repeat_masker: RepeatMasker.xml annotate

annotate RepeatMasker.xml @ 1:880265000696 draft

Uploaded

author	bgruening
date	Tue, 25 Jun 2013 08:58:21 -0400
parents	d4a2c739da3f
children	5673e72241aa

rev	line source
0 d4a2c739da3f Initial release under a consistent username. Fixes for stdout and the trailing semicolon. bgruening parents: diff changeset	1 <tool id="repeatmasker_wrapper" name="RepeatMasker" version="0.1.2">
d4a2c739da3f Initial release under a consistent username. Fixes for stdout and the trailing semicolon. bgruening parents: diff changeset	2 <description>Masks different kind of repeats</description>
d4a2c739da3f Initial release under a consistent username. Fixes for stdout and the trailing semicolon. bgruening parents: diff changeset	3 <command>
d4a2c739da3f Initial release under a consistent username. Fixes for stdout and the trailing semicolon. bgruening parents: diff changeset	4 ## The command is a Cheetah template which allows some Python based syntax.
d4a2c739da3f Initial release under a consistent username. Fixes for stdout and the trailing semicolon. bgruening parents: diff changeset	5 ## Lines starting hash hash are comments. Galaxy will turn newlines into spaces
d4a2c739da3f Initial release under a consistent username. Fixes for stdout and the trailing semicolon. bgruening parents: diff changeset	6
d4a2c739da3f Initial release under a consistent username. Fixes for stdout and the trailing semicolon. bgruening parents: diff changeset	7 ## create temp directory
d4a2c739da3f Initial release under a consistent username. Fixes for stdout and the trailing semicolon. bgruening parents: diff changeset	8 #import tempfile, os
d4a2c739da3f Initial release under a consistent username. Fixes for stdout and the trailing semicolon. bgruening parents: diff changeset	9 #set $dirname = os.path.abspath( tempfile.mkdtemp() )
d4a2c739da3f Initial release under a consistent username. Fixes for stdout and the trailing semicolon. bgruening parents: diff changeset	10 #set $input_filename = os.path.split( str($query) )[-1]
d4a2c739da3f Initial release under a consistent username. Fixes for stdout and the trailing semicolon. bgruening parents: diff changeset	11 #set $output_basename = os.path.join( $dirname, $input_filename )
d4a2c739da3f Initial release under a consistent username. Fixes for stdout and the trailing semicolon. bgruening parents: diff changeset	12
d4a2c739da3f Initial release under a consistent username. Fixes for stdout and the trailing semicolon. bgruening parents: diff changeset	13
d4a2c739da3f Initial release under a consistent username. Fixes for stdout and the trailing semicolon. bgruening parents: diff changeset	14 RepeatMasker
d4a2c739da3f Initial release under a consistent username. Fixes for stdout and the trailing semicolon. bgruening parents: diff changeset	15 -parallel 8
d4a2c739da3f Initial release under a consistent username. Fixes for stdout and the trailing semicolon. bgruening parents: diff changeset	16
d4a2c739da3f Initial release under a consistent username. Fixes for stdout and the trailing semicolon. bgruening parents: diff changeset	17 $nolow
d4a2c739da3f Initial release under a consistent username. Fixes for stdout and the trailing semicolon. bgruening parents: diff changeset	18 $noint
d4a2c739da3f Initial release under a consistent username. Fixes for stdout and the trailing semicolon. bgruening parents: diff changeset	19 $norna
d4a2c739da3f Initial release under a consistent username. Fixes for stdout and the trailing semicolon. bgruening parents: diff changeset	20
d4a2c739da3f Initial release under a consistent username. Fixes for stdout and the trailing semicolon. bgruening parents: diff changeset	21 #if str($species)!="all":
d4a2c739da3f Initial release under a consistent username. Fixes for stdout and the trailing semicolon. bgruening parents: diff changeset	22 $species
d4a2c739da3f Initial release under a consistent username. Fixes for stdout and the trailing semicolon. bgruening parents: diff changeset	23 #end if
d4a2c739da3f Initial release under a consistent username. Fixes for stdout and the trailing semicolon. bgruening parents: diff changeset	24
d4a2c739da3f Initial release under a consistent username. Fixes for stdout and the trailing semicolon. bgruening parents: diff changeset	25
d4a2c739da3f Initial release under a consistent username. Fixes for stdout and the trailing semicolon. bgruening parents: diff changeset	26 -dir $dirname
d4a2c739da3f Initial release under a consistent username. Fixes for stdout and the trailing semicolon. bgruening parents: diff changeset	27
d4a2c739da3f Initial release under a consistent username. Fixes for stdout and the trailing semicolon. bgruening parents: diff changeset	28 #if $adv_opts.adv_opts_selector=="advanced":
d4a2c739da3f Initial release under a consistent username. Fixes for stdout and the trailing semicolon. bgruening parents: diff changeset	29
d4a2c739da3f Initial release under a consistent username. Fixes for stdout and the trailing semicolon. bgruening parents: diff changeset	30 #if str($adv_opts.gc)!="0":
d4a2c739da3f Initial release under a consistent username. Fixes for stdout and the trailing semicolon. bgruening parents: diff changeset	31 -gc $adv_opts.gc
d4a2c739da3f Initial release under a consistent username. Fixes for stdout and the trailing semicolon. bgruening parents: diff changeset	32 #end if
d4a2c739da3f Initial release under a consistent username. Fixes for stdout and the trailing semicolon. bgruening parents: diff changeset	33
d4a2c739da3f Initial release under a consistent username. Fixes for stdout and the trailing semicolon. bgruening parents: diff changeset	34 $adv_opts.gccalc
d4a2c739da3f Initial release under a consistent username. Fixes for stdout and the trailing semicolon. bgruening parents: diff changeset	35
d4a2c739da3f Initial release under a consistent username. Fixes for stdout and the trailing semicolon. bgruening parents: diff changeset	36 #set $output_files_list = str($adv_opts.output_files).split(',')
d4a2c739da3f Initial release under a consistent username. Fixes for stdout and the trailing semicolon. bgruening parents: diff changeset	37 #if "gff" in $output_files_list:
d4a2c739da3f Initial release under a consistent username. Fixes for stdout and the trailing semicolon. bgruening parents: diff changeset	38 -gff
d4a2c739da3f Initial release under a consistent username. Fixes for stdout and the trailing semicolon. bgruening parents: diff changeset	39 #end if
d4a2c739da3f Initial release under a consistent username. Fixes for stdout and the trailing semicolon. bgruening parents: diff changeset	40 #if "html" in $output_files_list:
d4a2c739da3f Initial release under a consistent username. Fixes for stdout and the trailing semicolon. bgruening parents: diff changeset	41 -html
d4a2c739da3f Initial release under a consistent username. Fixes for stdout and the trailing semicolon. bgruening parents: diff changeset	42 #end if
d4a2c739da3f Initial release under a consistent username. Fixes for stdout and the trailing semicolon. bgruening parents: diff changeset	43
d4a2c739da3f Initial release under a consistent username. Fixes for stdout and the trailing semicolon. bgruening parents: diff changeset	44 $adv_opts.slow_search
d4a2c739da3f Initial release under a consistent username. Fixes for stdout and the trailing semicolon. bgruening parents: diff changeset	45 $adv_opts.quick_search
d4a2c739da3f Initial release under a consistent username. Fixes for stdout and the trailing semicolon. bgruening parents: diff changeset	46 $adv_opts.rush_search
d4a2c739da3f Initial release under a consistent username. Fixes for stdout and the trailing semicolon. bgruening parents: diff changeset	47 $adv_opts.only_alus
d4a2c739da3f Initial release under a consistent username. Fixes for stdout and the trailing semicolon. bgruening parents: diff changeset	48 $adv_opts.is_only
d4a2c739da3f Initial release under a consistent username. Fixes for stdout and the trailing semicolon. bgruening parents: diff changeset	49
d4a2c739da3f Initial release under a consistent username. Fixes for stdout and the trailing semicolon. bgruening parents: diff changeset	50 #else:
d4a2c739da3f Initial release under a consistent username. Fixes for stdout and the trailing semicolon. bgruening parents: diff changeset	51 ## Set defaults
d4a2c739da3f Initial release under a consistent username. Fixes for stdout and the trailing semicolon. bgruening parents: diff changeset	52 -gff
d4a2c739da3f Initial release under a consistent username. Fixes for stdout and the trailing semicolon. bgruening parents: diff changeset	53
d4a2c739da3f Initial release under a consistent username. Fixes for stdout and the trailing semicolon. bgruening parents: diff changeset	54 ## End of advanced options:
d4a2c739da3f Initial release under a consistent username. Fixes for stdout and the trailing semicolon. bgruening parents: diff changeset	55 #end if
d4a2c739da3f Initial release under a consistent username. Fixes for stdout and the trailing semicolon. bgruening parents: diff changeset	56
d4a2c739da3f Initial release under a consistent username. Fixes for stdout and the trailing semicolon. bgruening parents: diff changeset	57 $query
d4a2c739da3f Initial release under a consistent username. Fixes for stdout and the trailing semicolon. bgruening parents: diff changeset	58
d4a2c739da3f Initial release under a consistent username. Fixes for stdout and the trailing semicolon. bgruening parents: diff changeset	59 2>&1;
d4a2c739da3f Initial release under a consistent username. Fixes for stdout and the trailing semicolon. bgruening parents: diff changeset	60
d4a2c739da3f Initial release under a consistent username. Fixes for stdout and the trailing semicolon. bgruening parents: diff changeset	61 ## Copy the output files to galaxy
d4a2c739da3f Initial release under a consistent username. Fixes for stdout and the trailing semicolon. bgruening parents: diff changeset	62 ## AgR: if there are no repeats, the output files may not exist.
d4a2c739da3f Initial release under a consistent username. Fixes for stdout and the trailing semicolon. bgruening parents: diff changeset	63 ## This causes the job to fail, so touch files to ensure they exist.
d4a2c739da3f Initial release under a consistent username. Fixes for stdout and the trailing semicolon. bgruening parents: diff changeset	64 #if $adv_opts.adv_opts_selector=="advanced":
d4a2c739da3f Initial release under a consistent username. Fixes for stdout and the trailing semicolon. bgruening parents: diff changeset	65
d4a2c739da3f Initial release under a consistent username. Fixes for stdout and the trailing semicolon. bgruening parents: diff changeset	66 #if "summary" in $output_files_list:
d4a2c739da3f Initial release under a consistent username. Fixes for stdout and the trailing semicolon. bgruening parents: diff changeset	67 ## Write out the summary file (default)
d4a2c739da3f Initial release under a consistent username. Fixes for stdout and the trailing semicolon. bgruening parents: diff changeset	68 #set $summary_file = $output_basename + '.tbl'
1 880265000696 Uploaded bgruening parents: 0 diff changeset	69 touch $summary_file;
0 d4a2c739da3f Initial release under a consistent username. Fixes for stdout and the trailing semicolon. bgruening parents: diff changeset	70 cp $summary_file $output_summary;
d4a2c739da3f Initial release under a consistent username. Fixes for stdout and the trailing semicolon. bgruening parents: diff changeset	71 #end if
d4a2c739da3f Initial release under a consistent username. Fixes for stdout and the trailing semicolon. bgruening parents: diff changeset	72
d4a2c739da3f Initial release under a consistent username. Fixes for stdout and the trailing semicolon. bgruening parents: diff changeset	73 #if "gff" in $output_files_list:
d4a2c739da3f Initial release under a consistent username. Fixes for stdout and the trailing semicolon. bgruening parents: diff changeset	74 ## Write out the gff file (default)
d4a2c739da3f Initial release under a consistent username. Fixes for stdout and the trailing semicolon. bgruening parents: diff changeset	75 #set $gff_file = $output_basename + '.out.gff'
1 880265000696 Uploaded bgruening parents: 0 diff changeset	76 touch $gff_file;
0 d4a2c739da3f Initial release under a consistent username. Fixes for stdout and the trailing semicolon. bgruening parents: diff changeset	77 cp $gff_file $output_gff;
d4a2c739da3f Initial release under a consistent username. Fixes for stdout and the trailing semicolon. bgruening parents: diff changeset	78 #end if
d4a2c739da3f Initial release under a consistent username. Fixes for stdout and the trailing semicolon. bgruening parents: diff changeset	79
d4a2c739da3f Initial release under a consistent username. Fixes for stdout and the trailing semicolon. bgruening parents: diff changeset	80 #if "html" in $output_files_list:
d4a2c739da3f Initial release under a consistent username. Fixes for stdout and the trailing semicolon. bgruening parents: diff changeset	81 ## Write out the html file
d4a2c739da3f Initial release under a consistent username. Fixes for stdout and the trailing semicolon. bgruening parents: diff changeset	82 #set $html_file = $output_basename + '.out.html'
1 880265000696 Uploaded bgruening parents: 0 diff changeset	83 touch $html_file;
0 d4a2c739da3f Initial release under a consistent username. Fixes for stdout and the trailing semicolon. bgruening parents: diff changeset	84 cp $html_file $output_html;
d4a2c739da3f Initial release under a consistent username. Fixes for stdout and the trailing semicolon. bgruening parents: diff changeset	85 #end if
d4a2c739da3f Initial release under a consistent username. Fixes for stdout and the trailing semicolon. bgruening parents: diff changeset	86
d4a2c739da3f Initial release under a consistent username. Fixes for stdout and the trailing semicolon. bgruening parents: diff changeset	87 #else:
d4a2c739da3f Initial release under a consistent username. Fixes for stdout and the trailing semicolon. bgruening parents: diff changeset	88
d4a2c739da3f Initial release under a consistent username. Fixes for stdout and the trailing semicolon. bgruening parents: diff changeset	89 ## Write out the summary file (default)
d4a2c739da3f Initial release under a consistent username. Fixes for stdout and the trailing semicolon. bgruening parents: diff changeset	90 #set $summary_file = $output_basename + '.tbl'
1 880265000696 Uploaded bgruening parents: 0 diff changeset	91 touch $summary_file;
0 d4a2c739da3f Initial release under a consistent username. Fixes for stdout and the trailing semicolon. bgruening parents: diff changeset	92 cp $summary_file $output_summary;
d4a2c739da3f Initial release under a consistent username. Fixes for stdout and the trailing semicolon. bgruening parents: diff changeset	93
d4a2c739da3f Initial release under a consistent username. Fixes for stdout and the trailing semicolon. bgruening parents: diff changeset	94 ## Write out the gff file (default)
d4a2c739da3f Initial release under a consistent username. Fixes for stdout and the trailing semicolon. bgruening parents: diff changeset	95 #set $gff_file = $output_basename + '.out.gff'
1 880265000696 Uploaded bgruening parents: 0 diff changeset	96 touch $gff_file;
0 d4a2c739da3f Initial release under a consistent username. Fixes for stdout and the trailing semicolon. bgruening parents: diff changeset	97 cp $gff_file $output_gff;
d4a2c739da3f Initial release under a consistent username. Fixes for stdout and the trailing semicolon. bgruening parents: diff changeset	98
d4a2c739da3f Initial release under a consistent username. Fixes for stdout and the trailing semicolon. bgruening parents: diff changeset	99
d4a2c739da3f Initial release under a consistent username. Fixes for stdout and the trailing semicolon. bgruening parents: diff changeset	100 ## End of advanced options:
d4a2c739da3f Initial release under a consistent username. Fixes for stdout and the trailing semicolon. bgruening parents: diff changeset	101 #end if
d4a2c739da3f Initial release under a consistent username. Fixes for stdout and the trailing semicolon. bgruening parents: diff changeset	102
d4a2c739da3f Initial release under a consistent username. Fixes for stdout and the trailing semicolon. bgruening parents: diff changeset	103 ## Write out mask sequence file
d4a2c739da3f Initial release under a consistent username. Fixes for stdout and the trailing semicolon. bgruening parents: diff changeset	104 #set $mask_sequence_file = $output_basename + '.masked'
1 880265000696 Uploaded bgruening parents: 0 diff changeset	105 touch $mask_sequence_file;
0 d4a2c739da3f Initial release under a consistent username. Fixes for stdout and the trailing semicolon. bgruening parents: diff changeset	106 cp $mask_sequence_file $output_mask;
d4a2c739da3f Initial release under a consistent username. Fixes for stdout and the trailing semicolon. bgruening parents: diff changeset	107
d4a2c739da3f Initial release under a consistent username. Fixes for stdout and the trailing semicolon. bgruening parents: diff changeset	108 ## Write out standard file (default)
d4a2c739da3f Initial release under a consistent username. Fixes for stdout and the trailing semicolon. bgruening parents: diff changeset	109 ## The default '.out' file from RepeatMasker has a 3-line header and spaces rather
d4a2c739da3f Initial release under a consistent username. Fixes for stdout and the trailing semicolon. bgruening parents: diff changeset	110 ## than tabs. Remove the header and replace the whitespaces with tab
d4a2c739da3f Initial release under a consistent username. Fixes for stdout and the trailing semicolon. bgruening parents: diff changeset	111 #set $standard_file = $output_basename + '.out'
d4a2c739da3f Initial release under a consistent username. Fixes for stdout and the trailing semicolon. bgruening parents: diff changeset	112 tail -n +4 $standard_file \| tr -s ' ' '\t' > $output_std;
d4a2c739da3f Initial release under a consistent username. Fixes for stdout and the trailing semicolon. bgruening parents: diff changeset	113
d4a2c739da3f Initial release under a consistent username. Fixes for stdout and the trailing semicolon. bgruening parents: diff changeset	114 ## Delete all temporary files
d4a2c739da3f Initial release under a consistent username. Fixes for stdout and the trailing semicolon. bgruening parents: diff changeset	115 rm $dirname -r
d4a2c739da3f Initial release under a consistent username. Fixes for stdout and the trailing semicolon. bgruening parents: diff changeset	116
d4a2c739da3f Initial release under a consistent username. Fixes for stdout and the trailing semicolon. bgruening parents: diff changeset	117 </command>
d4a2c739da3f Initial release under a consistent username. Fixes for stdout and the trailing semicolon. bgruening parents: diff changeset	118 <inputs>
d4a2c739da3f Initial release under a consistent username. Fixes for stdout and the trailing semicolon. bgruening parents: diff changeset	119 <param name="query" type="data" format="fasta" label="Nucleotide query sequence(s)"/>
d4a2c739da3f Initial release under a consistent username. Fixes for stdout and the trailing semicolon. bgruening parents: diff changeset	120
d4a2c739da3f Initial release under a consistent username. Fixes for stdout and the trailing semicolon. bgruening parents: diff changeset	121 <param name="nolow" type="boolean" label="No low complexity DNA" truevalue="-nolow" falsevalue="" checked="false" help="Does not mask low_complexity DNA or simple repeats."/>
d4a2c739da3f Initial release under a consistent username. Fixes for stdout and the trailing semicolon. bgruening parents: diff changeset	122 <param name="noint" type="boolean" label="No interspersed repeats" truevalue="-noint" falsevalue="" checked="false" help="Only masks low complex/simple repeats (no interspersed repeats)."/>
d4a2c739da3f Initial release under a consistent username. Fixes for stdout and the trailing semicolon. bgruening parents: diff changeset	123
d4a2c739da3f Initial release under a consistent username. Fixes for stdout and the trailing semicolon. bgruening parents: diff changeset	124 <param name="norna" type="boolean" label="No small RNA genes" truevalue="-norna" falsevalue="" checked="false" help="Does not mask small RNA (pseudo) genes."/>
d4a2c739da3f Initial release under a consistent username. Fixes for stdout and the trailing semicolon. bgruening parents: diff changeset	125
d4a2c739da3f Initial release under a consistent username. Fixes for stdout and the trailing semicolon. bgruening parents: diff changeset	126 <!--
d4a2c739da3f Initial release under a consistent username. Fixes for stdout and the trailing semicolon. bgruening parents: diff changeset	127 Specify the species or clade of the input sequence. The species name
d4a2c739da3f Initial release under a consistent username. Fixes for stdout and the trailing semicolon. bgruening parents: diff changeset	128 must be a valid NCBI Taxonomy Database species name and be contained
d4a2c739da3f Initial release under a consistent username. Fixes for stdout and the trailing semicolon. bgruening parents: diff changeset	129 in the RepeatMasker repeat database. The following collection is not complete.
d4a2c739da3f Initial release under a consistent username. Fixes for stdout and the trailing semicolon. bgruening parents: diff changeset	130 -->
d4a2c739da3f Initial release under a consistent username. Fixes for stdout and the trailing semicolon. bgruening parents: diff changeset	131 <param name="species" type="select" label="Species" help="The list is not complete, if you need other species contact your administrator.">
d4a2c739da3f Initial release under a consistent username. Fixes for stdout and the trailing semicolon. bgruening parents: diff changeset	132 <option value="-species anopheles">anopheles</option>
d4a2c739da3f Initial release under a consistent username. Fixes for stdout and the trailing semicolon. bgruening parents: diff changeset	133 <option value="-species arabidopsis">arabidopsis</option>
d4a2c739da3f Initial release under a consistent username. Fixes for stdout and the trailing semicolon. bgruening parents: diff changeset	134 <option value="-species artiodactyl">artiodactyl</option>
d4a2c739da3f Initial release under a consistent username. Fixes for stdout and the trailing semicolon. bgruening parents: diff changeset	135 <option value="-species aspergillus">aspergillus</option>
d4a2c739da3f Initial release under a consistent username. Fixes for stdout and the trailing semicolon. bgruening parents: diff changeset	136 <option value="-species carnivore">carnivore</option>
d4a2c739da3f Initial release under a consistent username. Fixes for stdout and the trailing semicolon. bgruening parents: diff changeset	137 <option value="-species cat">cat</option>
d4a2c739da3f Initial release under a consistent username. Fixes for stdout and the trailing semicolon. bgruening parents: diff changeset	138 <option value="-species chicken">chicken</option>
d4a2c739da3f Initial release under a consistent username. Fixes for stdout and the trailing semicolon. bgruening parents: diff changeset	139 <option value="-species 'ciona intestinalis'">ciona intestinalis</option>
d4a2c739da3f Initial release under a consistent username. Fixes for stdout and the trailing semicolon. bgruening parents: diff changeset	140 <option value="-species 'ciona savignyi'">ciona savignyi</option>
d4a2c739da3f Initial release under a consistent username. Fixes for stdout and the trailing semicolon. bgruening parents: diff changeset	141 <option value="-species cow">cow</option>
d4a2c739da3f Initial release under a consistent username. Fixes for stdout and the trailing semicolon. bgruening parents: diff changeset	142 <option value="-species danio">danio</option>
d4a2c739da3f Initial release under a consistent username. Fixes for stdout and the trailing semicolon. bgruening parents: diff changeset	143 <option value="-species diatoaea">diatoaea</option>
d4a2c739da3f Initial release under a consistent username. Fixes for stdout and the trailing semicolon. bgruening parents: diff changeset	144 <option value="-species dog">dog</option>
d4a2c739da3f Initial release under a consistent username. Fixes for stdout and the trailing semicolon. bgruening parents: diff changeset	145 <option value="-species drosophila">drosophila</option>
d4a2c739da3f Initial release under a consistent username. Fixes for stdout and the trailing semicolon. bgruening parents: diff changeset	146 <option value="-species elegans">elegans</option>
d4a2c739da3f Initial release under a consistent username. Fixes for stdout and the trailing semicolon. bgruening parents: diff changeset	147 <option value="-species fugu">fugu</option>
d4a2c739da3f Initial release under a consistent username. Fixes for stdout and the trailing semicolon. bgruening parents: diff changeset	148 <option value="-species fungi" selected="true">fungi</option>
d4a2c739da3f Initial release under a consistent username. Fixes for stdout and the trailing semicolon. bgruening parents: diff changeset	149 <option value="-species human">human</option>
d4a2c739da3f Initial release under a consistent username. Fixes for stdout and the trailing semicolon. bgruening parents: diff changeset	150 <option value="-species maize">maize</option>
d4a2c739da3f Initial release under a consistent username. Fixes for stdout and the trailing semicolon. bgruening parents: diff changeset	151 <option value="-species mammal">mammal</option>
d4a2c739da3f Initial release under a consistent username. Fixes for stdout and the trailing semicolon. bgruening parents: diff changeset	152 <option value="-species mouse">mouse</option>
d4a2c739da3f Initial release under a consistent username. Fixes for stdout and the trailing semicolon. bgruening parents: diff changeset	153 <option value="-species pig">pig</option>
d4a2c739da3f Initial release under a consistent username. Fixes for stdout and the trailing semicolon. bgruening parents: diff changeset	154 <option value="-species rat">rat</option>
d4a2c739da3f Initial release under a consistent username. Fixes for stdout and the trailing semicolon. bgruening parents: diff changeset	155 <option value="-species rice">rice</option>
d4a2c739da3f Initial release under a consistent username. Fixes for stdout and the trailing semicolon. bgruening parents: diff changeset	156 <option value="-species rodentia">rodentia</option>
d4a2c739da3f Initial release under a consistent username. Fixes for stdout and the trailing semicolon. bgruening parents: diff changeset	157 <option value="-species wheat">wheat</option>
d4a2c739da3f Initial release under a consistent username. Fixes for stdout and the trailing semicolon. bgruening parents: diff changeset	158 </param>
d4a2c739da3f Initial release under a consistent username. Fixes for stdout and the trailing semicolon. bgruening parents: diff changeset	159
d4a2c739da3f Initial release under a consistent username. Fixes for stdout and the trailing semicolon. bgruening parents: diff changeset	160 <conditional name="adv_opts">
d4a2c739da3f Initial release under a consistent username. Fixes for stdout and the trailing semicolon. bgruening parents: diff changeset	161 <param name="adv_opts_selector" type="select" label="Advanced Options">
d4a2c739da3f Initial release under a consistent username. Fixes for stdout and the trailing semicolon. bgruening parents: diff changeset	162 <option value="basic" selected="True">Hide Advanced Options</option>
d4a2c739da3f Initial release under a consistent username. Fixes for stdout and the trailing semicolon. bgruening parents: diff changeset	163 <option value="advanced">Show Advanced Options</option>
d4a2c739da3f Initial release under a consistent username. Fixes for stdout and the trailing semicolon. bgruening parents: diff changeset	164 </param>
d4a2c739da3f Initial release under a consistent username. Fixes for stdout and the trailing semicolon. bgruening parents: diff changeset	165 <when value="basic" />
d4a2c739da3f Initial release under a consistent username. Fixes for stdout and the trailing semicolon. bgruening parents: diff changeset	166 <when value="advanced">
d4a2c739da3f Initial release under a consistent username. Fixes for stdout and the trailing semicolon. bgruening parents: diff changeset	167 <param name="is_only" type="boolean" label="Mask only E coli insertion elements" truevalue="-is_only" falsevalue="" checked="false" help="Only clips E coli insertion elements out of fasta and .qual files."/>
d4a2c739da3f Initial release under a consistent username. Fixes for stdout and the trailing semicolon. bgruening parents: diff changeset	168 <param name="slow_search" type="boolean" label="Slow search" truevalue="-s" falsevalue="" checked="false" help="0-5% more sensitive, 2-3 times slower than default."/>
d4a2c739da3f Initial release under a consistent username. Fixes for stdout and the trailing semicolon. bgruening parents: diff changeset	169 <param name="quick_search" type="boolean" label="Quick search" truevalue="-q" falsevalue="" checked="false" help="5-10% less sensitive, 2-5 times faster than default."/>
d4a2c739da3f Initial release under a consistent username. Fixes for stdout and the trailing semicolon. bgruening parents: diff changeset	170 <param name="rush_search" type="boolean" label="Rush search" truevalue="-qq" falsevalue="" checked="false" help="about 10% less sensitive, 4->10 times faster than default."/>
d4a2c739da3f Initial release under a consistent username. Fixes for stdout and the trailing semicolon. bgruening parents: diff changeset	171 <param name="only_alus" type="boolean" label="Only Alus" truevalue="-alu" falsevalue="" checked="false" help="Only masks Alus (and 7SLRNA, SVA and LTR5)(only for primate DNA)."/>
d4a2c739da3f Initial release under a consistent username. Fixes for stdout and the trailing semicolon. bgruening parents: diff changeset	172 <param name="gccalc" type="boolean" label="Use GC depended matrices, automaticly" truevalue="-gccalc" falsevalue="" checked="true" help="RepeatMasker calculates the GC content even for batch files/small seqs"/>
d4a2c739da3f Initial release under a consistent username. Fixes for stdout and the trailing semicolon. bgruening parents: diff changeset	173
d4a2c739da3f Initial release under a consistent username. Fixes for stdout and the trailing semicolon. bgruening parents: diff changeset	174 <param name="output_files" type="select" multiple="true" label="Additional output files">
d4a2c739da3f Initial release under a consistent username. Fixes for stdout and the trailing semicolon. bgruening parents: diff changeset	175 <option selected="true" value="summary">Summary file</option>
d4a2c739da3f Initial release under a consistent username. Fixes for stdout and the trailing semicolon. bgruening parents: diff changeset	176 <option value="gff">GFF file</option>
d4a2c739da3f Initial release under a consistent username. Fixes for stdout and the trailing semicolon. bgruening parents: diff changeset	177 <option value="html">HTML file</option>
d4a2c739da3f Initial release under a consistent username. Fixes for stdout and the trailing semicolon. bgruening parents: diff changeset	178 <option value="mask">Mask FastA file</option>
d4a2c739da3f Initial release under a consistent username. Fixes for stdout and the trailing semicolon. bgruening parents: diff changeset	179 </param>
d4a2c739da3f Initial release under a consistent username. Fixes for stdout and the trailing semicolon. bgruening parents: diff changeset	180
d4a2c739da3f Initial release under a consistent username. Fixes for stdout and the trailing semicolon. bgruening parents: diff changeset	181 <param name="gc" type="integer" value="0" label="Use GC depended matrices" help="Use matrices calculated for 'number' percentage background GC level">
d4a2c739da3f Initial release under a consistent username. Fixes for stdout and the trailing semicolon. bgruening parents: diff changeset	182 <validator type="in_range" min="0" />
d4a2c739da3f Initial release under a consistent username. Fixes for stdout and the trailing semicolon. bgruening parents: diff changeset	183 <validator type="in_range" max="100" />
d4a2c739da3f Initial release under a consistent username. Fixes for stdout and the trailing semicolon. bgruening parents: diff changeset	184 </param>
d4a2c739da3f Initial release under a consistent username. Fixes for stdout and the trailing semicolon. bgruening parents: diff changeset	185
d4a2c739da3f Initial release under a consistent username. Fixes for stdout and the trailing semicolon. bgruening parents: diff changeset	186 </when>
d4a2c739da3f Initial release under a consistent username. Fixes for stdout and the trailing semicolon. bgruening parents: diff changeset	187 </conditional>
d4a2c739da3f Initial release under a consistent username. Fixes for stdout and the trailing semicolon. bgruening parents: diff changeset	188
d4a2c739da3f Initial release under a consistent username. Fixes for stdout and the trailing semicolon. bgruening parents: diff changeset	189 </inputs>
d4a2c739da3f Initial release under a consistent username. Fixes for stdout and the trailing semicolon. bgruening parents: diff changeset	190 <outputs>
d4a2c739da3f Initial release under a consistent username. Fixes for stdout and the trailing semicolon. bgruening parents: diff changeset	191 <data name="output_std" format="tabular" label="${tool.name} on ${on_string}: Standard" />
d4a2c739da3f Initial release under a consistent username. Fixes for stdout and the trailing semicolon. bgruening parents: diff changeset	192 <data name="output_mask" format="fasta" label="${tool.name} on ${on_string}: Mask sequence">
d4a2c739da3f Initial release under a consistent username. Fixes for stdout and the trailing semicolon. bgruening parents: diff changeset	193 <filter>
d4a2c739da3f Initial release under a consistent username. Fixes for stdout and the trailing semicolon. bgruening parents: diff changeset	194 (adv_opts['adv_opts_selector'] == 'advanced' and 'mask' in adv_opts['output_files'])
d4a2c739da3f Initial release under a consistent username. Fixes for stdout and the trailing semicolon. bgruening parents: diff changeset	195 </filter>
d4a2c739da3f Initial release under a consistent username. Fixes for stdout and the trailing semicolon. bgruening parents: diff changeset	196 </data>
d4a2c739da3f Initial release under a consistent username. Fixes for stdout and the trailing semicolon. bgruening parents: diff changeset	197 <data name="output_summary" format="txt" label="${tool.name} on ${on_string}: Summary">
d4a2c739da3f Initial release under a consistent username. Fixes for stdout and the trailing semicolon. bgruening parents: diff changeset	198 <filter>(
d4a2c739da3f Initial release under a consistent username. Fixes for stdout and the trailing semicolon. bgruening parents: diff changeset	199 (adv_opts['adv_opts_selector'] == 'advanced' and 'summary' in adv_opts['output_files'])
d4a2c739da3f Initial release under a consistent username. Fixes for stdout and the trailing semicolon. bgruening parents: diff changeset	200 or
d4a2c739da3f Initial release under a consistent username. Fixes for stdout and the trailing semicolon. bgruening parents: diff changeset	201 (adv_opts['adv_opts_selector'] == 'basic')
d4a2c739da3f Initial release under a consistent username. Fixes for stdout and the trailing semicolon. bgruening parents: diff changeset	202 )
d4a2c739da3f Initial release under a consistent username. Fixes for stdout and the trailing semicolon. bgruening parents: diff changeset	203 </filter>
d4a2c739da3f Initial release under a consistent username. Fixes for stdout and the trailing semicolon. bgruening parents: diff changeset	204 </data>
d4a2c739da3f Initial release under a consistent username. Fixes for stdout and the trailing semicolon. bgruening parents: diff changeset	205 <data name="output_html" format="html" label="${tool.name} on ${on_string}: HTML">
d4a2c739da3f Initial release under a consistent username. Fixes for stdout and the trailing semicolon. bgruening parents: diff changeset	206 <filter>(adv_opts['adv_opts_selector'] == 'advanced' and 'html' in adv_opts['output_files'])</filter>
d4a2c739da3f Initial release under a consistent username. Fixes for stdout and the trailing semicolon. bgruening parents: diff changeset	207 </data>
d4a2c739da3f Initial release under a consistent username. Fixes for stdout and the trailing semicolon. bgruening parents: diff changeset	208 <data name="output_gff" format="gff" label="${tool.name} on ${on_string}: GFF">
d4a2c739da3f Initial release under a consistent username. Fixes for stdout and the trailing semicolon. bgruening parents: diff changeset	209 <filter>
d4a2c739da3f Initial release under a consistent username. Fixes for stdout and the trailing semicolon. bgruening parents: diff changeset	210 (adv_opts['adv_opts_selector'] == 'advanced' and 'gff' in adv_opts['output_files'])
d4a2c739da3f Initial release under a consistent username. Fixes for stdout and the trailing semicolon. bgruening parents: diff changeset	211 </filter>
d4a2c739da3f Initial release under a consistent username. Fixes for stdout and the trailing semicolon. bgruening parents: diff changeset	212 </data>
d4a2c739da3f Initial release under a consistent username. Fixes for stdout and the trailing semicolon. bgruening parents: diff changeset	213 </outputs>
d4a2c739da3f Initial release under a consistent username. Fixes for stdout and the trailing semicolon. bgruening parents: diff changeset	214 <requirements>
d4a2c739da3f Initial release under a consistent username. Fixes for stdout and the trailing semicolon. bgruening parents: diff changeset	215 <requirement type="binary">RepeatMasker</requirement>
d4a2c739da3f Initial release under a consistent username. Fixes for stdout and the trailing semicolon. bgruening parents: diff changeset	216 </requirements>
d4a2c739da3f Initial release under a consistent username. Fixes for stdout and the trailing semicolon. bgruening parents: diff changeset	217 <help>
d4a2c739da3f Initial release under a consistent username. Fixes for stdout and the trailing semicolon. bgruening parents: diff changeset	218
d4a2c739da3f Initial release under a consistent username. Fixes for stdout and the trailing semicolon. bgruening parents: diff changeset	219 .. class:: warningmark
d4a2c739da3f Initial release under a consistent username. Fixes for stdout and the trailing semicolon. bgruening parents: diff changeset	220
d4a2c739da3f Initial release under a consistent username. Fixes for stdout and the trailing semicolon. bgruening parents: diff changeset	221 What it does
d4a2c739da3f Initial release under a consistent username. Fixes for stdout and the trailing semicolon. bgruening parents: diff changeset	222
d4a2c739da3f Initial release under a consistent username. Fixes for stdout and the trailing semicolon. bgruening parents: diff changeset	223 RepeatMasker is a program that screens DNA sequences for interspersed repeats
d4a2c739da3f Initial release under a consistent username. Fixes for stdout and the trailing semicolon. bgruening parents: diff changeset	224 and low complexity DNA sequences. The output of the program is a detailed
d4a2c739da3f Initial release under a consistent username. Fixes for stdout and the trailing semicolon. bgruening parents: diff changeset	225 annotation of the repeats that are present in the query sequence as well as a
d4a2c739da3f Initial release under a consistent username. Fixes for stdout and the trailing semicolon. bgruening parents: diff changeset	226 modified version of the query sequence in which all the annotated repeats have
d4a2c739da3f Initial release under a consistent username. Fixes for stdout and the trailing semicolon. bgruening parents: diff changeset	227 been masked (default: replaced by Ns).
d4a2c739da3f Initial release under a consistent username. Fixes for stdout and the trailing semicolon. bgruening parents: diff changeset	228
d4a2c739da3f Initial release under a consistent username. Fixes for stdout and the trailing semicolon. bgruening parents: diff changeset	229 -----
d4a2c739da3f Initial release under a consistent username. Fixes for stdout and the trailing semicolon. bgruening parents: diff changeset	230
d4a2c739da3f Initial release under a consistent username. Fixes for stdout and the trailing semicolon. bgruening parents: diff changeset	231 How to read the results
d4a2c739da3f Initial release under a consistent username. Fixes for stdout and the trailing semicolon. bgruening parents: diff changeset	232
d4a2c739da3f Initial release under a consistent username. Fixes for stdout and the trailing semicolon. bgruening parents: diff changeset	233
d4a2c739da3f Initial release under a consistent username. Fixes for stdout and the trailing semicolon. bgruening parents: diff changeset	234
d4a2c739da3f Initial release under a consistent username. Fixes for stdout and the trailing semicolon. bgruening parents: diff changeset	235 The annotation file contains the cross_match output lines. It lists all best matches
d4a2c739da3f Initial release under a consistent username. Fixes for stdout and the trailing semicolon. bgruening parents: diff changeset	236 (above a set minimum score) between the query sequence and any of the sequences in
d4a2c739da3f Initial release under a consistent username. Fixes for stdout and the trailing semicolon. bgruening parents: diff changeset	237 the repeat database or with low complexity DNA. The term "best matches" reflects
d4a2c739da3f Initial release under a consistent username. Fixes for stdout and the trailing semicolon. bgruening parents: diff changeset	238 that a match is not shown if its domain is over 80% contained within the domain
d4a2c739da3f Initial release under a consistent username. Fixes for stdout and the trailing semicolon. bgruening parents: diff changeset	239 of a higher scoring match, where the "domain" of a match is the region in
d4a2c739da3f Initial release under a consistent username. Fixes for stdout and the trailing semicolon. bgruening parents: diff changeset	240 the query sequence that is defined by the alignment start and stop. These domains
d4a2c739da3f Initial release under a consistent username. Fixes for stdout and the trailing semicolon. bgruening parents: diff changeset	241 have been masked in the returned masked sequence file. In the output, matches are
d4a2c739da3f Initial release under a consistent username. Fixes for stdout and the trailing semicolon. bgruening parents: diff changeset	242 ordered by query name, and for each query by position of the start of the alignment.
d4a2c739da3f Initial release under a consistent username. Fixes for stdout and the trailing semicolon. bgruening parents: diff changeset	243
d4a2c739da3f Initial release under a consistent username. Fixes for stdout and the trailing semicolon. bgruening parents: diff changeset	244 Example:
d4a2c739da3f Initial release under a consistent username. Fixes for stdout and the trailing semicolon. bgruening parents: diff changeset	245
d4a2c739da3f Initial release under a consistent username. Fixes for stdout and the trailing semicolon. bgruening parents: diff changeset	246 ======== ========= ========= ========= ========== =========== ========= ========= ============ =============== =================== ================ ============== ======= ==
d4a2c739da3f Initial release under a consistent username. Fixes for stdout and the trailing semicolon. bgruening parents: diff changeset	247 SW score perc div. perc del. perc ins. query seq. q-pos begin q-pos end (left) w complement matching repeat repeat class/family repeat-pos begin repeat-pos end (left) ID
d4a2c739da3f Initial release under a consistent username. Fixes for stdout and the trailing semicolon. bgruening parents: diff changeset	248 ======== ========= ========= ========= ========== =========== ========= ========= ============ =============== =================== ================ ============== ======= ==
d4a2c739da3f Initial release under a consistent username. Fixes for stdout and the trailing semicolon. bgruening parents: diff changeset	249 1306 15.6 6.2 0.0 HSU08988 6563 6781 \(22462) C MER7A DNA/MER2_type 336 103 \(0) 1
d4a2c739da3f Initial release under a consistent username. Fixes for stdout and the trailing semicolon. bgruening parents: diff changeset	250 12204 10.0 2.4 1.8 HSU08988 6782 7714 \(21529) C TIGGER1 DNA/MER2_type 2418 1493 \(0) 2
d4a2c739da3f Initial release under a consistent username. Fixes for stdout and the trailing semicolon. bgruening parents: diff changeset	251 279 3.0 0.0 0.0 HSU08988 7719 7751 \(21492) + (TTTTA)n Simple_repeat 1 33 \(0) 3
d4a2c739da3f Initial release under a consistent username. Fixes for stdout and the trailing semicolon. bgruening parents: diff changeset	252 1765 13.4 6.5 1.8 HSU08988 7752 8022 \(21221) C AluSx SINE/Alu 289 1 \(23) 4
d4a2c739da3f Initial release under a consistent username. Fixes for stdout and the trailing semicolon. bgruening parents: diff changeset	253 12204 10.0 2.4 1.8 HSU08988 8023 8694 \(20549) C TIGGER1 DNA/MER2_type 1493 827 \(925) 5
d4a2c739da3f Initial release under a consistent username. Fixes for stdout and the trailing semicolon. bgruening parents: diff changeset	254 1984 11.1 0.3 0.7 HSU08988 8695 9000 \(20243) C AluSg SINE/Alu 305 1 \(5) 6
d4a2c739da3f Initial release under a consistent username. Fixes for stdout and the trailing semicolon. bgruening parents: diff changeset	255 12204 10.0 2.4 1.8 HSU08988 9001 9695 \(19548) C TIGGER1 DNA/MER2_type 827 2 \(1591) 7
d4a2c739da3f Initial release under a consistent username. Fixes for stdout and the trailing semicolon. bgruening parents: diff changeset	256 711 21.2 1.4 0.0 HSU08988 9696 9816 \(19427) C MER7A DNA/MER2_type 122 2 \(224) 8
d4a2c739da3f Initial release under a consistent username. Fixes for stdout and the trailing semicolon. bgruening parents: diff changeset	257 ======== ========= ========= ========= ========== =========== ========= ========= ============ =============== =================== ================ ============== ======= ==
d4a2c739da3f Initial release under a consistent username. Fixes for stdout and the trailing semicolon. bgruening parents: diff changeset	258
d4a2c739da3f Initial release under a consistent username. Fixes for stdout and the trailing semicolon. bgruening parents: diff changeset	259 This is a sequence in which a Tigger1 DNA transposon has integrated into a MER7 DNA transposon copy.
d4a2c739da3f Initial release under a consistent username. Fixes for stdout and the trailing semicolon. bgruening parents: diff changeset	260 Subsequently two Alus integrated in the Tigger1 sequence. The simple repeat is derived from the
d4a2c739da3f Initial release under a consistent username. Fixes for stdout and the trailing semicolon. bgruening parents: diff changeset	261 poly A of the Alu element. The first line is interpreted like this:
d4a2c739da3f Initial release under a consistent username. Fixes for stdout and the trailing semicolon. bgruening parents: diff changeset	262
d4a2c739da3f Initial release under a consistent username. Fixes for stdout and the trailing semicolon. bgruening parents: diff changeset	263 :Table description:
d4a2c739da3f Initial release under a consistent username. Fixes for stdout and the trailing semicolon. bgruening parents: diff changeset	264
d4a2c739da3f Initial release under a consistent username. Fixes for stdout and the trailing semicolon. bgruening parents: diff changeset	265 1. 1306 = Smith-Waterman score of the match, usually complexity adjusted
d4a2c739da3f Initial release under a consistent username. Fixes for stdout and the trailing semicolon. bgruening parents: diff changeset	266 The SW scores are not always directly comparable. Sometimes
d4a2c739da3f Initial release under a consistent username. Fixes for stdout and the trailing semicolon. bgruening parents: diff changeset	267 the complexity adjustment has been turned off, and a variety of
d4a2c739da3f Initial release under a consistent username. Fixes for stdout and the trailing semicolon. bgruening parents: diff changeset	268 scoring-matrices are used.
d4a2c739da3f Initial release under a consistent username. Fixes for stdout and the trailing semicolon. bgruening parents: diff changeset	269
d4a2c739da3f Initial release under a consistent username. Fixes for stdout and the trailing semicolon. bgruening parents: diff changeset	270 #. 15.6 = % substitutions in matching region compared to the consensus
d4a2c739da3f Initial release under a consistent username. Fixes for stdout and the trailing semicolon. bgruening parents: diff changeset	271 #. 6.2 = % of bases opposite a gap in the query sequence (deleted bp)
d4a2c739da3f Initial release under a consistent username. Fixes for stdout and the trailing semicolon. bgruening parents: diff changeset	272 #. 0.0 = % of bases opposite a gap in the repeat consensus (inserted bp)
d4a2c739da3f Initial release under a consistent username. Fixes for stdout and the trailing semicolon. bgruening parents: diff changeset	273 #. HSU08988 = name of query sequence
d4a2c739da3f Initial release under a consistent username. Fixes for stdout and the trailing semicolon. bgruening parents: diff changeset	274 #. 6563 = starting position of match in query sequence
d4a2c739da3f Initial release under a consistent username. Fixes for stdout and the trailing semicolon. bgruening parents: diff changeset	275 #. 7714 = ending position of match in query sequence
d4a2c739da3f Initial release under a consistent username. Fixes for stdout and the trailing semicolon. bgruening parents: diff changeset	276 #. (22462) = no. of bases in query sequence past the ending position of match
d4a2c739da3f Initial release under a consistent username. Fixes for stdout and the trailing semicolon. bgruening parents: diff changeset	277 #. C = match is with the Complement of the consensus sequence in the database
d4a2c739da3f Initial release under a consistent username. Fixes for stdout and the trailing semicolon. bgruening parents: diff changeset	278 #. MER7A = name of the matching interspersed repeat
d4a2c739da3f Initial release under a consistent username. Fixes for stdout and the trailing semicolon. bgruening parents: diff changeset	279 #. DNA/MER2_type = the class of the repeat, in this case a DNA transposon fossil of the MER2 group (see below for list and references)
d4a2c739da3f Initial release under a consistent username. Fixes for stdout and the trailing semicolon. bgruening parents: diff changeset	280 #. 2418 = starting position of match in database sequence (using top-strand numbering)
d4a2c739da3f Initial release under a consistent username. Fixes for stdout and the trailing semicolon. bgruening parents: diff changeset	281 #. 1465 = ending position of match in database sequence
d4a2c739da3f Initial release under a consistent username. Fixes for stdout and the trailing semicolon. bgruening parents: diff changeset	282 #. (0) = no. of bases in (complement of) the repeat consensus sequence prior to beginning of the match (so 0 means that the match extended all the way to the end of the repeat consensus sequence)
d4a2c739da3f Initial release under a consistent username. Fixes for stdout and the trailing semicolon. bgruening parents: diff changeset	283 #. 1 = Identifier
d4a2c739da3f Initial release under a consistent username. Fixes for stdout and the trailing semicolon. bgruening parents: diff changeset	284
d4a2c739da3f Initial release under a consistent username. Fixes for stdout and the trailing semicolon. bgruening parents: diff changeset	285 An asterisk (\*) in the final column (no example shown) indicates that there is
d4a2c739da3f Initial release under a consistent username. Fixes for stdout and the trailing semicolon. bgruening parents: diff changeset	286 a higher-scoring match whose domain partly (<80%) includes the domain of this match.
d4a2c739da3f Initial release under a consistent username. Fixes for stdout and the trailing semicolon. bgruening parents: diff changeset	287
d4a2c739da3f Initial release under a consistent username. Fixes for stdout and the trailing semicolon. bgruening parents: diff changeset	288 Note that the SW score and divergence numbers for the three Tigger1 lines are identical.
d4a2c739da3f Initial release under a consistent username. Fixes for stdout and the trailing semicolon. bgruening parents: diff changeset	289 This is because the information is derived from a single alignment (the Alus were deleted
d4a2c739da3f Initial release under a consistent username. Fixes for stdout and the trailing semicolon. bgruening parents: diff changeset	290 from the query before the alignment with the Tigger element was performed).
d4a2c739da3f Initial release under a consistent username. Fixes for stdout and the trailing semicolon. bgruening parents: diff changeset	291 The program makes educated guesses about many fragments if they are derived from
d4a2c739da3f Initial release under a consistent username. Fixes for stdout and the trailing semicolon. bgruening parents: diff changeset	292 the same element (e.g. it knows that the MER7A fragments represent one insert).
d4a2c739da3f Initial release under a consistent username. Fixes for stdout and the trailing semicolon. bgruening parents: diff changeset	293 In a next version I can identify each element with a unique ID, if interest exists
d4a2c739da3f Initial release under a consistent username. Fixes for stdout and the trailing semicolon. bgruening parents: diff changeset	294 (this could help to represent repeats cleaner in graphic displays).
d4a2c739da3f Initial release under a consistent username. Fixes for stdout and the trailing semicolon. bgruening parents: diff changeset	295
d4a2c739da3f Initial release under a consistent username. Fixes for stdout and the trailing semicolon. bgruening parents: diff changeset	296
d4a2c739da3f Initial release under a consistent username. Fixes for stdout and the trailing semicolon. bgruening parents: diff changeset	297 -------
d4a2c739da3f Initial release under a consistent username. Fixes for stdout and the trailing semicolon. bgruening parents: diff changeset	298
d4a2c739da3f Initial release under a consistent username. Fixes for stdout and the trailing semicolon. bgruening parents: diff changeset	299 References
d4a2c739da3f Initial release under a consistent username. Fixes for stdout and the trailing semicolon. bgruening parents: diff changeset	300
d4a2c739da3f Initial release under a consistent username. Fixes for stdout and the trailing semicolon. bgruening parents: diff changeset	301 Smit, AFA, Hubley, R and Green, P. RepeatMasker Open-3.0.
d4a2c739da3f Initial release under a consistent username. Fixes for stdout and the trailing semicolon. bgruening parents: diff changeset	302
d4a2c739da3f Initial release under a consistent username. Fixes for stdout and the trailing semicolon. bgruening parents: diff changeset	303 http://www.repeatmasker.org/
d4a2c739da3f Initial release under a consistent username. Fixes for stdout and the trailing semicolon. bgruening parents: diff changeset	304
d4a2c739da3f Initial release under a consistent username. Fixes for stdout and the trailing semicolon. bgruening parents: diff changeset	305 </help>
d4a2c739da3f Initial release under a consistent username. Fixes for stdout and the trailing semicolon. bgruening parents: diff changeset	306 </tool>

Mercurial > repos > bgruening > repeat_masker

annotate RepeatMasker.xml @ 1:880265000696 draft