ucsc_blat: blat.xml annotate

annotate blat.xml @ 9:c4f0808a68ad draft

planemo upload commit e948e26e96631447718ac125a92dd5fef0cecdcf

author	yating-l
date	Thu, 02 Feb 2017 12:55:12 -0500
parents	5e4e16939d3b
children	3511cb739854

rev	line source
5 70d7377d5e24 planemo upload commit 7856c637db5bd4ea0b8b4db63e242618421a9cc6-dirty yating-l parents: 0 diff changeset	1 <?xml version="1.0"?>
0 9e56efe1c371 planemo upload yating-l parents: diff changeset	2 <tool id="ucsc_blat" name="UCSC BLAT Alignment Tool" version="1.0">
5 70d7377d5e24 planemo upload commit 7856c637db5bd4ea0b8b4db63e242618421a9cc6-dirty yating-l parents: 0 diff changeset	3 <description>Standalone blat sequence search command line tool</description>
0 9e56efe1c371 planemo upload yating-l parents: diff changeset	4 <requirements>
9e56efe1c371 planemo upload yating-l parents: diff changeset	5 <requirement type="package" version="1.0">ucsc_tools_340_for_BLAT</requirement>
9e56efe1c371 planemo upload yating-l parents: diff changeset	6 </requirements>
9e56efe1c371 planemo upload yating-l parents: diff changeset	7 <command detect_errors="exit_code"><![CDATA[
9e56efe1c371 planemo upload yating-l parents: diff changeset	8 blat
9e56efe1c371 planemo upload yating-l parents: diff changeset	9 #if $noHead
9e56efe1c371 planemo upload yating-l parents: diff changeset	10 -noHead
9e56efe1c371 planemo upload yating-l parents: diff changeset	11 #end if
9e56efe1c371 planemo upload yating-l parents: diff changeset	12 -q=$query_type
9e56efe1c371 planemo upload yating-l parents: diff changeset	13 -t=$database_type
9e56efe1c371 planemo upload yating-l parents: diff changeset	14 -mask=$mask
9e56efe1c371 planemo upload yating-l parents: diff changeset	15 '${database}'
9e56efe1c371 planemo upload yating-l parents: diff changeset	16 '${query}'
5 70d7377d5e24 planemo upload commit 7856c637db5bd4ea0b8b4db63e242618421a9cc6-dirty yating-l parents: 0 diff changeset	17 output
70d7377d5e24 planemo upload commit 7856c637db5bd4ea0b8b4db63e242618421a9cc6-dirty yating-l parents: 0 diff changeset	18 && sort -k 10,10 -k 12,12n output > '${output_sorted}'
70d7377d5e24 planemo upload commit 7856c637db5bd4ea0b8b4db63e242618421a9cc6-dirty yating-l parents: 0 diff changeset	19 #if $filter_param.filter =="yes"
9 c4f0808a68ad planemo upload commit e948e26e96631447718ac125a92dd5fef0cecdcf yating-l parents: 8 diff changeset	20 && pslReps -minAli=0.25 '${output_sorted}' output.reps.psl output.reps.psr
c4f0808a68ad planemo upload commit e948e26e96631447718ac125a92dd5fef0cecdcf yating-l parents: 8 diff changeset	21 && faPolyASizes '${query}' query.polyA
5 70d7377d5e24 planemo upload commit 7856c637db5bd4ea0b8b4db63e242618421a9cc6-dirty yating-l parents: 0 diff changeset	22 && pslCDnaFilter
70d7377d5e24 planemo upload commit 7856c637db5bd4ea0b8b4db63e242618421a9cc6-dirty yating-l parents: 0 diff changeset	23 #if $filter_param.assembly_type == "native"
70d7377d5e24 planemo upload commit 7856c637db5bd4ea0b8b4db63e242618421a9cc6-dirty yating-l parents: 0 diff changeset	24 -localNearBest=0.001
70d7377d5e24 planemo upload commit 7856c637db5bd4ea0b8b4db63e242618421a9cc6-dirty yating-l parents: 0 diff changeset	25 #if $filter_param.assembly_category == "finished"
70d7377d5e24 planemo upload commit 7856c637db5bd4ea0b8b4db63e242618421a9cc6-dirty yating-l parents: 0 diff changeset	26 -minId=0.95
70d7377d5e24 planemo upload commit 7856c637db5bd4ea0b8b4db63e242618421a9cc6-dirty yating-l parents: 0 diff changeset	27 -minCover=0.25
70d7377d5e24 planemo upload commit 7856c637db5bd4ea0b8b4db63e242618421a9cc6-dirty yating-l parents: 0 diff changeset	28 #else if $filter_param.assembly_category == "well-ordered"
70d7377d5e24 planemo upload commit 7856c637db5bd4ea0b8b4db63e242618421a9cc6-dirty yating-l parents: 0 diff changeset	29 -minId=0.95
70d7377d5e24 planemo upload commit 7856c637db5bd4ea0b8b4db63e242618421a9cc6-dirty yating-l parents: 0 diff changeset	30 -minCover=0.15
70d7377d5e24 planemo upload commit 7856c637db5bd4ea0b8b4db63e242618421a9cc6-dirty yating-l parents: 0 diff changeset	31 #else
70d7377d5e24 planemo upload commit 7856c637db5bd4ea0b8b4db63e242618421a9cc6-dirty yating-l parents: 0 diff changeset	32 -minId=0.94
70d7377d5e24 planemo upload commit 7856c637db5bd4ea0b8b4db63e242618421a9cc6-dirty yating-l parents: 0 diff changeset	33 -minAlnSize=80
70d7377d5e24 planemo upload commit 7856c637db5bd4ea0b8b4db63e242618421a9cc6-dirty yating-l parents: 0 diff changeset	34 #end if
70d7377d5e24 planemo upload commit 7856c637db5bd4ea0b8b4db63e242618421a9cc6-dirty yating-l parents: 0 diff changeset	35 #else
70d7377d5e24 planemo upload commit 7856c637db5bd4ea0b8b4db63e242618421a9cc6-dirty yating-l parents: 0 diff changeset	36 -localNearBest=0.010
70d7377d5e24 planemo upload commit 7856c637db5bd4ea0b8b4db63e242618421a9cc6-dirty yating-l parents: 0 diff changeset	37 #if $filter_param.assembly_category == "finished"
70d7377d5e24 planemo upload commit 7856c637db5bd4ea0b8b4db63e242618421a9cc6-dirty yating-l parents: 0 diff changeset	38 -minId=0.35
70d7377d5e24 planemo upload commit 7856c637db5bd4ea0b8b4db63e242618421a9cc6-dirty yating-l parents: 0 diff changeset	39 -minCover=0.25
70d7377d5e24 planemo upload commit 7856c637db5bd4ea0b8b4db63e242618421a9cc6-dirty yating-l parents: 0 diff changeset	40 #else if $filter_param.assembly_category == "well-ordered"
70d7377d5e24 planemo upload commit 7856c637db5bd4ea0b8b4db63e242618421a9cc6-dirty yating-l parents: 0 diff changeset	41 -minId=0.35
70d7377d5e24 planemo upload commit 7856c637db5bd4ea0b8b4db63e242618421a9cc6-dirty yating-l parents: 0 diff changeset	42 -minCover=0.15
70d7377d5e24 planemo upload commit 7856c637db5bd4ea0b8b4db63e242618421a9cc6-dirty yating-l parents: 0 diff changeset	43 #else
70d7377d5e24 planemo upload commit 7856c637db5bd4ea0b8b4db63e242618421a9cc6-dirty yating-l parents: 0 diff changeset	44 -minId=0.33
70d7377d5e24 planemo upload commit 7856c637db5bd4ea0b8b4db63e242618421a9cc6-dirty yating-l parents: 0 diff changeset	45 -minAlnSize=80
70d7377d5e24 planemo upload commit 7856c637db5bd4ea0b8b4db63e242618421a9cc6-dirty yating-l parents: 0 diff changeset	46 #end if
70d7377d5e24 planemo upload commit 7856c637db5bd4ea0b8b4db63e242618421a9cc6-dirty yating-l parents: 0 diff changeset	47 #end if
70d7377d5e24 planemo upload commit 7856c637db5bd4ea0b8b4db63e242618421a9cc6-dirty yating-l parents: 0 diff changeset	48 -minQSize=20
70d7377d5e24 planemo upload commit 7856c637db5bd4ea0b8b4db63e242618421a9cc6-dirty yating-l parents: 0 diff changeset	49 -ignoreIntrons
70d7377d5e24 planemo upload commit 7856c637db5bd4ea0b8b4db63e242618421a9cc6-dirty yating-l parents: 0 diff changeset	50 -repsAsMatch
70d7377d5e24 planemo upload commit 7856c637db5bd4ea0b8b4db63e242618421a9cc6-dirty yating-l parents: 0 diff changeset	51 -ignoreNs
70d7377d5e24 planemo upload commit 7856c637db5bd4ea0b8b4db63e242618421a9cc6-dirty yating-l parents: 0 diff changeset	52 -bestOverlap
70d7377d5e24 planemo upload commit 7856c637db5bd4ea0b8b4db63e242618421a9cc6-dirty yating-l parents: 0 diff changeset	53 -polyASizes=query.polyA
70d7377d5e24 planemo upload commit 7856c637db5bd4ea0b8b4db63e242618421a9cc6-dirty yating-l parents: 0 diff changeset	54 output.reps.psl
70d7377d5e24 planemo upload commit 7856c637db5bd4ea0b8b4db63e242618421a9cc6-dirty yating-l parents: 0 diff changeset	55 '${output_filtered}'
70d7377d5e24 planemo upload commit 7856c637db5bd4ea0b8b4db63e242618421a9cc6-dirty yating-l parents: 0 diff changeset	56 #end if
0 9e56efe1c371 planemo upload yating-l parents: diff changeset	57 ]]></command>
9e56efe1c371 planemo upload yating-l parents: diff changeset	58 <inputs>
9e56efe1c371 planemo upload yating-l parents: diff changeset	59 <param type="data" name="database" format="fasta" />
9e56efe1c371 planemo upload yating-l parents: diff changeset	60 <param type="data" name="query" format="fasta" />
9e56efe1c371 planemo upload yating-l parents: diff changeset	61 <param type="select" name="database_type" format="text" multiple="false" label="database type" help="Choose your database type, the default is dna">
9e56efe1c371 planemo upload yating-l parents: diff changeset	62 <option value="dna">DNA sequence</option>
9e56efe1c371 planemo upload yating-l parents: diff changeset	63 <option value="prot">protein sequence</option>
9e56efe1c371 planemo upload yating-l parents: diff changeset	64 <option value="dnax">DNA sequence translated in six frames to protein</option>
9e56efe1c371 planemo upload yating-l parents: diff changeset	65 </param>
9e56efe1c371 planemo upload yating-l parents: diff changeset	66 <param type="select" name="query_type" format="text" multiple="false" label="query type" help="Choose your query type, the default is dna">
9e56efe1c371 planemo upload yating-l parents: diff changeset	67 <option value="dna">DNA sequence</option>
9e56efe1c371 planemo upload yating-l parents: diff changeset	68 <option value="rna">RNA sequence</option>
9e56efe1c371 planemo upload yating-l parents: diff changeset	69 <option value="prot">protein sequence</option>
9e56efe1c371 planemo upload yating-l parents: diff changeset	70 <option value="dnax">DNA sequence translated in six frames to protein</option>
9e56efe1c371 planemo upload yating-l parents: diff changeset	71 <option value="rnax">DNA sequence translated in three frames to protein</option>
9e56efe1c371 planemo upload yating-l parents: diff changeset	72 </param>
9e56efe1c371 planemo upload yating-l parents: diff changeset	73 <param name="noHead" type="boolean" value="false" label="Suppresses .psl header (so it's just a tab-separated file)." />
9e56efe1c371 planemo upload yating-l parents: diff changeset	74 <param name="mask" type="select" label="Mask out repeats" help="Alignments won't be started in masked region
9e56efe1c371 planemo upload yating-l parents: diff changeset	75 but may extend through it in nucleotide searches. Masked areas
9e56efe1c371 planemo upload yating-l parents: diff changeset	76 are ignored entirely in protein or translated searches.">
9e56efe1c371 planemo upload yating-l parents: diff changeset	77 <option value="lower">lower - mask out lower-cased sequence</option>
9e56efe1c371 planemo upload yating-l parents: diff changeset	78 <option value="upper">upper - mask out upper-cased sequence</option>
9e56efe1c371 planemo upload yating-l parents: diff changeset	79 <option value="out">out - mask according to database.out RepeatMasker .out file</option>
9e56efe1c371 planemo upload yating-l parents: diff changeset	80 <option value="file.out">file.out - mask database according to RepeatMasker file.out</option>
9e56efe1c371 planemo upload yating-l parents: diff changeset	81 </param>
5 70d7377d5e24 planemo upload commit 7856c637db5bd4ea0b8b4db63e242618421a9cc6-dirty yating-l parents: 0 diff changeset	82 <conditional name="filter_param">
70d7377d5e24 planemo upload commit 7856c637db5bd4ea0b8b4db63e242618421a9cc6-dirty yating-l parents: 0 diff changeset	83 <param name="filter" type="select" label="Filter BLAT results with pslCDnaFilter">
70d7377d5e24 planemo upload commit 7856c637db5bd4ea0b8b4db63e242618421a9cc6-dirty yating-l parents: 0 diff changeset	84 <option value="no" selected="true">No</option>
70d7377d5e24 planemo upload commit 7856c637db5bd4ea0b8b4db63e242618421a9cc6-dirty yating-l parents: 0 diff changeset	85 <option value="yes">Yes</option>
0 9e56efe1c371 planemo upload yating-l parents: diff changeset	86 </param>
6 6f06b6d68c0b planemo upload commit 7856c637db5bd4ea0b8b4db63e242618421a9cc6-dirty yating-l parents: 5 diff changeset	87 <when value="no"/>
5 70d7377d5e24 planemo upload commit 7856c637db5bd4ea0b8b4db63e242618421a9cc6-dirty yating-l parents: 0 diff changeset	88 <when value="yes">
70d7377d5e24 planemo upload commit 7856c637db5bd4ea0b8b4db63e242618421a9cc6-dirty yating-l parents: 0 diff changeset	89 <param name="assembly_type" type="select" label="Choose your type of cDNA sequence">
70d7377d5e24 planemo upload commit 7856c637db5bd4ea0b8b4db63e242618421a9cc6-dirty yating-l parents: 0 diff changeset	90 <option value="native">Same species</option>
70d7377d5e24 planemo upload commit 7856c637db5bd4ea0b8b4db63e242618421a9cc6-dirty yating-l parents: 0 diff changeset	91 <option value="xeno">Across species</option>
70d7377d5e24 planemo upload commit 7856c637db5bd4ea0b8b4db63e242618421a9cc6-dirty yating-l parents: 0 diff changeset	92 </param>
70d7377d5e24 planemo upload commit 7856c637db5bd4ea0b8b4db63e242618421a9cc6-dirty yating-l parents: 0 diff changeset	93 <param name="assembly_category" type="select" label="Choose your genome assembly category">
70d7377d5e24 planemo upload commit 7856c637db5bd4ea0b8b4db63e242618421a9cc6-dirty yating-l parents: 0 diff changeset	94 <option value="finished">finished assemblies (high quality)</option>
70d7377d5e24 planemo upload commit 7856c637db5bd4ea0b8b4db63e242618421a9cc6-dirty yating-l parents: 0 diff changeset	95 <option value="well-ordered">well-ordered assemblies (well ordered, whole genome shotgun)</option>
70d7377d5e24 planemo upload commit 7856c637db5bd4ea0b8b4db63e242618421a9cc6-dirty yating-l parents: 0 diff changeset	96 <option value="low-coverage">low-coverage assemblies (low coverage (< 4x"), lots of contigs, N50 scaffold size < 1mb) </option>
70d7377d5e24 planemo upload commit 7856c637db5bd4ea0b8b4db63e242618421a9cc6-dirty yating-l parents: 0 diff changeset	97 </param>
70d7377d5e24 planemo upload commit 7856c637db5bd4ea0b8b4db63e242618421a9cc6-dirty yating-l parents: 0 diff changeset	98 </when>
70d7377d5e24 planemo upload commit 7856c637db5bd4ea0b8b4db63e242618421a9cc6-dirty yating-l parents: 0 diff changeset	99 </conditional>
0 9e56efe1c371 planemo upload yating-l parents: diff changeset	100 </inputs>
9e56efe1c371 planemo upload yating-l parents: diff changeset	101 <outputs>
6 6f06b6d68c0b planemo upload commit 7856c637db5bd4ea0b8b4db63e242618421a9cc6-dirty yating-l parents: 5 diff changeset	102 <data format="psl" name="output_sorted" label="${tool.name} on ${on_string}"></data>
8 5e4e16939d3b planemo upload commit 7856c637db5bd4ea0b8b4db63e242618421a9cc6-dirty yating-l parents: 7 diff changeset	103 <data format="psl" name="output_filtered" label="${tool.name} on ${on_string}:filtered BLAT results">
5e4e16939d3b planemo upload commit 7856c637db5bd4ea0b8b4db63e242618421a9cc6-dirty yating-l parents: 7 diff changeset	104 <filter>filter_param['filter'] == "yes"</filter>
5e4e16939d3b planemo upload commit 7856c637db5bd4ea0b8b4db63e242618421a9cc6-dirty yating-l parents: 7 diff changeset	105 </data>
0 9e56efe1c371 planemo upload yating-l parents: diff changeset	106 </outputs>
9e56efe1c371 planemo upload yating-l parents: diff changeset	107 <tests>
9e56efe1c371 planemo upload yating-l parents: diff changeset	108 <test>
9 c4f0808a68ad planemo upload commit e948e26e96631447718ac125a92dd5fef0cecdcf yating-l parents: 8 diff changeset	109 <param name="database" value="amaVit1_Gallus/amaVit1.fa" />
c4f0808a68ad planemo upload commit e948e26e96631447718ac125a92dd5fef0cecdcf yating-l parents: 8 diff changeset	110 <param name="query" value="amaVit1_Gallus/Gallus_gallus_RefSeq.fa" />
0 9e56efe1c371 planemo upload yating-l parents: diff changeset	111 <param name="database_type" value="dnax" />
9e56efe1c371 planemo upload yating-l parents: diff changeset	112 <param name="query_type" value="rnax" />
9e56efe1c371 planemo upload yating-l parents: diff changeset	113 <param name="noHead" value="true" />
9e56efe1c371 planemo upload yating-l parents: diff changeset	114 <param name="mask" value="lower" />
5 70d7377d5e24 planemo upload commit 7856c637db5bd4ea0b8b4db63e242618421a9cc6-dirty yating-l parents: 0 diff changeset	115 <param name="filter" value="yes" />
70d7377d5e24 planemo upload commit 7856c637db5bd4ea0b8b4db63e242618421a9cc6-dirty yating-l parents: 0 diff changeset	116 <param name="assembly_type" value="xeno" />
70d7377d5e24 planemo upload commit 7856c637db5bd4ea0b8b4db63e242618421a9cc6-dirty yating-l parents: 0 diff changeset	117 <param name="assembly_category" value="well-ordered" />
9 c4f0808a68ad planemo upload commit e948e26e96631447718ac125a92dd5fef0cecdcf yating-l parents: 8 diff changeset	118 <output name="output_sorted" value="amaVit1_Gallus/amaVit1_Gallus_gallus.psl" />
c4f0808a68ad planemo upload commit e948e26e96631447718ac125a92dd5fef0cecdcf yating-l parents: 8 diff changeset	119 <output name="output_filtered" value="amaVit1_Gallus/amaVit1_Gallus_gallus_filtered.psl" />
0 9e56efe1c371 planemo upload yating-l parents: diff changeset	120 </test>
9 c4f0808a68ad planemo upload commit e948e26e96631447718ac125a92dd5fef0cecdcf yating-l parents: 8 diff changeset	121 <test>
c4f0808a68ad planemo upload commit e948e26e96631447718ac125a92dd5fef0cecdcf yating-l parents: 8 diff changeset	122 <param name="database" value="dbia3/dbia3.fa" />
c4f0808a68ad planemo upload commit e948e26e96631447718ac125a92dd5fef0cecdcf yating-l parents: 8 diff changeset	123 <param name="query" value="dbia3/dmel-all-translation-r6.11.fasta" />
c4f0808a68ad planemo upload commit e948e26e96631447718ac125a92dd5fef0cecdcf yating-l parents: 8 diff changeset	124 <param name="database_type" value="dnax" />
c4f0808a68ad planemo upload commit e948e26e96631447718ac125a92dd5fef0cecdcf yating-l parents: 8 diff changeset	125 <param name="query_type" value="prot" />
c4f0808a68ad planemo upload commit e948e26e96631447718ac125a92dd5fef0cecdcf yating-l parents: 8 diff changeset	126 <param name="noHead" value="true" />
c4f0808a68ad planemo upload commit e948e26e96631447718ac125a92dd5fef0cecdcf yating-l parents: 8 diff changeset	127 <param name="mask" value="lower" />
c4f0808a68ad planemo upload commit e948e26e96631447718ac125a92dd5fef0cecdcf yating-l parents: 8 diff changeset	128 <param name="filter" value="yes" />
c4f0808a68ad planemo upload commit e948e26e96631447718ac125a92dd5fef0cecdcf yating-l parents: 8 diff changeset	129 <param name="assembly_type" value="xeno" />
c4f0808a68ad planemo upload commit e948e26e96631447718ac125a92dd5fef0cecdcf yating-l parents: 8 diff changeset	130 <param name="assembly_category" value="well-ordered" />
c4f0808a68ad planemo upload commit e948e26e96631447718ac125a92dd5fef0cecdcf yating-l parents: 8 diff changeset	131 <output name="output_sorted" value="dbia3/dbia3.sorted.psl" />
c4f0808a68ad planemo upload commit e948e26e96631447718ac125a92dd5fef0cecdcf yating-l parents: 8 diff changeset	132 <output name="output_filtered" value="dbia3/dbia3_dmel_filtered.psl" />
c4f0808a68ad planemo upload commit e948e26e96631447718ac125a92dd5fef0cecdcf yating-l parents: 8 diff changeset	133 </test>
c4f0808a68ad planemo upload commit e948e26e96631447718ac125a92dd5fef0cecdcf yating-l parents: 8 diff changeset	134
5 70d7377d5e24 planemo upload commit 7856c637db5bd4ea0b8b4db63e242618421a9cc6-dirty yating-l parents: 0 diff changeset	135 </tests>
70d7377d5e24 planemo upload commit 7856c637db5bd4ea0b8b4db63e242618421a9cc6-dirty yating-l parents: 0 diff changeset	136 <help>
70d7377d5e24 planemo upload commit 7856c637db5bd4ea0b8b4db63e242618421a9cc6-dirty yating-l parents: 0 diff changeset	137 <![CDATA[
70d7377d5e24 planemo upload commit 7856c637db5bd4ea0b8b4db63e242618421a9cc6-dirty yating-l parents: 0 diff changeset	138 BLAT
70d7377d5e24 planemo upload commit 7856c637db5bd4ea0b8b4db63e242618421a9cc6-dirty yating-l parents: 0 diff changeset	139 ====
70d7377d5e24 planemo upload commit 7856c637db5bd4ea0b8b4db63e242618421a9cc6-dirty yating-l parents: 0 diff changeset	140 BLAT is a bioinformatics software a tool which performs rapid mRNA/DNA and cross-species protein alignments.
70d7377d5e24 planemo upload commit 7856c637db5bd4ea0b8b4db63e242618421a9cc6-dirty yating-l parents: 0 diff changeset	141
70d7377d5e24 planemo upload commit 7856c637db5bd4ea0b8b4db63e242618421a9cc6-dirty yating-l parents: 0 diff changeset	142 blat (version: v340)- Standalone blat sequence search command line tool.
7 bd3352c46beb planemo upload commit 7856c637db5bd4ea0b8b4db63e242618421a9cc6-dirty yating-l parents: 6 diff changeset	143 -------------------------------------------------------------------------
bd3352c46beb planemo upload commit 7856c637db5bd4ea0b8b4db63e242618421a9cc6-dirty yating-l parents: 6 diff changeset	144
5 70d7377d5e24 planemo upload commit 7856c637db5bd4ea0b8b4db63e242618421a9cc6-dirty yating-l parents: 0 diff changeset	145 usage:
70d7377d5e24 planemo upload commit 7856c637db5bd4ea0b8b4db63e242618421a9cc6-dirty yating-l parents: 0 diff changeset	146 ++++++
7 bd3352c46beb planemo upload commit 7856c637db5bd4ea0b8b4db63e242618421a9cc6-dirty yating-l parents: 6 diff changeset	147
bd3352c46beb planemo upload commit 7856c637db5bd4ea0b8b4db63e242618421a9cc6-dirty yating-l parents: 6 diff changeset	148 $ blat database query [-ooc=11.ooc] output.psl
bd3352c46beb planemo upload commit 7856c637db5bd4ea0b8b4db63e242618421a9cc6-dirty yating-l parents: 6 diff changeset	149
5 70d7377d5e24 planemo upload commit 7856c637db5bd4ea0b8b4db63e242618421a9cc6-dirty yating-l parents: 0 diff changeset	150 where:
70d7377d5e24 planemo upload commit 7856c637db5bd4ea0b8b4db63e242618421a9cc6-dirty yating-l parents: 0 diff changeset	151 database and query are each either a .fa, .nib or .2bit file,
7 bd3352c46beb planemo upload commit 7856c637db5bd4ea0b8b4db63e242618421a9cc6-dirty yating-l parents: 6 diff changeset	152 or a list of these files with one file name per line.
5 70d7377d5e24 planemo upload commit 7856c637db5bd4ea0b8b4db63e242618421a9cc6-dirty yating-l parents: 0 diff changeset	153 -ooc=11.ooc tells the program to load over-occurring 11-mers from
7 bd3352c46beb planemo upload commit 7856c637db5bd4ea0b8b4db63e242618421a9cc6-dirty yating-l parents: 6 diff changeset	154 an external file. This will increase the speed
bd3352c46beb planemo upload commit 7856c637db5bd4ea0b8b4db63e242618421a9cc6-dirty yating-l parents: 6 diff changeset	155 by a factor of 40 in many cases, but is not required.
bd3352c46beb planemo upload commit 7856c637db5bd4ea0b8b4db63e242618421a9cc6-dirty yating-l parents: 6 diff changeset	156 output.psl is the name of the output file.
bd3352c46beb planemo upload commit 7856c637db5bd4ea0b8b4db63e242618421a9cc6-dirty yating-l parents: 6 diff changeset	157
5 70d7377d5e24 planemo upload commit 7856c637db5bd4ea0b8b4db63e242618421a9cc6-dirty yating-l parents: 0 diff changeset	158 documentation:
70d7377d5e24 planemo upload commit 7856c637db5bd4ea0b8b4db63e242618421a9cc6-dirty yating-l parents: 0 diff changeset	159 ++++++++++++++
7 bd3352c46beb planemo upload commit 7856c637db5bd4ea0b8b4db63e242618421a9cc6-dirty yating-l parents: 6 diff changeset	160
bd3352c46beb planemo upload commit 7856c637db5bd4ea0b8b4db63e242618421a9cc6-dirty yating-l parents: 6 diff changeset	161 See Blat documentation (http://genome.ucsc.edu/goldenPath/help/blatSpec.html)
bd3352c46beb planemo upload commit 7856c637db5bd4ea0b8b4db63e242618421a9cc6-dirty yating-l parents: 6 diff changeset	162
5 70d7377d5e24 planemo upload commit 7856c637db5bd4ea0b8b4db63e242618421a9cc6-dirty yating-l parents: 0 diff changeset	163 Source code:
70d7377d5e24 planemo upload commit 7856c637db5bd4ea0b8b4db63e242618421a9cc6-dirty yating-l parents: 0 diff changeset	164 ++++++++++++
7 bd3352c46beb planemo upload commit 7856c637db5bd4ea0b8b4db63e242618421a9cc6-dirty yating-l parents: 6 diff changeset	165
5 70d7377d5e24 planemo upload commit 7856c637db5bd4ea0b8b4db63e242618421a9cc6-dirty yating-l parents: 0 diff changeset	166 http://hgdownload.cse.ucsc.edu/admin/exe/
7 bd3352c46beb planemo upload commit 7856c637db5bd4ea0b8b4db63e242618421a9cc6-dirty yating-l parents: 6 diff changeset	167
5 70d7377d5e24 planemo upload commit 7856c637db5bd4ea0b8b4db63e242618421a9cc6-dirty yating-l parents: 0 diff changeset	168 pslCDnaFilter (version: v340)
7 bd3352c46beb planemo upload commit 7856c637db5bd4ea0b8b4db63e242618421a9cc6-dirty yating-l parents: 6 diff changeset	169 -----------------------------
5 70d7377d5e24 planemo upload commit 7856c637db5bd4ea0b8b4db63e242618421a9cc6-dirty yating-l parents: 0 diff changeset	170 Filter cDNA alignments in psl format. Filtering criteria are comparative, selecting near best in genome alignments for each given cDNA and non-comparative, based only on the quality of an individual alignment.
7 bd3352c46beb planemo upload commit 7856c637db5bd4ea0b8b4db63e242618421a9cc6-dirty yating-l parents: 6 diff changeset	171
5 70d7377d5e24 planemo upload commit 7856c637db5bd4ea0b8b4db63e242618421a9cc6-dirty yating-l parents: 0 diff changeset	172 usage:
70d7377d5e24 planemo upload commit 7856c637db5bd4ea0b8b4db63e242618421a9cc6-dirty yating-l parents: 0 diff changeset	173 ++++++
7 bd3352c46beb planemo upload commit 7856c637db5bd4ea0b8b4db63e242618421a9cc6-dirty yating-l parents: 6 diff changeset	174
bd3352c46beb planemo upload commit 7856c637db5bd4ea0b8b4db63e242618421a9cc6-dirty yating-l parents: 6 diff changeset	175 $ pslCDnaFilter [options] inPsl outPsl
bd3352c46beb planemo upload commit 7856c637db5bd4ea0b8b4db63e242618421a9cc6-dirty yating-l parents: 6 diff changeset	176
5 70d7377d5e24 planemo upload commit 7856c637db5bd4ea0b8b4db63e242618421a9cc6-dirty yating-l parents: 0 diff changeset	177 Source code:
70d7377d5e24 planemo upload commit 7856c637db5bd4ea0b8b4db63e242618421a9cc6-dirty yating-l parents: 0 diff changeset	178 ++++++++++++
7 bd3352c46beb planemo upload commit 7856c637db5bd4ea0b8b4db63e242618421a9cc6-dirty yating-l parents: 6 diff changeset	179
5 70d7377d5e24 planemo upload commit 7856c637db5bd4ea0b8b4db63e242618421a9cc6-dirty yating-l parents: 0 diff changeset	180 http://hgdownload.cse.ucsc.edu/admin/exe/
70d7377d5e24 planemo upload commit 7856c637db5bd4ea0b8b4db63e242618421a9cc6-dirty yating-l parents: 0 diff changeset	181
70d7377d5e24 planemo upload commit 7856c637db5bd4ea0b8b4db63e242618421a9cc6-dirty yating-l parents: 0 diff changeset	182 Licence
70d7377d5e24 planemo upload commit 7856c637db5bd4ea0b8b4db63e242618421a9cc6-dirty yating-l parents: 0 diff changeset	183 =======
70d7377d5e24 planemo upload commit 7856c637db5bd4ea0b8b4db63e242618421a9cc6-dirty yating-l parents: 0 diff changeset	184 Please note that commercial download and installation of the Blat and In-Silico PCR software may be licensed through Kent Informatics (http://www.kentinformatics.com).
70d7377d5e24 planemo upload commit 7856c637db5bd4ea0b8b4db63e242618421a9cc6-dirty yating-l parents: 0 diff changeset	185 ]]>
70d7377d5e24 planemo upload commit 7856c637db5bd4ea0b8b4db63e242618421a9cc6-dirty yating-l parents: 0 diff changeset	186 </help>
70d7377d5e24 planemo upload commit 7856c637db5bd4ea0b8b4db63e242618421a9cc6-dirty yating-l parents: 0 diff changeset	187 <citations>
70d7377d5e24 planemo upload commit 7856c637db5bd4ea0b8b4db63e242618421a9cc6-dirty yating-l parents: 0 diff changeset	188 <citation type="bibtex">@article{kent2002blat,
70d7377d5e24 planemo upload commit 7856c637db5bd4ea0b8b4db63e242618421a9cc6-dirty yating-l parents: 0 diff changeset	189 title={BLAT—the BLAST-like alignment tool},
70d7377d5e24 planemo upload commit 7856c637db5bd4ea0b8b4db63e242618421a9cc6-dirty yating-l parents: 0 diff changeset	190 author={Kent, W James},
70d7377d5e24 planemo upload commit 7856c637db5bd4ea0b8b4db63e242618421a9cc6-dirty yating-l parents: 0 diff changeset	191 journal={Genome research},
70d7377d5e24 planemo upload commit 7856c637db5bd4ea0b8b4db63e242618421a9cc6-dirty yating-l parents: 0 diff changeset	192 volume={12},
70d7377d5e24 planemo upload commit 7856c637db5bd4ea0b8b4db63e242618421a9cc6-dirty yating-l parents: 0 diff changeset	193 number={4},
70d7377d5e24 planemo upload commit 7856c637db5bd4ea0b8b4db63e242618421a9cc6-dirty yating-l parents: 0 diff changeset	194 pages={656--664},
70d7377d5e24 planemo upload commit 7856c637db5bd4ea0b8b4db63e242618421a9cc6-dirty yating-l parents: 0 diff changeset	195 year={2002},
70d7377d5e24 planemo upload commit 7856c637db5bd4ea0b8b4db63e242618421a9cc6-dirty yating-l parents: 0 diff changeset	196 publisher={Cold Spring Harbor Lab}
70d7377d5e24 planemo upload commit 7856c637db5bd4ea0b8b4db63e242618421a9cc6-dirty yating-l parents: 0 diff changeset	197 }</citation>
70d7377d5e24 planemo upload commit 7856c637db5bd4ea0b8b4db63e242618421a9cc6-dirty yating-l parents: 0 diff changeset	198 </citations>
0 9e56efe1c371 planemo upload yating-l parents: diff changeset	199 </tool>
9e56efe1c371 planemo upload yating-l parents: diff changeset	200
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Mercurial > repos > yating-l > ucsc_blat

annotate blat.xml @ 9:c4f0808a68ad draft