read segments from a file, instead of discovering
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	478 them via seeding. Replaces other seeding or gap-free extension
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	479 options
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	480 --[no]census[=<file>] count/report how many times each target base aligns
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	481 (default is to not report census)
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	482 --identity=<min>[..<max>] filter alignments by percent identity
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	483 0<=min<=max<=100; blocks (or HSPs) outside min..max
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	484 are discarded
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	485 (default is no identity filtering)
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	486 --coverage=<min>[..<max>] filter alignments by percentage pf query covered
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	487 0<=min<=max<=100; blocks (or HSPs) outside min..max
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	488 are discarded
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	489 (default is no query coverage filtering)
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	490 --notrivial do not output trivial self-alignment block if the target and query
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	491 sequences are identical. Using --self enables this option automatically
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	492 --output=<output_file> write the alignments to the specified file name instead of stdout
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	493 --code=<file> give quantum code for query sequence (only for display)
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	494 --format=<type> specify output format; one of lav, axt, maf, maf+, maf-, text,
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	495 lav+text, cigar, text, rdplot, general, or general:<fields>
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	496 (by default output is LAV)
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	497 --rdotplot=<file> create an additional output file suitable for plotting the alignments
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	498 with the R statistical package.
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	499 --markend Just before normal completion, write "# lastz end-of-file" to output file
3c13c9c09ad9 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: diff changeset	500 --census[=<output_file>] count and report how many times each target base aligns, up

1

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1 <tool id="lastz_wrapper_2" name="Lastz" version="1.2.2">

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2 <requirements>

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3 <requirement type="package" version="1.02.00">lastz</requirement>

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4 </requirements>

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5 <description> map short reads against reference sequence</description>

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6 <command interpreter="python">lastz_wrapper.py

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7 #if $seq_name.how_to_name=="yes":

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8 --ref_name="${seq_name.ref_name}"

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9 #end if

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10 --ref_source="${source.ref_source}"

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11 --source_select="${params.source_select}"

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12 --out_format="${out_format}"

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13 --input2="${input2}"

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14 #if $source.ref_source=="history":

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15 --input1="${source.input1}"

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16 --ref_sequences="${input1.metadata.sequences}"

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17 #else:

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18 --input1="${source.input1_2bit.fields.path}"

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19 --ref_sequences="None"

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20 #end if

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21 #if $params.source_select=="pre_set":

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22 --pre_set_options="${params.pre_set_options}"

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23 #else:

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24 --strand="${params.strand}"

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25 --seed="${params.seed}"

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26 --gfextend="${params.gfextend}"

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27 --chain="${params.chain}"

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28 --transition="${params.transition}"

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29 --O="${params.O}"

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30 --E="${params.E}"

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31 --X="${params.X}"

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32 --Y="${params.Y}"

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33 --K="${params.K}"

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34 --L="${params.L}"

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35 --entropy="${params.entropy}"

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36 #end if

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37 --identity_min="${min_ident}"

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38 --identity_max="${max_ident}"

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39 --coverage="${min_cvrg}"

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40 --output="${output1}"

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41 --unmask="${unmask}"

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42 --lastzSeqsFileDir="${GALAXY_DATA_INDEX_DIR}"

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43 </command>

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44 <inputs>

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45 <param name="input2" format="fasta" type="data" label="Align sequencing reads in" />

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46 <conditional name="source">

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47 <param name="ref_source" type="select" label="Against reference sequences that are">

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48 <option value="cached">locally cached</option>

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49 <option value="history">in your history</option>

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50 </param>

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51 <when value="cached">

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52 <param name="input1_2bit" type="select" label="Using reference genome" help="If your genome of interest is not listed, contact the Galaxy team">

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53 <options from_data_table="lastz_seqs" />

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54 </param>

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55 </when>

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56 <when value="history">

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57 <param name="input1" type="data" format="fasta" label="Select a reference dataset" />

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58 </when>

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59 </conditional>

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60 <param name="out_format" type="select" label="Output format">

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61 <option value="sam">SAM</option>

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62 <option value="diffs">Polymorphisms</option>

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63 <option value="tabular">Tabular</option>

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64 </param>

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65 <conditional name="params">

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66 <param name="source_select" type="select" label="Lastz settings to use" help="For most mapping needs use Commonly used settings. If you want full control use Full List">

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67 <option value="pre_set">Commonly used</option>

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68 <option value="full">Full Parameter List</option>

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69 </param>

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70 <when value="pre_set">

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71 <param name="pre_set_options" type="select" label="Select mapping mode">

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72 <option value="yasra98">Roche-454 98% identity</option>

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73 <option value="yasra95">Roche-454 95% identity</option>

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74 <option value="yasra90">Roche-454 90% identity</option>

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75 <option value="yasra85">Roche-454 85% identity</option>

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76 <option value="yasra75">Roche-454 75% identity</option>

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77 <option value="yasra95short">Illumina 95% identity</option>

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78 <option value="yasra85short">Illumina 85% identity</option>

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79 </param>

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80 </when>

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81 <when value="full">

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82 <param name="strand" type="select" label="Which strand to search?">

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83 <option value="both">Both</option>

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84 <option value="plus">Search forward strand only (the one in the reference)</option>

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85 <option value="minus">Search the reverse complement strand only (opposite of the reference)</option>

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86 </param>

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87 <param name="seed" type="select" label="Select seeding settings" help="allows you set word size and number of mismatches">

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88 <option value="12of19">Seed hits require a 19 bp word with matches in 12 specific positions</option>

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89 <option value="14of22">Seed hits require a 22 bp word with matches in 14 specific positions</option>

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90 </param>

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91 <param name="transition" type="select" label="Select transition settings" help="affects the number of allowed transition substitutions">

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92 <option value="transition">Allow one transition in each seed hit</option>

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93 <option value="transition=2">Allow two transitions in a seed hit </option>

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94 <option value="notransition">Don't allow any transitions in seed hits</option>

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95 </param>

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96 <param name="gfextend" type="select" label="Perform gap-free extension of seed hits to HSPs (high scoring segment pairs)?">

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97 <option value="nogfextend">No</option>

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98 <option value="gfextend">Yes</option>

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99 </param>

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100 <param name="chain" type="select" label="Perform chaining of HSPs?">

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101 <option value="nochain">No</option>

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102 <option value="chain">Yes</option>

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103 </param>

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104 <param name="O" type="integer" value="400" label="Gap opening penalty"/>

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105 <param name="E" type="integer" value="30" label="Gap extension penalty"/>

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106 <param name="X" type="integer" value="910" label="X-drop threshold"/>

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107 <param name="Y" type="integer" value="9370" label="Y-drop threshold"/>

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108 <param name="K" type="integer" value="3000" label="Set the threshold for HSPs (ungapped extensions scoring lower are discarded)"/>

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109 <param name="L" type="integer" value="3000" label="Set the threshold for gapped alignments (gapped extensions scoring lower are discarded)"/>

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110 <param name="entropy" type="select" label="Involve entropy when filtering HSPs?">

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111 <option value="noentropy">No</option>

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112 <option value="entropy">Yes</option>

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113 </param>

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114 </when>

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115 </conditional>

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116 <conditional name="seq_name">

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117 <param name="how_to_name" type="select" label="Do you want to modify the reference name?">

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118 <option value="no">No</option>

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119 <option value="yes">Yes</option>

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120 </param>

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121 <when value="yes">

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122 <param name="ref_name" type="text" value="Type sequence name here" label="Enter name for the Reference sequence"/>

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123 </when>

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124 <when value="no" />

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125 </conditional>

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126 <param name="min_ident" type="integer" value="0" label="Do not report matches below this identity (%)"/>

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127 <param name="max_ident" type="integer" value="100" label="Do not report matches above this identity (%)"/>

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128 <param name="min_cvrg" type="integer" value="0" label="Do not report matches that cover less than this percentage of each read"/>

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129 <param name="unmask" type="select" label="Convert lowercase bases to uppercase">

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130 <option value="yes">Yes</option>

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131 <option value="no">No</option>

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132 </param>

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133 </inputs>

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134 <outputs>

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135 <data format="tabular" name="output1" label="${tool.name} on ${on_string}: mapped reads">

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136 <change_format>

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137 <when input="out_format" value="sam" format="sam" />

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138 </change_format>

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139 </data>

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140 </outputs>

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141 <tests>

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142 <test>

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143 <!--

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144 Lastz command:

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145 lastz phiX.2bit/phiX174[nickname=Ref] test-data/b1.fasta +nogfextend +nochain +gapped +strand=both +seed=12of19 +transition O=400 E=30 X=910 Y=9370 K=3000 L=3000 +noentropy +ambiguousn +nolaj +identity=0..100 +coverage=0 +format=sam- > lastz_wrapper_out2.sam

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146 You need to point to phiX.2bit somewhere on your system. b1.fasta is located in galaxy's test-data. You will have to replace all the pluses before the

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147 commands with 2 dashes, as double-dash can't appear in an XML comment.

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148 -->

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149 <param name="input2" value="b1.fasta" ftype="fasta" />

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150 <param name="ref_source" value="cached" />

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151 <param name="input1_2bit" value="phiX174" />

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152 <param name="out_format" value="sam" />

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153 <param name="source_select" value="full" />

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154 <param name="strand" value="both" />

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155 <param name="seed" value="12of19" />

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156 <param name="transition" value="transition" />

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157 <param name="gfextend" value="nogfextend" />

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158 <param name="chain" value="nochain" />

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159 <param name="O" value="400" />

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160 <param name="E" value="30" />

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161 <param name="X" value="910" />

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162 <param name="Y" value="9370" />

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163 <param name="K" value="3000" />

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164 <param name="L" value="3000" />

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165 <param name="entropy" value="noentropy" />

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166 <!--

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167 how_to_name is not the default. It is changed to modify

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168 input1_2bit by adding the ref_name as a nickname

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169 -->

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170 <param name="how_to_name" value="yes" />

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171 <param name="ref_name" value="Ref" />

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172 <param name="min_ident" value="0" />

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173 <param name="max_ident" value="100" />

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174 <param name="min_cvrg" value="0" />

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175 <param name="unmask" value="yes" />

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176 <output name="output1" file="lastz_wrapper_out2.sam" />

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177 </test>

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178 <test>

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179 <!--

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180 Lastz command:

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181 lastz test-data/phiX.fasta test-data/b1.fasta[fullnames] +yasra95short +ambiguousn +nolaj +identity=0..100 +coverage=0 +format=diffs > lastz_wrapper_out3.tabular

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182 phiX.fasta and b1.fasta are located in galaxy's test-data. You will have to replace all the pluses before the commands with 2 dashes,

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183 as double-dash can't appear in an XML comment.

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184 -->

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185 <param name="input2" value="b1.fasta" ftype="fasta" />

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186 <param name="ref_source" value="history" />

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187 <param name="input1" value="phiX.fasta" ftype="fasta" />

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188 <param name="out_format" value="diffs" />

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189 <param name="source_select" value="pre_set" />

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190 <param name="pre_set_options" value="yasra95short" />

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191 <param name="how_to_name" value="no" />

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192 <param name="min_ident" value="0" />

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193 <param name="max_ident" value="100" />

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194 <param name="min_cvrg" value="0" />

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195 <param name="unmask" value="yes" />

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196 <output name="output1" file="lastz_wrapper_out3.tabular" />

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197 </test>

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198 <test>

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199 <!--

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200 Lastz command: first you will need to split the file phiX_split.fasta into two files,

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201 phiX1.fasta and phiX2.fasta, each with 1 sequence (phiX1 and phiX2, respectively). Then:

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202 lastz phiX1.fasta test-data/b1.fasta *yasra95short *ambiguousn *nolaj *identity=0..100 *coverage=0 *format=general-:score,name1,strand1,size1,start1,zstart1,end1,length1,text1,name2,strand2,size2,start2,zstart2,end2,start2+,zstart2+,end2+,length2,text2,diff,cigar,identity,coverage,gaprate,diagonal,shingle > lastz_wrapper_out4.tabular

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203 lastz phiX2.fasta test-data/b1.fasta *yasra95short *ambiguousn *nolaj *identity=0..100 *coverage=0 *format=general-:score,name1,strand1,size1,start1,zstart1,end1,length1,text1,name2,strand2,size2,start2,zstart2,end2,start2+,zstart2+,end2+,length2,text2,diff,cigar,identity,coverage,gaprate,diagonal,shingle >> lastz_wrapper_out4.tabular

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204 You need to point to phiX1.fasta and phiX2.fasta somewhere on your system.

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205 phiX_split.fasta and b1.fasta are located in galaxy's test-data

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206 You will have to replace all the asterisks before the commands with 2 dashes,

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207 as double-dash can't appear in an XML comment

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208

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209 NOTE: since the input file include more than 1 sequence, the output must be sorted in

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210 order for functional test to pass. This is done using the sort="True" attribute on the output.

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211 -->

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212 <param name="input2" value="b1.fasta" ftype="fasta" />

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213 <param name="ref_source" value="history" />

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214 <param name="input1" value="phiX_split.fasta" ftype="fasta" />

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215 <param name="out_format" value="tabular" />

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216 <param name="source_select" value="pre_set" />

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217 <param name="pre_set_options" value="yasra95short" />

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218 <param name="how_to_name" value="no" />

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219 <param name="min_ident" value="0" />

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220 <param name="max_ident" value="100" />

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221 <param name="min_cvrg" value="0" />

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222 <param name="unmask" value="yes" />

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223 <output name="output1" file="lastz_wrapper_out4.tabular" sort="True" />

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224 </test>

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225 </tests>

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226 <help>

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227

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228 **What it does**

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229

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230 **LASTZ** is a high performance pairwise sequence aligner derived from BLASTZ. It is written by Bob Harris in Webb Miller's laboratory at Penn State University. Special scoring sets were derived to improve runtime performance and quality. This Galaxy version of LASTZ is geared towards aligning short (Illumina/Solexa, AB/SOLiD) and medium (Roche/454) reads against a reference sequence. There is excellent, extensive documentation on LASTZ available here_.

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231

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232 .. _here: http://www.bx.psu.edu/miller_lab/dist/README.lastz-1.02.00/README.lastz-1.02.00.html

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233

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234 ------

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235

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236 **Input formats**

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237

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238 LASTZ accepts reference and reads in FASTA format. However, because Galaxy supports implicit format conversion the tool will recognize fastq and other method specific formats.

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239

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240 ------

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241

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242 **Outputs**

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243

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244 LASTZ generates one output. Depending on the choice you make in the *Select output format* drop-down, LASTZ will produce a SAM file showing sequence alignments, a list of differences between the reads and reference (Polymorphisms), or a general table with one line per alignment block (Tabular). Examples of these outputs are shown below.

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245

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246 **SAM output**

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247

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248 SAM has 12 columns::

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249

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250 1 2 3 4 5 6 7 8 9 10 11 12

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251 ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------

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252 HWI-EAS91_1_30788AAXX:1:2:1670:915 99 chr9 58119878 60 36M = 58120234 392 GACCCCTACCCCACCGTGCTCTGGATCTCAGTGTTT IIIIIIIIIIIIIIIIEIIIIIII7IIIIIIIIIII XT:A:U NM:i:0 SM:i:37 AM:i:37 X0:i:1 X1:i:0 XM:i:0 XO:i:0 XG:i:0 MD:Z:36

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253 HWI-EAS91_1_30788AAXX:1:2:1670:915 147 chr9 58120234 60 36M = 58119878 -392 ATGAGTCGAATTCTATTTTCCAAACTGTTAACAAAA IFIIDI;IIICIIIIIIIIIIIIIIIIIIIIIIIII XT:A:U NM:i:0 SM:i:37 AM:i:37 X0:i:1 X1:i:0 XM:i:0 XO:i:0 XG:i:0 MD:Z:36

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254

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255

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256 where::

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257

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258 Column Description

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259 --------- ---------------------------------------------------------------------

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260 1. QNAME Query (pair) NAME

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261 2. FLAG bitwise FLAG

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262 3. RNAME Reference sequence NAME

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263 4. POS 1-based leftmost POSition/coordinate of clipped sequence

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264 5. MAPQ MAPping Quality (Phred-scaled)

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265 6. CIGAR extended CIGAR string

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266 7. MRNM Mate Reference sequence NaMe ('=' if same as RNAME)

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267 8. MPOS 1-based Mate POSition

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268 9. ISIZE Inferred insert SIZE

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269 10. SEQ query SEQuence on the same strand as the reference

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270 11. QUAL query QUALity (ASCII-33 gives the Phred base quality)

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271 12. OPT variable OPTional fields in the format TAG:VTYPE:VALUE, tab-separated

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272

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273 The flags are as follows::

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274

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275 Flag Description

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276 ------ -------------------------------------

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277 0x0001 the read is paired in sequencing

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278 0x0002 the read is mapped in a proper pair

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279 0x0004 the query sequence itself is unmapped

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280 0x0008 the mate is unmapped

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281 0x0010 strand of the query (1 for reverse)

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282 0x0020 strand of the mate

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283 0x0040 the read is the first read in a pair

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284 0x0080 the read is the second read in a pair

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285 0x0100 the alignment is not primary

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286

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287 **Polymorphism (SNP or differences) output**

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288

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289 Polymorphism output contains 14 columns::

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290

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291 1 2 3 4 5 6 7 8 9 10 11 12 13 14

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292 --------------------------------------------------------------------------------------------------------------------------------------------------------------

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293 chrM 2490 2491 + 5386 HWI-EAS91_1_306UPAAXX:6:1:486:822 10 11 - 36 C A ACCTGTTTTACAGACACCTAAAGCTACATCGTCAAC ACCTGTTTTAAAGACACCTAAAGCTACATCGTCAAC

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294 chrM 2173 2174 + 5386 HWI-EAS91_1_306UPAAXX:6:1:259:1389 26 27 + 36 G T GCGTACTTATTCGCCACCATGATTATGACCAGTGTT GCGTACTTATTCGCCACCATGATTATTACCAGTGTT

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295

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296 where::

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297

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298 1. (chrM) - Reference sequence id

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299 2. (2490) - Start position of the difference in the reference

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300 3. (2491) - End position of the difference in the reference

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301 4. (+) - Strand of the reference (always plus)

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302 5. (5386) - Length of the reference sequence

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303 6. (HWI...) - read id

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304 7. (10) - Start position of the difference in the read

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305 8. (11) - End position of the difference in the read

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306 9. (+) - Strand of the read

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307 10. (36) - Length of the read

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308 11. (C) - Nucleotide in the reference

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309 12. (A) - Nucleotide in the read

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310 13. (ACC...) - Reference side os the alignment

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311 14. (ACC...) - Read side of the alignment

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312

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313 **Tabular output**

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314

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315 Tabular output is a tab-separated format with 30 columns::

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316

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317 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30

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318 -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------

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319 14 PHIX174 + 5386 4648 4647 4661 14 ATTTTCGTGATATT EYKX4VC01BV8HS + 204 154 153 167 154 153 167 14 ATTTTCGTGATATT .............. 14M 14/14 100.0% 14/204 6.9% 0/14 0.0% 4494 NA

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320 16 PHIX174 + 5386 3363 3362 3378 16 GACGCCGGATTTGAGA EYKX4VC01AWJ88 - 259 36 35 51 209 208 224 16 GACGCCGGATTTGAGA ................ 16M 16/16 100.0% 16/259 6.2% 0/16 0.0% 3327 NA

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321

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322 The following columns are present::

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323

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324 Field Meaning

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325 ---------------- -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------

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326 1. score Score of the alignment block. The scale and meaning of this number will vary, depending on the final stage performed and other command-line options.

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327 2. name1 Name of the target sequence.

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328 3. strand1 Target sequence strand, either "+" or "−".

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329 4. size1 Size of the entire target sequence.

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330 5. start1 Starting position of the alignment block in the target, origin-one.

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331 6. zstart1 Starting position of the alignment block in the target, origin-zero.

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332 7. end1 Ending position of the alignment block in the target, expressed either as origin-one closed or origin-zero half-open (the ending value is the same in both systems).

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333 8. length1 Length of the alignment block in the target (excluding gaps).

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334 9. text1 Aligned characters in the target, including gap characters.

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335 10. name2 Name of the query sequence.

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336 11. strand2 Query sequence strand, either "+" or "−".

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337 12. size2 Size of the entire query sequence.

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338 13. start2 Starting position of the alignment block in the query, origin-one.

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339 14. zstart2 Starting position of the alignment block in the query, origin-zero.

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340 15. end2 Ending position of the alignment block in the query, expressed either as origin-one closed or origin-zero half-open (the ending value is the same in both systems).

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341 16. start2+ Starting position of the alignment block in the query, counting along the query sequence's positive strand (regardless of which query strand was aligned), origin-one. Note that if strand2 is "−", then this is the other end of the block from start2.

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342 17. zstart2+ Starting position of the alignment block in the query, counting along the query sequence's positive strand (regardless of which query strand was aligned), origin-zero. Note that if strand2 is "−", then this is the other end of the block from zstart2.

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343 18. end2+ Ending position of the alignment block in the query, counting along the query sequence's positive strand (regardless of which query strand was aligned), expressed either as origin-one closed or origin-zero half-open (the ending value is the same in both systems). Note that if strand2 is "−", then this is the other end of the block from end2.

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344 19. length2 Length of the alignment block in the query (excluding gaps).

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345 20. text2 Aligned characters in the query, including gap characters.

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346 21. diff Differences between what would be written for text1 and text2. Matches are written as . (period), transitions as : (colon), transversions as X, and gaps as - (hyphen).

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347 22. cigar A CIGAR-like representation of the alignment's path through the Dynamic Programming matrix. This is the short representation, without spaces, described in the Ensembl CIGAR specification.

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348 23./24. identity Fraction of aligned bases in the block that are matches (see Identity). This is written as two fields. The first field is a fraction, written as <n>/<d>. The second field contains the same value, computed as a percentage.

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349 25./26. coverage Fraction of the entire input sequence (target or query, whichever is shorter) that is covered by the alignment block (see Coverage). This is written as two fields. The first field is a fraction, written as <n>/<d>. The second field contains the same value, computed as a percentage.

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350 27./28. gaprate Rate of gaps (also called indels) in the alignment block. This is written as two fields. The first field is a fraction, written as <n>/<d>, with the numerator being the number of alignment columns containing gaps and the denominator being the number without gaps. The second field contains the same value, computed as a percentage.

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351 29. diagonal The diagonal of the start of the alignment block in the dynamic programming matrix, expressed as an identifying number start1-start2.

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352 30. shingle A measurement of the shingle overlap between the target and the query. This is intended for the case where both the target and query are relatively short, and their ends are expected to overlap.

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353

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354 -------

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355

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356 **LASTZ Settings**

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357

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358 There are two setting modes: (1) **Commonly used settings** and (2) **Full Parameter List**.

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359

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360 **Commonly used settings**

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361

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362 There are seven modes::

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363

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364 Illumina-Solexa/AB-SOLiD 95% identity

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365 Illumina-Solexa/AB-SOLiD 85% identity

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366 Roche-454 98% identity

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367 Roche-454 95% identity

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368 Roche-454 90% identity

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369 Roche-454 85% identity

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370 Roche-454 75% identity

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371

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372 When deciding which one to use, consider the following: a 36 bp read with two differences will be 34/36 = 94% identical to the reference.

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373

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374 **Full Parameter List**

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375

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376 This mode gives you fuller control over lastz. The description of these and other parameters is found at the end of this page. Note that not all parameters are included in this interface. If you would like to make additional options available through Galaxy, e-mail us at galaxy-bugs@bx.psu.edu.

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377

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378 ------

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379

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380 **Do you want to modify the reference name?**

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381

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382 This option allows you to set the name of the reference sequence manually. This is helpful when, for example, you would like to make the reference name compatible with the UCSC naming conventions to be able to display your lastz results as a custom track at the UCSC Genome Browser.

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383

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384 ------

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385

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386 **LASTZ parameter list**

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387

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388 This is an exhaustive list of LASTZ options. Once again, please note that not all options are included in this interface. If you would like to make additional options available through Galaxy, e-mail us at galaxy-bugs@bx.psu.edu::

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389

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390 target[[s..e]][-] spec/file containing target sequence (fasta or nib)

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391 [s..e] defines a subrange of the file

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392 - indicates reverse-complement

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393 (use --help=files for more details)

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394 query[[s..e]][-] spec/file containing query sequences (fasta or nib)

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395 if absent, queries come from stdin (unless they

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396 aren't needed, as for --self or --tableonly)

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397 (use --help=files for more details)

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398 --self the target sequence is also the query

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399 --quantum the query sequence contains quantum DNA

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400 --seed=match<length> use a word with no gaps instead of a seed pattern

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401 --seed=half<length> use space-free half-weight word instead of seed pattern

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402 --match=<reward>[,<penalty>] set the score values for a match (+<reward>)

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403 and mismatch (-<penalty>)

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404 --[no]trans[ition][=2] allow one or two transitions in a seed hit

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405 (by default a transition is allowed)

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406 --word=<bits> set max bits for word hash; use this to trade time for

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407 memory, eliminating thrashing for heavy seeds

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408 (default is 28 bits)

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409 --[no]filter=[<T>:]<M> filter half-weight seed hits, requiring at least M

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410 matches and allowing no more than T transversions

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411 (default is no filtering)

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412 --notwins require just one seed hit

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413 --twins=[<min>:]<maxgap> require two nearby seed hits on the same diagonal

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414 (default is twins aren't required)

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415 --notwins allow single, isolated seeds

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416 --[no]recoverseeds avoid losing seeds in hash collisions. Cannot be used with --twins

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417 --seedqueue=<entries> set number of entries in seed hit queue

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418 (default is 262144)

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419 --anchors=<file> read anchors from a file, instead of discovering anchors

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420 via seeding

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421 --recoverhits recover hash-collision seed hits

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422 (default is not to recover seed hits)

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423 --step=<length> set step length (default is 1)

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424 --maxwordcount=<limit> words occurring more often than <limit> in the target

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425 are not eligible for seeds

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426 --strand=both search both strands

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427 --strand=plus search + strand only (matching strand of query spec)

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428 --strand=minus search - strand only (opposite strand of query spec)

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429 (by default both strands are searched)

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430 --ambiguousn treat N as an ambiguous nucleotide

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431 (by default N is treated as a sequence splicing character)

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432 --[no]gfextend perform gap-free extension of seed hits to HSPs

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433 (by default no extension is performed)

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434 --[no]chain perform chaining

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435 --chain=<diag,anti> perform chaining with given penalties for diagonal and

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436 anti-diagonal

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437 (by default no chaining is performed)

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438 --[no]gapped perform gapped alignment (instead of gap-free)

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439 (by default gapped alignment is performed)

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440 --score[s]=<file> read substitution scores from a file

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441 (default is HOXD70)

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442 --unitscore[s] scores are +1/-1 for match/mismatch

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443 --gap=<[open,]extend> set gap open and extend penalties (default is 400,30)

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444 --xdrop=<score> set x-drop threshold (default is 10*sub[A][A])

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445 --ydrop=<score> set y-drop threshold (default is open+300extend)

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446 --infer[=<control>] infer scores from the sequences, then use them

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447 --inferonly[=<control>] infer scores, but don't use them (requires --infscores)

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448 all inference options are read from the control file

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449 --infscores[=<file>] write inferred scores to a file

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450 --hspthresh=<score> set threshold for high scoring pairs (default is 3000)

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451 ungapped extensions scoring lower are discarded

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452 <score> can also be a percentage or base count

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453 --entropy adjust for entropy when qualifying HSPs in the x-drop extension

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454 method

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455 --noentropy don't adjust for entropy when qualifying HSPs

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456 --exact=<length> set threshold for exact matches

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457 if specified, exact matches are found rather than high

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458 scoring pairs (replaces --hspthresh)

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459 --inner=<score> set threshold for HSPs during interpolation

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460 (default is no interpolation)

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461 --gappedthresh=<score> set threshold for gapped alignments

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462 gapped extensions scoring lower are discarded

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463 <score> can also be a percentage or base count

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464 (default is to use same value as --hspthresh)

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465 --ball=<score> set minimum score required of words 'in' a quantum ball

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466 --[no]entropy involve entropy in filtering high scoring pairs

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467 (default is "entropy")

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468 --[no]mirror report/use mirror image of all gap-free alignments

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469 (default is "mirror" for self-alignments only)

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470 --traceback=<bytes> space for trace-back information

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471 (default is 80.0M)

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472 --masking=<count> mask any position in target hit this many times

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473 zero indicates no masking

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474 (default is no masking)

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475 --targetcapsule=<capsule_file> the target seed word position table and seed

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476 (as well as the target sequence)are read from specified file

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477 --segments=<segment_file> read segments from a file, instead of discovering

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478 them via seeding. Replaces other seeding or gap-free extension

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479 options

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480 --[no]census[=<file>] count/report how many times each target base aligns

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481 (default is to not report census)

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482 --identity=<min>[..<max>] filter alignments by percent identity

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483 0<=min<=max<=100; blocks (or HSPs) outside min..max

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484 are discarded

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485 (default is no identity filtering)

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486 --coverage=<min>[..<max>] filter alignments by percentage pf query covered

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487 0<=min<=max<=100; blocks (or HSPs) outside min..max

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488 are discarded

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489 (default is no query coverage filtering)

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490 --notrivial do not output trivial self-alignment block if the target and query

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491 sequences are identical. Using --self enables this option automatically

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492 --output=<output_file> write the alignments to the specified file name instead of stdout

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493 --code=<file> give quantum code for query sequence (only for display)

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494 --format=<type> specify output format; one of lav, axt, maf, maf+, maf-, text,

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495 lav+text, cigar, text, rdplot, general, or general:<fields>

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496 (by default output is LAV)

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497 --rdotplot=<file> create an additional output file suitable for plotting the alignments

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498 with the R statistical package.

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499 --markend Just before normal completion, write "# lastz end-of-file" to output file

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500 --census[=<output_file>] count and report how many times each target base aligns, up

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501 to 255. Ns are included in the count

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502 --census16[=<output_file>] count and report how many times each target base aligns, up

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503 up 65 thousand

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504 --census32[=<output_file>] count and report how many times each target bas aligns, up

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505 to 4 billion

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506 --writecapsule=<capsule_file> just write out a target capsule file and quit; don't

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507 search for seeds or perform subsequent stages

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508 --verbosity=<level> set info level (0 is minimum, 10 is everything)

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509 (default is 0)

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510 --[no]runtime report runtime in the output file

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511 (default is to not report runtime)

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512 --tableonly[=count] just produce the target position table, don't

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513 search for seeds

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514 --[no]stats[=<file>] show search statistics (or don't)

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515 (not available in this build)

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516 --version report the program version and quit

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517 --help list all options

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518 --help=files list information about file specifiers

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519 --help=short[cuts] list blastz-compatible shortcuts

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520 --help=yasra list yasra-specific shortcuts

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521

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522 </help>

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523 </tool>

Mercurial > repos > devteam > lastz

annotate lastz_wrapper.xml @ 1:3c13c9c09ad9 draft