Mercurial > repos > jjohnson > gmap
diff gmap.xml @ 3:488e9d642566 draft
GMAP wrappers v3.0.1 after linting and cleanup, still untested work-in-progress
| author | peterjc |
|---|---|
| date | Wed, 28 Sep 2016 10:47:28 -0400 |
| parents | f6ba0f12cca2 |
| children | 14561eb803a5 |
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--- a/gmap.xml Wed Sep 28 10:43:44 2016 -0400 +++ b/gmap.xml Wed Sep 28 10:47:28 2016 -0400 @@ -1,9 +1,9 @@ -<tool id="gmap" name="GMAP" version="3.0.0"> +<tool id="gmap" name="GMAP" version="3.0.1"> <description>Genomic Mapping and Alignment Program for mRNA and EST sequences</description> <requirements> <requirement type="package" version="2013-05-09">gmap</requirement> </requirements> - <version_string>gmap --version</version_string> + <version_command>gmap --version</version_command> <command> #import os,os.path gmap @@ -41,7 +41,7 @@ --protein_gen #elif $result.format == "sam": --format=$result.sam_paired_read - $result.no_sam_headers + $result.no_sam_headers $result.sam_use_0M $result.force_xs_dir $result.md_lowercase_snp @@ -127,7 +127,7 @@ ${i.added_input} #end for #if $split_output == True - 2> $gmap_stderr + 2> $gmap_stderr #else 2> $gmap_stderr > $output #end if @@ -194,7 +194,7 @@ </param> </when> <when value="gmapdb"> - <param name="gmapdb" type="data" format="gmapdb" metadata_name="dbkey" label="Select a gmapdb" + <param name="gmapdb" type="data" format="gmapdb" 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> @@ -208,12 +208,12 @@ </param> </when> <when value="history"> - <param name="ownFile" type="data" format="fasta" metadata_name="dbkey" label="Select the reference genome" + <param name="ownFile" type="data" format="fasta" 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=""> @@ -223,56 +223,56 @@ <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." > + <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)" > + <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)" > + <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)" > + <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 0" > + <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 0" > <validator type="in_range" message="chimera_margin must be positive" min="0" /> </param> - <param name="direction" type="select" label="cDNA direction"> + <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)" > + <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="find_shifted_canonical" type="boolean" truevalue="--find-shifted-canonical-species" falsevalue="" checked="false" label="find-shifted-canonical Use a more sensitive search for canonical splicing" help=""/> <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"> + + <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"> + <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 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"> + <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 + <!-- 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" /> --> @@ -293,25 +293,25 @@ <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)"> + <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)"> + <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." > + 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." > + 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)" > + <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="" + <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> @@ -383,9 +383,9 @@ <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"/> <param name="sam_use_0M" type="boolean" truevalue="--sam-use-0M" falsevalue="" checked="false" label="Insert 0M in CIGAR between adjacent insertions and deletions" help="Required by Picard, but can cause errors in other tools"/> - <param name="force_xs_dir" type="boolean" truevalue="--force-xs-dir" falsevalue="" checked="false" label="Force direction (disallow XS:A:?)" + <param name="force_xs_dir" type="boolean" truevalue="--force-xs-dir" falsevalue="" checked="false" label="Force direction (disallow XS:A:?)" help="For RNA-Seq alignments, disallows XS:A:? when the sense direction is unclear, and replaces this value arbitrarily with XS:A:+. May be useful for some programs, such as Cufflinks, that cannot handle XS:A:?. However, if you use this flag, the reported value of XS:A:+ in these cases will not be meaningful."/> - <param name="md_lowercase_snp" type="boolean" truevalue="--md-lowercase-snp" falsevalue="" checked="false" label="MD lowercase SNP" + <param name="md_lowercase_snp" type="boolean" truevalue="--md-lowercase-snp" falsevalue="" checked="false" label="MD lowercase SNP" help="In MD string, when known SNPs are given by the -v flag, prints difference nucleotides as lower-case when they, differ from reference but match a known alternate allele"/> </when> </conditional> <!-- name="result" --> @@ -393,7 +393,7 @@ <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 @@ -401,7 +401,7 @@ print-comment Show comment line for each hit --> - <!-- + <!-- min-trimmed-coverage=FLOAT Do not print alignments with trimmed coverage less this value (default=0.0, which means no filtering) Note that chimeric alignments will be output regardless @@ -484,13 +484,13 @@ </data> </outputs> <tests> - </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. +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 @@ -506,7 +506,9 @@ You will want to read the README_ .. _README: http://research-pub.gene.com/gmap/src/README - </help> + <citations> + <citation type="doi">10.1093/bioinformatics/bti310</citation> + </citations> </tool>