gmap: gsnap.xml comparison

comparison gsnap.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

comparison

equal deleted inserted replaced

-:f6ba0f12cca2
+:488e9d642566
-<tool id="gsnap" name="GSNAP" version="3.0.0">
+<tool id="gsnap" name="GSNAP" version="3.0.1">
 <description>Genomic Short-read Nucleotide Alignment Program</description>
 <requirements>
 <requirement type="package" version="2013-05-09">gmap</requirement>
 </requirements>
-<version_string>gsnap --version</version_string>
+<version_command>gsnap --version</version_command>
 <command>
 #import os.path, re
 gsnap
 --nthreads="4" --ordered
 #if $refGenomeSource.genomeSource == "gmapdb":
 #if $output.options == "advanced":
 #if $output.npath.__str__ != '':
 --npath=$output.npath
 #end if
 #if $output.maxsearch.__str__ != '':
 --maxsearch=$output.maxsearch
 #end if
 $output.quiet_if_excessive
 $output.show_refdiff
 $output.clip_overlap
 #end if
 <option value="RF">rev-fwd, for circularized inserts</option>
 <option value="FF">fwd-fwd, same strand</option>
 </param>
 <param name="pairmax_dna"  type="integer" value="" optional="true" label="Max total genomic length for DNA-Seq paired reads, or other reads without splicing (default 1000)." help="Used if no splice file is provided and novelsplicing is off."/>
 <param name="pairmax_rna"  type="integer" value="" optional="true" label="Max total genomic length for RNA-Seq paired reads, or other reads that could have a splice (default 200000)." help="Used when novel splicing is specified or a splice file is provided.  Should probably match the value for localsplicedist."/>
 <param name="pairexpect"  type="integer" value="" optional="true" label="Expected paired-end length"
 help="Used for calling splices in medial part of paired-end reads (default 200)"/>
 <param name="pairdev"  type="integer" value="" optional="true" label="Allowable deviation from expected paired-end length"
 help="Used for calling splices in medial part of paired-end reads (default 25)"/>
 </when>
 </conditional>
 <param name="barcode_length" type="integer" value="" optional="true"  label="Amount of barcode to remove from start of read (default 0)" />
 <param name="fastq_id_start" type="integer" value="" optional="true"  label="Starting field  of identifier in FASTQ header, whitespace-delimited, starting from 1" />
 <param name="fastq_id_end" type="integer" value="" optional="true"  label="Ending field  of identifier in FASTQ header, whitespace-delimited, starting from 1"
 help="Examples:
 &lt;br&gt;@HWUSI-EAS100R:6:73:941:1973#0/1
 &lt;br&gt; . start=1, end=1 (default)  => identifier is HWUSI-EAS100R:6:73:941:1973#0/1
 &lt;br&gt;@SRR001666.1 071112_SLXA-EAS1_s_7:5:1:817:345 length=36
 &lt;br&gt; . start=1, end=1  => identifier is SRR001666.1
 &lt;br&gt; . start=2, end=2  => identifier is 071112_SLXA-EAS1_s_7:5:1:817:345
 &lt;br&gt; . start=1, end=2  => identifier is SRR001666.1 071112_SLXA-EAS1_s_7:5:1:817:345"
 />
 <param name="filter_chastity" type="select" label="Skip reads marked by the Illumina chastity program"
 help="String after the accession having a  'Y'  after the first colon, like this:
 &lt;br&gt;@accession 1:Y:0:CTTGTA
 &lt;br&gt;where the  'Y'  signifies filtering by chastity.
 &lt;br&gt; For 'either', a  'Y'  on either end of a paired-end read will be filtered.
 &lt;br&gt;  For 'both', a  'Y'  is required on both ends of a paired-end read (or on the only end of a single-end read)"
 >
 -->
 <when value="gsnap_fasta">
 <param name="gsnap" type="data" format="fasta" label="Select a single-end dataset" help="GSNAP fasta must have the sequence entirely on one line, a second line is interpreted as the paired-end sequence"/>
 <param name="circularinput" type="boolean" checked="false" truevalue="--circular-input=true" falsevalue="" label="Circular-end data (paired reads are on same strand)"/>
 </when>
 </conditional>
 <!-- No longer in options as of version 2011-11-30
 <param name="mapq_unique_score"  type="integer" value="" optional="true" label="MAPQ score threshold"
 help="For multiple results, consider as a unique result if only one of the results has a MAPQ score equal or greater than this
 (if not selected, then reports all multiple results, up to npaths)" />
 -->
 <!-- GMAPDB for alignment -->
 <option value="atoi-stranded">atoi-stranded   for RNA-editing tolerance (A-to-G changes)</option>
 <option value="atoi-nonstranded">atoi-nonstranded   for RNA-editing tolerance (A-to-G changes)</option>
 </param>
 <conditional name="use_splicing">
 <param name="src" type="select" label="&lt;HR&gt;Known Splicesite and Introns"
 help="Look for splicing involving known sites or known introns at short or long distances
 See README instructions for the distinction between known sites and known introns">
 <option value="none" selected="true">None</option>
 <option value="gmapdb">From the GMAP Database</option>
 <option value="history">A Map in your history</option>
 </param>
 <when value="none"/>
 <when value="history">
-<param name="splicemap" type="data" format="splicesites.iit,introns.iit" metadata_name="dbkey" label="Select a splicesite map"
+<param name="splicemap" type="data" format="splicesites.iit,introns.iit" label="Select a splicesite map"
 help="built with GMAP IIT"/>
 </when>
 <when value="gmapdb">
 <param name="splicemap" type="select" data_ref="gmapindex" label="Use map for splicing involving known sites or known introns" help="">
 <options from_file="gmap_indices.loc">
 <option value="gmapdb">From the GMAP Database</option>
 <option value="history">A SNP Index in your history</option>
 </param>
 <when value="none"/>
 <when value="history">
-<param name="snpindex" type="data" format="gmapsnpindex" metadata_name="dbkey" label="Select a snpindex"
+<param name="snpindex" type="data" format="gmapsnpindex" label="Select a snpindex"
 help="built with GMAP SNP Index"/>
 </when>
 <when value="gmapdb">
 <param name="snpindex" type="select" data_ref="gmapindex" label="Use database containing known SNPs" help="">
 <options from_file="gmap_indices.loc">
 </when>
 </conditional>
 </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>
 <filter type="data_meta" ref="gmapdb" key="kmers" multiple="True" separator=","/>
 </options>
 <option value="atoi-stranded">atoi-stranded   for RNA-editing tolerance (A-to-G changes)</option>
 <option value="atoi-nonstranded">atoi-nonstranded   for RNA-editing tolerance (A-to-G changes)</option>
 </param>
 <conditional name="use_splicing">
 <param name="src" type="select" label="&lt;HR&gt;Known Splicesite and Introns"
 help="Look for splicing involving known sites or known introns at short or long distances
 See README instructions for the distinction between known sites and known introns">
 <option value="none" selected="true">None</option>
 <option value="gmapdb">From the GMAP Database</option>
 <option value="history">A Map in your history</option>
 </param>
 <when value="none"/>
 <when value="history">
-<param name="splicemap" type="data" format="splicesites.iit,introns.iit" metadata_name="dbkey" label="Select a splicesite map"
+<param name="splicemap" type="data" format="splicesites.iit,introns.iit" label="Select a splicesite map"
 help="built with GMAP IIT"/>
 <param name="ambig_splice_noclip"  type="boolean" checked="false" truevalue="--ambig-splice-noclip" falsevalue="" label="Do not clip at ambiguous splice sites"
 help="For ambiguous known splicing at ends of the read, do not clip at the splice site, but extend instead into the intron.
 This flag makes sense only if you are trying to eliminate all soft clipping with --trim-mismatch-score=0"/>
 </when>
 <when value="gmapdb">
 <param name="splicemap" 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>
 <param name="ambig_splice_noclip"  type="boolean" checked="false" truevalue="--ambig-splice-noclip" falsevalue="" label="Do not clip at ambiguous splice sites"
 help="For ambiguous known splicing at ends of the read, do not clip at the splice site, but extend instead into the intron.
 This flag makes sense only if you are trying to eliminate all soft clipping with --trim-mismatch-score=0"/>
 </when>
 </conditional>
 <conditional name="use_snps">
 <option value="gmapdb">From the GMAP Database</option>
 <option value="history">A SNP Index in your history</option>
 </param>
 <when value="none"/>
 <when value="history">
-<param name="snpindex" type="data" format="gmapsnpindex" metadata_name="dbkey" label="Select a snpindex"
+<param name="snpindex" type="data" format="gmapsnpindex" label="Select a snpindex"
 help="built with GMAP SNP Index"/>
 </when>
 <when value="gmapdb">
 <param name="snpindex" type="select"  data_ref="gmapdb" label="Use database containing known SNPs" help="">
 <options>
 <option value="default">Use default settings</option>
 <option value="advanced">Set Computation Options</option>
 </param>
 <when value="default"/>
 <when value="advanced">
 <param name="max_mismatches" type="float" value="" optional="true" label="Maximum number of mismatches allowed (uses default when negative)"
 help="Maximum number of mismatches allowed (if not specified, then
 defaults to the ultrafast level of ((readlength+index_interval-1)/kmer - 2))
 (By default, the genome index interval is 3, but this can be changed
 by providing a different value for -q to gmap_build when processing the genome.)
 		    If specified between 0.0 and 1.0, then treated as a fraction
 <param name="maxsearch" type="integer" value="" optional="true" label="Maximum number of alignments to find (default 1000)"
 help="Must be larger than paths, which is the number to report.
 Keeping this number large will allow for random selection among multiple alignments.
 Reducing this number can speed up the program. "/>
 <param name="terminal_threshold"  type="integer" value="" optional="true" label="Threshold for searching for a terminal alignment"
 help="Threshold for searching for a terminal alignment (from one end of the
 read to the best possible position at the other end) (default 2
 for standard, atoi-stranded, and atoi-nonstranded mode; default 100
 for cmet-stranded and cmet-nonstranded mode).
 For example, if this value is 2, then if GSNAP finds an exact or
 obtain terminal alignments for very short reads, although such reads
 probably don't have enough specificity for terminal alignments anyway.
 To turn off terminal alignments, set this to a high value, greater
 than the value for max-mismatches.
 "/>
 <param name="indel_penalty"  type="integer" value="" optional="true" label="Penalty for an indel (default 2)"
 help="Counts against mismatches allowed.  To find indels, make indel-penalty less than or equal to max-mismatches.  A value &lt; 2 can lead to false positives at read ends" />
 <param name="indel_endlength"  type="integer" value="" optional="true" label="Minimum length at end required for indel alignments (default 4)" />
 <param name="max_middle_insertions"  type="integer" value="" optional="true" label="Maximum number of middle insertions allowed (default 9)" />
 <param name="max_middle_deletions"  type="integer" value="" optional="true" label="Maximum number of middle deletions allowed (default 30)" />
 <param name="max_end_insertions"  type="integer" value="" optional="true" label="Maximum number of end insertions allowed (default 3)" />
 <param name="max_end_deletions"  type="integer" value="" optional="true" label="Maximum number of end deletions allowed (default 6)" />
 <param name="suboptimal_levels"  type="integer" value="" optional="true" label="Report suboptimal hits beyond best hit (default 0)"
 help="All hits with best score plus suboptimal-levels are reported" />
 <param name="adapter_strip"  type="select" label="Method for removing adapters from reads"
 help="Default is 'off'.  To turn on, specify 'paired', which removes adapters
 from paired-end reads if they appear to be present.">
 <option value="paired">paired</option>
 <option value="off" selected="true">off</option>
 </param>
 <param name="trim_mismatch_score" type="integer" value="" optional="true" label="Score to use for mismatches when trimming at ends (default is -3)"
 help="to turn off trimming, specify 0 (Warning: turning trimming off will give false positive mismatches at the ends of reads)"/>
 <param name="trim_indel_score" type="integer" value="" optional="true" label="Score to use for indels when trimming at ends (default is -4)"
 help="to turn off trimming, specify 0 (Warning: turning trimming off will give false positive indels at the ends of reads)"/>
-<param name="use_tally" type="data" format="tally.iit" optional="true" metadata_name="dbkey" label="Select a tally IIT file to resolve concordant multiple results"
+<param name="use_tally" type="data" format="tally.iit" optional="true" label="Select a tally IIT file to resolve concordant multiple results"
 help="generated by gsnap_tally and iit_store"/>
 <!--
 tallydir=STRING              Directory for tally IIT file to resolve concordant multiple results (default is
 location of genome index files specified using -D and -d).  Note: can
 runlengthdir=STRING          Directory for runlength IIT file to resolve concordant multiple results (default is
 location of genome index files specified using -D and -d).  Note: can
 just give full path name to use-runlength instead.
 use-runlength=STRING         Use this runlength IIT file to resolve concordant multiple results
 -->
 <!-- Options for GMAP alignment within GSNAP -->
 <param name="gmap_mode" type="select" multiple="true" optional="true" display="checkboxes" label="Cases to use GMAP for complex alignments containing multiple splices or indels"
 help="Default: pairsearch,terminal,improve">
 <option value="pairsearch" selected="true">pairsearch</option>
 <option value="indel_knownsplice" selected="true">indel_knownsplice</option>
 <option value="terminal" selected="true">terminal</option>
 <option value="improve" selected="true">improve</option>
 </param>
 <param name="trigger_score_for_gmap" type="integer" value="" optional="true" label="GMAP pairsearch threshold (default 5)"
 help="Try GMAP pairsearch on nearby genomic regions if best score (the total of both ends if paired-end) exceeds this value (default 5)" />
 <param name="max_gmap_pairsearch" type="integer" value="" optional="true" label="GMAP pairsearch threshold (default 3)"
 help="Perform GMAP pairsearch on nearby genomic regions up to this many candidate ends (default 3)." />
 <param name="max_gmap_terminal" type="integer" value="" optional="true" label="GMAP terminal threshold (default 3)"
 help="Perform GMAP terminal on nearby genomic regions up to this many candidate ends (default 3)." />
 <param name="max_gmap_improvement" type="integer" value="" optional="true" label="GMAP improvement threshold (default 3)"
 help="Perform GMAP improvement on nearby genomic regions up to this many candidate ends (default 3)." />
 <param name="microexon_spliceprob"  type="float" value="" optional="true" label="GMAP microexons threshold (default .90)"
 help="Allow microexons only if one of the splice site probabilities is greater than this value." >
 <validator type="in_range" message="The microexons  probability must be between 0. and 1." min="0." max="1."/>
 </param>
 </when>
 </conditional>
 <option value="advanced">Set Splicing Options</option>
 </param>
 <when value="default"/>
 <when value="advanced">
 <!-- Splicing options for RNA-Seq -->
 <!-- use-splicing This should be either a select list from the gmapdb maps or a data type using splicesdir and use-splicing -->
 <!-- Neither novel splicing (-N) nor known splicing (-s) turned on => assume reads are DNA-Seq (genomic) -->
 <param name="novelsplicing" type="boolean" checked="false" truevalue="--novelsplicing=1" falsevalue="" label="Look for novel splicing "/>
 <param name="localsplicedist"  type="integer" value="" optional="true" label="Definition of local novel splicing event (default 200000)"/>
 <param name="local_splice_penalty"  type="integer" value="" optional="true" label="Penalty for a local splice (default 0).  Counts against mismatches allowed"/>
 <param name="distant_splice_penalty"  type="integer" value="" optional="true" label="Penalty for a distant splice (default 3).  Counts against mismatches allowed"
 <param name="distant_splice_endlength"  type="integer" value="" optional="true" label="Minimum length at end required for distant spliced alignments"
 help="(default 16, min is the kmer length)"/>
 <param name="shortend_splice_endlength"  type="integer" value="" optional="true" label="Minimum length at end required for short-end spliced alignments"
 help="(default 2, but unless known splice sites are provided,  GSNAP may still need the end length to be the value of kmer size to find a given splice"/>
 <param name="distant_splice_identity"  type="float" value="" optional="true" label="Minimum identity at end required for distant spliced alignments (default 0.95)"/>
 <param name="antistranded_penalty"  type="integer" value="" optional="true" label="Penalty for antistranded splicing when using stranded RNA-Seq protocols"
 help="A positive value, such as 1, expects antisense on the first read and sense on the second read.
 Default is 0, which treats sense and antisense equally well"/>
 </when>
 </conditional>
 <!-- Output data -->
 <option value="advanced">Set Output Options</option>
 </param>
 <when value="default"/>
 <when value="advanced">
 <param name="npath"  type="integer" value="" optional="true" label="Maximum number of paths to print (default 100)"/>
 <param name="quiet_if_excessive" type="boolean" checked="false" truevalue="--quiet-if-excessive" falsevalue="" label="Quiet if Excessive"
 help="If more than maximum number of paths are found, then nothing is printed."/>
 <param name="show_refdiff" type="boolean" checked="false" truevalue="--show-refdiff" falsevalue="" label="Show SNP-tolerant alignment"
 help="For GSNAP output in SNP-tolerant alignment, shows all differences relative to the reference genome as lower case (otherwise, it shows all differences relative to both the reference and alternate genome)"/>
 <param name="clip_overlap" type="boolean" checked="false" truevalue="--clip-overlap" falsevalue="" label="Clip Overlap"
 help="For paired-end reads whose alignments overlap, clip the overlapping region."/>
 </when>
 </conditional>
 <conditional name="result">
 <param name="format" type="select" label="Select the output format" help="">
 -->
 </conditional>
 <!-- TODO combine fails and split_output -->
 <conditional name="results">
 <param name="split_output" type="select" label="&lt;HR&gt;Split outputs"
 help="Separate outputs for: nomapping, halfmapping_uniq, halfmapping_mult, unpaired_uniq, unpaired_mult, paired_uniq, paired_mult, concordant_uniq, and concordant_mult results">
 <option value="no">no</option>
 <option value="yes">yes</option>
 </param>
 <when value="no">
 <conditional name="fails">
 <option value="failsonly">failsonly - only output failing results</option>
 </param>
 <when value="default"/>
 <when value="nofails"/>
 <when value="failsonly">
 <param name="fails_as_input" type="boolean" truevalue="--fails-as-input" falsevalue="" checked="false" label="Print completely failed alignments as input FASTA or FASTQ format"
 help=""/>
 </when>
 </conditional>
 </when>
 <when value="yes">
 <conditional name="fails">
 </param>
 <when value="default"/>
 <when value="nofails"/>
 <when value="failsonly"/>
 </conditional>
 <param name="fails_as_input" type="boolean" truevalue="--fails-as-input" falsevalue="" checked="false" label="Print completely failed alignments as input FASTA or FASTQ format"
 help=""/>
 </when>
 </conditional>
 </inputs>
 <outputs>
 </data>
 -->
 </outputs>
 <tests>
 </tests>
 <help>
 **What it does**
 GSNAP_ (Genomic Short-read Nucleotide Alignment Program) is a short read aligner which can align both single- and paired-end reads as short as 14nt and of arbitrarily long length. It can detect short- and long-distance splicing, including interchromosomal splicing, in individual reads, using probabilistic models or a database of known splice sites. Our program also permits SNP-tolerant alignment to a reference space of all possible combinations of major and minor alleles, and can align reads from bisulfite-treated DNA for the study of methylation state. It is developed by Thomas D. Wu of Genentech, Inc.
 Publication_ citation: Thomas D. Wu, Serban Nacu "Fast and SNP-tolerant detection of complex variants and splicing in short reads. Bioinformatics. 2010 Apr 1;26(7):873-81. Epub 2010 Feb 10.
 .. _GSNAP: http://research-pub.gene.com/gmap/
 .. _Publication: http://bioinformatics.oupjournals.org/cgi/content/full/26/7/873
-http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2844994/?tool=pubmed
+https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2844994/?tool=pubmed
 ------
 **Know what you are doing**
 ------
 **Input formats**
 Input to GSNAP should be either in FASTQ or FASTA format.
 The FASTQ input may include quality scores, which will then be included in SAM
 output, if that output format is selected.
 For FASTA format, you should include one line per read (or end of a
 paired-end read).  The same FASTA file can have a mixture of
 single-end and paired-end reads of varying lengths, if desired.
 SAM output format
 Default GSNAP format
 See the README_
 </help>
+<citations>
+<citation type="doi">10.1093/bioinformatics/btq057</citation>
+</citations>
 </tool>

Mercurial > repos > jjohnson > gmap

comparison gsnap.xml @ 3:488e9d642566 draft