Mercurial > repos > bjoern-gruening > repeat_masker
diff tools/RepeatMasker.xml @ 0:13df908a02b0
Initial commit
| author | bjoern-gruening |
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| date | Wed, 11 Jan 2012 04:50:59 -0500 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tools/RepeatMasker.xml Wed Jan 11 04:50:59 2012 -0500 @@ -0,0 +1,309 @@ +<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>