Mercurial > repos > bjoern-gruening > repeat_masker
diff tools/RepeatMasker.xml @ 1:f8f1a3878edd draft default tip
0.1.1 version, prevent a crash if no repeat is found. Thanks to Simon Guest
| author | bjoern-gruening |
|---|---|
| date | Fri, 01 Feb 2013 03:29:37 -0500 |
| parents | 13df908a02b0 |
| children |
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--- a/tools/RepeatMasker.xml Wed Jan 11 04:50:59 2012 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,309 +0,0 @@ -<tool id="repeatmasker_wrapper" name="RepeatMasker" version="0.1"> - <description>Masks different kind of repeats</description> - <command> -## The command is a Cheetah template which allows some Python based syntax. -## Lines starting hash hash are comments. Galaxy will turn newlines into spaces - -## create temp directory -#import tempfile, os -#set $dirname = os.path.abspath(tempfile.mkdtemp()) -#set $input_filename = os.path.split(str($query))[-1] -#set $output_basename = os.path.join($dirname, $input_filename) - - -RepeatMasker --parallel 8 - -$nolow -$noint -$norna - -#if str($species)!="all": - $species -#end if - - --dir $dirname - -#if $adv_opts.adv_opts_selector=="advanced": - - #if str($adv_opts.gc)!="0": - -gc $adv_opts.gc - #end if - - $adv_opts.gccalc - - #set $output_files_list = str($adv_opts.output_files).split(',') - #if "gff" in $output_files_list: - -gff - #end if - #if "html" in $output_files_list: - -html - #end if - - $adv_opts.slow_search - $adv_opts.quick_search - $adv_opts.rush_search - $adv_opts.only_alus - $adv_opts.is_only - -#else: - ## Set defaults - -gff - -## End of advanced options: -#end if - -$query - - -> /dev/null 2> /dev/null; -## Copy the output files to galaxy -#if $adv_opts.adv_opts_selector=="advanced": - - #if "summary" in $output_files_list: - ## Write out the summary file (default) - #set $summary_file = $output_basename + '.tbl' - cp $summary_file $output_summary; - #end if - - #if "gff" in $output_files_list: - ## Write out the gff file (default) - #set $gff_file = $output_basename + '.out.gff' - cp $gff_file $output_gff; - #end if - - #if "html" in $output_files_list: - ## Write out the html file - #set $html_file = $output_basename + '.out.html' - cp $html_file $output_html; - #end if - -#else: - - ## Write out the summary file (default) - #set $summary_file = $output_basename + '.tbl' - cp $summary_file $output_summary; - - ## Write out the gff file (default) - #set $gff_file = $output_basename + '.out.gff' - cp $gff_file $output_gff; - - -## End of advanced options: -#end if - -## Write out mask sequence file -#set $mask_sequence_file = $output_basename + '.masked' -cp $mask_sequence_file $output_mask; - -## Write out standard file (default) -## The default '.out' file from RepeatMasker has a 3-line header and spaces rather -## than tabs. Remove the header and replace the whitespaces with tab -#set $standard_file = $output_basename + '.out' -tail -n +4 $standard_file | tr -s ' ' '\t' > $output_std; - -## Delete all temporary files -rm $dirname -r; - - - </command> - <inputs> - <param name="query" type="data" format="fasta" label="Nucleotide query sequence(s)"/> - - <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."/> - <param name="noint" type="boolean" label="No interspersed repeats" truevalue="-noint" falsevalue="" checked="false" help="Only masks low complex/simple repeats (no interspersed repeats)."/> - - <param name="norna" type="boolean" label="No small RNA genes" truevalue="-norna" falsevalue="" checked="false" help="Does not mask small RNA (pseudo) genes."/> - - <!-- - Specify the species or clade of the input sequence. The species name - must be a valid NCBI Taxonomy Database species name and be contained - in the RepeatMasker repeat database. The following collection is not complete. - --> - <param name="species" type="select" label="Species" help="The list is not complete, if you need other species contact your administrator."> - <option value="-species anopheles">anopheles</option> - <option value="-species arabidopsis">arabidopsis</option> - <option value="-species artiodactyl">artiodactyl</option> - <option value="-species aspergillus">aspergillus</option> - <option value="-species carnivore">carnivore</option> - <option value="-species cat">cat</option> - <option value="-species chicken">chicken</option> - <option value="-species 'ciona intestinalis'">ciona intestinalis</option> - <option value="-species 'ciona savignyi'">ciona savignyi</option> - <option value="-species cow">cow</option> - <option value="-species danio">danio</option> - <option value="-species diatoaea">diatoaea</option> - <option value="-species dog">dog</option> - <option value="-species drosophila">drosophila</option> - <option value="-species elegans">elegans</option> - <option value="-species fugu">fugu</option> - <option value="-species fungi" selected="true">fungi</option> - <option value="-species human">human</option> - <option value="-species maize">maize</option> - <option value="-species mammal">mammal</option> - <option value="-species mouse">mouse</option> - <option value="-species pig">pig</option> - <option value="-species rat">rat</option> - <option value="-species rice">rice</option> - <option value="-species rodentia">rodentia</option> - <option value="-species wheat">wheat</option> - </param> - - <conditional name="adv_opts"> - <param name="adv_opts_selector" type="select" label="Advanced Options"> - <option value="basic" selected="True">Hide Advanced Options</option> - <option value="advanced">Show Advanced Options</option> - </param> - <when value="basic" /> - <when value="advanced"> - - - <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."/> - - - <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."/> - <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."/> - <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."/> - - <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)."/> - - <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"/> - - <param name="output_files" type="select" multiple="true" label="Additional output files"> - <option selected="true" value="summary">Summary file</option> - <option value="gff">GFF file</option> - <option value="html">HTML file</option> - <option value="mask">Mask FastA file</option> - </param> - - - <param name="gc" type="integer" value="0" label="Use GC depended matrices" help="Use matrices calculated for 'number' percentage background GC level"> - <validator type="in_range" min="0" /> - <validator type="in_range" max="100" /> - </param> - - </when> - </conditional> - - </inputs> - <outputs> - <data name="output_std" format="tabular" label="${tool.name} on ${on_string}: Standard" /> - <data name="output_mask" format="fasta" label="${tool.name} on ${on_string}: Mask sequence"> - <filter> - (adv_opts['adv_opts_selector'] == 'advanced' and 'mask' in adv_opts['output_files']) - </filter> - </data> - <data name="output_summary" format="txt" label="${tool.name} on ${on_string}: Summary"> - <filter>( - (adv_opts['adv_opts_selector'] == 'advanced' and 'summary' in adv_opts['output_files']) - or - (adv_opts['adv_opts_selector'] == 'basic') - ) - </filter> - </data> - <data name="output_html" format="html" label="${tool.name} on ${on_string}: HTML"> - <filter>(adv_opts['adv_opts_selector'] == 'advanced' and 'html' in adv_opts['output_files'])</filter> - </data> - <data name="output_gff" format="gff" label="${tool.name} on ${on_string}: GFF"> - <filter> - (adv_opts['adv_opts_selector'] == 'advanced' and 'gff' in adv_opts['output_files']) - </filter> - </data> - </outputs> - <requirements> - <requirement type="binary">RepeatMasker</requirement> - </requirements> - <help> - -.. class:: warningmark - - ------ - -**What it does** - -RepeatMasker is a program that screens DNA sequences for *interspersed repeats* -and *low complexity* DNA sequences. The output of the program is a detailed -annotation of the repeats that are present in the query sequence as well as a -modified version of the query sequence in which all the annotated repeats have -been masked (default: replaced by Ns). - ------ - -**How to read the results** - - - -The annotation file contains the cross_match output lines. It lists all best matches -(above a set minimum score) between the query sequence and any of the sequences in -the repeat database or with low complexity DNA. The term "best matches" reflects -that a match is not shown if its domain is over 80% contained within the domain -of a higher scoring match, where the "domain" of a match is the region in -the query sequence that is defined by the alignment start and stop. These domains -have been masked in the returned masked sequence file. In the output, matches are -ordered by query name, and for each query by position of the start of the alignment. - -Example: - -======== ========= ========= ========= ========== =========== ========= ========= ============ =============== =================== ================ ============== ======= == -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 -======== ========= ========= ========= ========== =========== ========= ========= ============ =============== =================== ================ ============== ======= == - 1306 15.6 6.2 0.0 HSU08988 6563 6781 \(22462) C MER7A DNA/MER2_type 336 103 \(0) 1 - 12204 10.0 2.4 1.8 HSU08988 6782 7714 \(21529) C TIGGER1 DNA/MER2_type 2418 1493 \(0) 2 - 279 3.0 0.0 0.0 HSU08988 7719 7751 \(21492) + (TTTTA)n Simple_repeat 1 33 \(0) 3 - 1765 13.4 6.5 1.8 HSU08988 7752 8022 \(21221) C AluSx SINE/Alu 289 1 \(23) 4 - 12204 10.0 2.4 1.8 HSU08988 8023 8694 \(20549) C TIGGER1 DNA/MER2_type 1493 827 \(925) 5 - 1984 11.1 0.3 0.7 HSU08988 8695 9000 \(20243) C AluSg SINE/Alu 305 1 \(5) 6 - 12204 10.0 2.4 1.8 HSU08988 9001 9695 \(19548) C TIGGER1 DNA/MER2_type 827 2 \(1591) 7 - 711 21.2 1.4 0.0 HSU08988 9696 9816 \(19427) C MER7A DNA/MER2_type 122 2 \(224) 8 -======== ========= ========= ========= ========== =========== ========= ========= ============ =============== =================== ================ ============== ======= == - -This is a sequence in which a Tigger1 DNA transposon has integrated into a MER7 DNA transposon copy. -Subsequently two Alus integrated in the Tigger1 sequence. The simple repeat is derived from the -poly A of the Alu element. The first line is interpreted like this: - -:Table description: - -1. **1306** = Smith-Waterman score of the match, usually complexity adjusted - The SW scores are not always directly comparable. Sometimes - the complexity adjustment has been turned off, and a variety of - scoring-matrices are used. - -#. **15.6** = % substitutions in matching region compared to the consensus -#. **6.2** = % of bases opposite a gap in the query sequence (deleted bp) -#. **0.0** = % of bases opposite a gap in the repeat consensus (inserted bp) -#. **HSU08988** = name of query sequence -#. **6563** = starting position of match in query sequence -#. **7714** = ending position of match in query sequence -#. **(22462)** = no. of bases in query sequence past the ending position of match -#. **C** = match is with the Complement of the consensus sequence in the database -#. **MER7A** = name of the matching interspersed repeat -#. **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) -#. **2418** = starting position of match in database sequence (using top-strand numbering) -#. **1465** = ending position of match in database sequence -#. **(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) -#. **1** = Identifier - -An asterisk (\*) in the final column (no example shown) indicates that there is -a higher-scoring match whose domain partly (<80%) includes the domain of this match. - -Note that the SW score and divergence numbers for the three Tigger1 lines are identical. -This is because the information is derived from a single alignment (the Alus were deleted -from the query before the alignment with the Tigger element was performed). -The program makes educated guesses about many fragments if they are derived from -the same element (e.g. it knows that the MER7A fragments represent one insert). -In a next version I can identify each element with a unique ID, if interest exists -(this could help to represent repeats cleaner in graphic displays). - - -------- - -**References** - -Smit, AFA, Hubley, R and Green, P. RepeatMasker Open-3.0. - -http://www.repeatmasker.org/ - - </help> -</tool>