Mercurial > repos > jjohnson > gmap
diff gmap.xml @ 11:6adc485b6dc0 draft default tip
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| author | jjohnson |
|---|---|
| date | Tue, 31 Jul 2012 08:19:46 -0400 |
| parents | 93911bac43da |
| children |
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--- a/gmap.xml Thu Jan 05 14:31:24 2012 -0600 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,482 +0,0 @@ -<tool id="gmap" name="GMAP" version="2.0.1"> - <description>Genomic Mapping and Alignment Program for mRNA and EST sequences</description> - <requirements> - <requirement type="binary">gmap</requirement> - </requirements> - <version_string>gmap --version</version_string> - <command> - #import os,os.path - gmap - --nthreads=4 --ordered - #if $refGenomeSource.genomeSource == "history": - --gseg=$refGenomeSource.ownFile - #elif $refGenomeSource.genomeSource == "gmapdb": - #set $gmapdb = $os.listdir($refGenomeSource.gmapdb.extra_files_path)[0] - --dir=$refGenomeSource.gmapdb.extra_files_path --db=$gmapdb - #if $refGenomeSource.kmer != None and len($refGenomeSource.kmer.__str__) == 2: - --kmer=$refGenomeSource.kmer - #end if - #else: - --dir=$os.path.dirname($refGenomeSource.gmapindex.value) --db=$os.path.basename($refGenomeSource.gmapindex.value) - #if $refGenomeSource.kmer != None and len($refGenomeSource.kmer.__str__) == 2: - --kmer=$refGenomeSource.kmer - #end if - #end if - #if $result.format == "summary": - --summary - #elif $result.format == "align": - --align - #elif $result.format == "continuous": - --continuous - #elif $result.format == "continuous-by-exon": - --continuous-by-exon - #elif $result.format == "compress": - --compress - #elif $result.format == "exons_dna": - --exons=cdna - #elif $result.format == "exons_gen": - --exons=genomic - #elif $result.format == "protein_dna": - --protein_dna - #elif $result.format == "protein_gen": - --protein_gen - #elif $result.format == "sam": - --format=$result.sam_paired_read - $result.no_sam_headers - #* Removed in gmap version 2011-11-30 - #if len($result.noncanonical_splices.__str__) > 0 - --noncanonical-splices=$result.noncanonical_splices - #end if - *# - #if len($result.read_group_id.__str__) > 0 - --read-group-id=$result.read_group_id - #end if - #if len($result.read_group_name.__str__) > 0 - --read-group-name=$result.read_group_name - #end if - #if len($result.read_group_library.__str__) > 0 - --read-group-library=$result.read_group_library - #end if - #if len($result.read_group_platform.__str__) > 0 - --read-group-platform=$result.read_group_platform - #end if - #elif $result.format != "gmap": - --format=$result.format - #end if - #if $computation.options == "advanced": - $computation.nosplicing - $computation.cross_species - #if len($computation.min_intronlength.__str__) > 0 - --min-intronlength=$computation.min_intronlength - #end if - #if len($computation.intronlength.__str__) > 0 - --intronlength=$computation.intronlength - #end if - #if len($computation.localsplicedist.__str__) > 0 - --localsplicedist=$computation.localsplicedist - #end if - #if len($computation.totallength.__str__) > 0 - --totallength=$computation.totallength - #end if - #if len($computation.trimendexons.__str__) > 0 - --trimendexons=$computation.trimendexons - #end if - --direction=$computation.direction - --canonical-mode=$computation.canonical - --prunelevel=$computation.prunelevel - --allow-close-indels=$computation.allow_close_indels - #if len($computation.microexon_spliceprob.__str__) >= 0: - --microexon-spliceprob=$computation.microexon_spliceprob - #end if - #if len($computation.chimera_margin.__str__) >= 0: - --chimera-margin=$computation.chimera_margin - #end if - #end if - #if $advanced.options == "used": - #if len($advanced.npaths.__str__) > 0: - --npaths=$advanced.npaths - #end if - #if len($advanced.suboptimal_score.__str__) > 0: - --suboptimal-score=$advanced.suboptimal_score - #end if - #if len($advanced.chimera_overlap.__str__) > 0: - --chimera_overlap=$advanced.chimera_overlap - #end if - $advanced.protein - $advanced.tolerant - $advanced.nolengths - $advanced.invertmode - #if len($advanced.introngap.__str__) > 0: - --introngap=$advanced.introngap - #end if - #if len($advanced.wraplength.__str__) > 0: - --wraplength=$advanced.wraplength - #end if - #end if - #if $split_output == True - $split_output - #end if - #if len($quality_protocol.__str__) > 0: - --quality-protocol=$quality_protocol - #end if - $input - #for $i in $inputs: - ${i.added_input} - #end for - #if $split_output == True - 2> $gmap_stderr - #else - 2> $gmap_stderr > $output - #end if - </command> - <inputs> - <!-- Input data --> - <param name="input" type="data" format="fasta,fastqsanger,fastqillumina" label="<H2>Input Sequences</H2>Select an mRNA or EST dataset to map" /> - <repeat name="inputs" title="addtional mRNA or EST dataset to map"> - <param name="added_input" type="data" format="fasta,fastqsanger,fastqillumina" label=""/> - </repeat> - <param name="quality_protocol" type="select" label="Protocol for input quality scores"> - <option value="">No quality scores</option> - <option value="sanger">Sanger quality scores</option> - <option value="illumina">Illumina quality scores</option> - </param> - - <!-- GMAPDB for mapping --> - <conditional name="refGenomeSource"> - <param name="genomeSource" type="select" label="<HR><H2>Map To</H2>Will you map to a reference genome from your history or use a built-in index?" help="Built-ins were indexed using default options"> - <option value="indexed">Use a built-in index</option> - <option value="gmapdb">Use gmapdb from the history</option> - <option value="history">Use a fasta reference sequence from the history</option> - </param> - <when value="indexed"> - <param name="gmapindex" type="select" label="Select a reference genome" help="if your genome of interest is not listed - contact Galaxy team"> - <options from_file="gmap_indices.loc"> - <column name="uid" index="0" /> - <column name="dbkey" index="1" /> - <column name="name" index="2" /> - <column name="kmers" index="3" /> - <column name="maps" index="4" /> - <column name="snps" index="5" /> - <column name="value" index="6" /> - </options> - </param> - <param name="kmer" type="select" data_ref="gmapindex" label="kmer size" help="Defaults to highest available kmer size"> - <options from_file="gmap_indices.loc"> - <column name="name" index="3"/> - <column name="value" index="3"/> - <filter type="param_value" ref="gmapindex" column="6"/> - <filter type="multiple_splitter" column="3" separator=","/> - <filter type="add_value" name="" value=""/> - <filter type="sort_by" column="3"/> - </options> - </param> - <param name="map" type="select" data_ref="gmapindex" label="Look for splicing involving known sites or known introns" help=""> - <options from_file="gmap_indices.loc"> - <column name="name" index="4"/> - <column name="value" index="4"/> - <filter type="param_value" ref="gmapindex" column="6"/> - <filter type="multiple_splitter" column="4" separator=","/> - <filter type="add_value" name="" value=""/> - <filter type="sort_by" column="4"/> - </options> - </param> - </when> - <when value="gmapdb"> - <param name="gmapdb" type="data" format="gmapdb" metadata_name="dbkey" label="Select a gmapdb" - help="A GMAP database built with GMAP Build"/> - <param name="kmer" type="select" data_ref="gmapdb" label="kmer size" help="Defaults to highest available kmer size"> - <options> - <filter type="data_meta" ref="gmapdb" key="kmers" multiple="True" separator=","/> - </options> - </param> - <param name="map" type="select" data_ref="gmapdb" label="Use map for splicing involving known sites or known introns" help=""> - <options> - <filter type="data_meta" ref="gmapdb" key="maps" multiple="True"/> - </options> - </param> - </when> - <when value="history"> - <param name="ownFile" type="data" format="fasta" metadata_name="dbkey" label="Select the reference genome" - help="Fasta containing genomic DNA sequence"/> - </when> - </conditional> - - - <!-- Computation options --> - <conditional name="computation"> - <param name="options" type="select" label="<HR>Computational Settings" help=""> - <option value="default">Use default settings</option> - <option value="advanced">Set Computation Options</option> - </param> - <when value="default"/> - <when value="advanced"> - <param name="nosplicing" type="boolean" truevalue="--nosplicing" falsevalue="" checked="false" label="Turn off splicing" help="(useful for aligning genomic sequences onto a genome)"/> - <param name="min_intronlength" type="integer" value="" optional="true" label="Min length for one internal intron (default 9)." help="Below this size, a genomic gap will be considered a deletion rather than an intron." > - <validator type="in_range" message="min_intronlength must be positive" min="0" /> - </param> - <param name="intronlength" type="integer" value="" optional="true" label="Max length for one intron (default 1000000)" > - <validator type="in_range" message="intronlength must be positive" min="0" /> - </param> - <param name="localsplicedist" type="integer" value="" optional="true" label="Max length for known splice sites at ends of sequence (default 200000)" > - <validator type="in_range" message="localsplicedist must be positive" min="0" /> - </param> - <param name="totallength" type="integer" value="" optional="true" label="Max total intron length (default 2400000)" > - <validator type="in_range" message="totallength must be positive" min="0" /> - </param> - <param name="chimera_margin" type="integer" value="" optional="true" label="Amount of unaligned sequence that triggers search for a chimera" - help=" default is 40, To turn off, set to a large value (greater than the query length)" > - <validator type="in_range" message="chimera_margin must be positive" min="0" /> - </param> - <param name="direction" type="select" label="cDNA direction"> - <option value="auto">auto</option> - <option value="sense_force">sense_force</option> - <option value="antisense_force">antisense_force</option> - <option value="sense_filter">sense_filter</option> - <option value="antisense_filter">antisense_filter</option> - </param> - <param name="trimendexons" type="integer" value="" optional="true" label="Trim end exons with fewer than given number of matches (in nt, default 12)" > - <validator type="in_range" message="trimendexons must be positive" min="1" /> - </param> - <param name="cross_species" type="boolean" truevalue="--cross-species" falsevalue="" checked="false" label="Cross-species alignment" help="For cross-species alignments, use a more sensitive search for canonical splicing"/> - - <param name="canonical" type="select" label="Reward for canonical and semi-canonical introns"> - <option value="1">high reward (default)</option> - <option value="0">low reward</option> - <option value="2">low reward for high-identity sequences</option> - </param> - <param name="allow_close_indels" type="select" label="Allow an insertion and deletion close to each other"> - <option value="1" selected="true">yes (default)</option> - <option value="0">no</option> - <option value="2">only for high-quality alignments</option> - </param> - <param name="microexon_spliceprob" type="float" value="" optional="true" label="Micro Exon splice probablility threshold" - help="Allow microexons only if one of the splice site probabilities is greater than this value (default 0.90)" > - <validator type="in_range" message="slice probability between 0.00 and 1.00" min="0" max="1"/> - </param> - <param name="prunelevel" type="select" label="Pruning level"> - <option value="0">no pruning (default)</option> - <option value="1">poor sequences</option> - <option value="2">repetitive sequences</option> - <option value="3">poor and repetitive sequences</option> - </param> - <!-- could do this as a config file - <param name="chrsubsetfile" type="data" format="fasta" label="User-supplied chromosome subset file" /> - <param name="chrsubset" type="text" label="Chromosome subset to search" /> - --> - </when> - </conditional> - - <!-- Advanced Settings --> - <conditional name="advanced"> - <param name="options" type="select" label="<HR>Advanced Settings" help=""> - <option value="default">Use default settings</option> - <option value="used">Set Options</option> - </param> - <when value="default"/> - <when value="used"> - <param name="nolengths" type="boolean" checked="false" truevalue="--nolengths=true" falsevalue="" label="No intron lengths in alignment"/> - <param name="invertmode" type="select" label=" Mode for alignments to genomic (-) strand" help=""> - <option value="">Don't invert the cDNA (default)</option> - <option value="--invertmode=1">Invert cDNA and print genomic (-) strand</option> - <option value="--invertmode=2">Invert cDNA and print genomic (+) strand</option> - </param> - <param name="introngap" type="integer" value="" optional="true" label="Nucleotides to show on each end of intron (default=3)"> - <validator type="in_range" message="introngap must be positive" min="0" /> - </param> - <param name="wraplength" type="integer" value="" optional="true" label="Line Wrap length for alignment (default=50)"> - <validator type="in_range" message="wraplength must be positive" min="1" /> - </param> - <param name="npaths" type="integer" value="" optional="true" - label="Maximum number of paths to show. Ignored if negative. If 0, prints two paths if chimera detected, else one." > - <validator type="in_range" message="npaths must be positive" min="0" /> - </param> - <param name="suboptimal_score" type="integer" value="" optional="true" - label="Report only paths whose score is within this value of the best path" - help="By default the program prints all paths found." > - <validator type="in_range" message="suboptimal_score must be positive" min="0" /> - </param> - <param name="chimera_overlap" type="integer" value="" optional="true" label="Overlap to show, if any, at chimera breakpoint (default 0)" > - <validator type="in_range" message="chimera_overlap must be positive" min="0" /> - </param> - <param name="tolerant" type="boolean" checked="false" truevalue="--tolerant=true" falsevalue="" - label="Translates cDNA with corrections for frameshifts"/> - <param name="protein" type="select" label="Protein alignment" help=""> - <option value="">default</option> - <option value="--fulllength=true">Assume full-length protein, starting with Met</option> - <option value="--truncate=true">Truncate alignment around full-length protein, Met to Stop</option> - </param> - </when> - </conditional> - - <!-- Output data --> - <conditional name="result"> - <param name="format" type="select" label="<HR><H2>Output</H2>Select the output format" help=""> - <option value="gmap">GMAP default output</option> - <option value="summary">Summary of alignments</option> - <option value="align">Alignment</option> - <option value="continuous">Alignment in three continuous lines</option> - <option value="continuous-by-exon">Alignment in three lines per exon</option> - <option value="compress">Print output in compressed format</option> - <option value="exons_dna">Print exons cDNA</option> - <option value="exons_gen">Print exons genomic</option> - <option value="protein_dna">Print protein sequence (cDNA)</option> - <option value="protein_gen">Print protein sequence (genomic)</option> - <option value="psl">PSL (BLAT) format</option> - <option value="gff3_gene">GFF3 gene format</option> - <option value="gff3_match_cdna">GFF3 match cDNA format</option> - <option value="gff3_match_est">GFF3 match EST format</option> - <option value="splicesites">splicesites output (for GSNAP)</option> - <option value="introns">introns output (for GSNAP)</option> - <option value="map_exons">IIT FASTA exon map format</option> - <option value="map_genes">IIT FASTA map format</option> - <option value="coords">coords in table format</option> - <option value="sam" selected="true">SAM format</option> - </param> - <when value="gmap"> - </when> - <when value="summary"/> - <when value="align"> - </when> - <when value="continuous"> - </when> - <when value="continuous-by-exon"> - </when> - <when value="compress"/> - <when value="exons_dna"/> - <when value="exons_gen"/> - <when value="protein_dna"/> - <when value="protein_gen"/> - <when value="psl"/> - <when value="gff3_gene"/> - <when value="gff3_match_cdna"/> - <when value="gff3_match_est"/> - <when value="splicesites"/> - <when value="introns"/> - <when value="map_exons"/> - <when value="map_genes"/> - <when value="coords"/> - <when value="sam"> - <param name="sam_paired_read" type="boolean" truevalue="sampe" falsevalue="samse" checked="false" label="SAM paired reads"/> - <param name="no_sam_headers" type="boolean" truevalue="--no-sam-headers" falsevalue="" checked="false" label="Do not print headers beginning with '@'"/> - <!-- Removed in gmap version 2011-11-30 - <param name="noncanonical_splices" type="select" label="Print non-canonical genomic gaps greater than 20 nt in CIGAR string as STRING."> - <option value="">Use default</option> - <option value="N">N</option> - <option value="D">D</option> - </param> - --> - <param name="read_group_id" type="text" value="" label="Value to put into read-group id (RG-ID) field"/> - <param name="read_group_name" type="text" value="" label="Value to put into read-group name (RG-SM) field"/> - <param name="read_group_library" type="text" value="" label="Value to put into read-group library (RG-LB) field"/> - <param name="read_group_platform" type="text" value="" label="Value to put into read-group library platform (RG-PL) field"/> - </when> - </conditional> <!-- name="result" --> - - <param name="split_output" type="boolean" truevalue="--split-output=gmap_out" falsevalue="" checked="false" label="Separate outputs for nomapping, uniq, mult, and chimera" help="(chimera only when chimera-margin is selected)"/> - - - <!-- - map=iitfile Map file. If argument is '?' (with the quotes), this lists available map files. - mapexons Map each exon separately - mapboth Report hits from both strands of genome - flanking=INT Show flanking hits (default 0) - print-comment Show comment line for each hit - --> - - - </inputs> - <outputs> - <data format="txt" name="gmap_stderr" label="${tool.name} on ${on_string}: stderr"/> - <data format="txt" name="output" label="${tool.name} on ${on_string} ${result.format}" > - <filter>(split_output == False)</filter> - <change_format> - <when input="result['format']" value="gff3_gene" format="gff3"/> - <when input="result['format']" value="gff3_match_cdna" format="gff3"/> - <when input="result['format']" value="gff3_match_est" format="gff3"/> - <when input="result['format']" value="sam" format="sam"/> - <when input="result['format']" value="splicesites" format="gmap_splicesites"/> - <when input="result['format']" value="introns" format="gmap_introns"/> - <when input="result['format']" value="map_genes" format="gmap_annotation"/> - <when input="result['format']" value="map_exons" format="gmap_annotation"/> - </change_format> - </data> - <data format="txt" name="uniq" label="${tool.name} on ${on_string} uniq.${result.format}" from_work_dir="gmap_out.uniq"> - <filter>(split_output == True)</filter> - <change_format> - <when input="result['format']" value="gff3_gene" format="gff3"/> - <when input="result['format']" value="gff3_match_cdna" format="gff3"/> - <when input="result['format']" value="gff3_match_est" format="gff3"/> - <when input="result['format']" value="sam" format="sam"/> - <when input="result['format']" value="splicesites" format="gmap_splicesites"/> - <when input="result['format']" value="introns" format="gmap_introns"/> - <when input="result['format']" value="map_genes" format="gmap_annotation"/> - <when input="result['format']" value="map_exons" format="gmap_annotation"/> - </change_format> - </data> - <data format="txt" name="transloc" label="${tool.name} on ${on_string} transloc.${result.format}" from_work_dir="gmap_out.transloc"> - <filter>(split_output == True)</filter> - <change_format> - <when input="result['format']" value="gff3_gene" format="gff3"/> - <when input="result['format']" value="gff3_match_cdna" format="gff3"/> - <when input="result['format']" value="gff3_match_est" format="gff3"/> - <when input="result['format']" value="sam" format="sam"/> - <when input="result['format']" value="splicesites" format="gmap_splicesites"/> - <when input="result['format']" value="introns" format="gmap_introns"/> - <when input="result['format']" value="map_genes" format="gmap_annotation"/> - <when input="result['format']" value="map_exons" format="gmap_annotation"/> - </change_format> - </data> - <data format="txt" name="nomapping" label="${tool.name} on ${on_string} nomapping.${result.format}" from_work_dir="gmap_out.nomapping"> - <filter>(split_output == True)</filter> - <change_format> - <when input="result['format']" value="gff3_gene" format="gff3"/> - <when input="result['format']" value="gff3_match_cdna" format="gff3"/> - <when input="result['format']" value="gff3_match_est" format="gff3"/> - <when input="result['format']" value="sam" format="sam"/> - <when input="result['format']" value="splicesites" format="gmap_splicesites"/> - <when input="result['format']" value="introns" format="gmap_introns"/> - <when input="result['format']" value="map_genes" format="gmap_annotation"/> - <when input="result['format']" value="map_exons" format="gmap_annotation"/> - </change_format> - </data> - <data format="txt" name="mult" label="${tool.name} on ${on_string} mult.${result.format}" from_work_dir="gmap_out.mult"> - <filter>(split_output == True)</filter> - <change_format> - <when input="result['format']" value="gff3_gene" format="gff3"/> - <when input="result['format']" value="gff3_match_cdna" format="gff3"/> - <when input="result['format']" value="gff3_match_est" format="gff3"/> - <when input="result['format']" value="sam" format="sam"/> - <when input="result['format']" value="splicesites" format="gmap_splicesites"/> - <when input="result['format']" value="introns" format="gmap_introns"/> - <when input="result['format']" value="map_genes" format="gmap_annotation"/> - <when input="result['format']" value="map_exons" format="gmap_annotation"/> - </change_format> - </data> - </outputs> - <tests> - </tests> - - <help> - -**What it does** - -GMAP_ (Genomic Mapping and Alignment Program) The functionality provided by gmap allows a user to: (1) map and align a single cDNA interactively against a large genome in about a second, without the startup time of several minutes typically needed by existing mapping programs; (2) switch arbitrarily among different genomes, without the need for a preloaded server dedicated to each genome; (3) run the program on computers with as little as 128 MB of RAM (random access memory); (4) perform high-throughput batch processing of cDNAs by using memory mapping and multithreading when appropriate memory and hardware are available; (5) generate accurate gene models, even in the presence of substantial polymorphisms and sequence errors; (6) locate splice sites accurately without the use of probabilistic splice site models, allowing generalized use of the program across species; (7) detect statistically significant microexons and incorporate them into the alignment; and (8) handle mapping and alignment tasks on genomes having alternate assemblies, linkage groups or strains. It is developed by Thomas D. Wu of Genentech, Inc. - -Publication_ citation: Thomas D. Wu, Colin K. Watanabe Bioinformatics 2005 21(9):1859-1875; doi:10.1093/bioinformatics/bti310 - -.. _GMAP: http://research-pub.gene.com/gmap/ -.. _Publication: http://bioinformatics.oxfordjournals.org/cgi/content/full/21/9/1859 - ------- - -**Know what you are doing** - -.. class:: warningmark - -You will want to read the README_ - -.. _README: http://research-pub.gene.com/gmap/src/README - - </help> -</tool> -