Mercurial > repos > iuc > vsearch
diff search.xml @ 0:fae6527990af draft
Imported from capsule None
| author | iuc |
|---|---|
| date | Thu, 21 May 2015 03:58:09 -0400 |
| parents | |
| children | f29e21388219 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/search.xml Thu May 21 03:58:09 2015 -0400 @@ -0,0 +1,391 @@ +<tool id="vsearch_search" name="VSearch search" version="@VERSION@.0"> + <description></description> + <macros> + <import>vsearch_macros.xml</import> + </macros> + <expand macro="requirements" /> + <expand macro="stdio" /> + <expand macro="version_command" /> + <command> +<![CDATA[ + vsearch + + @GENERAL@ + --db $dbfile + --dbmask $dbmask + + ##--fulldp full dynamic programming alignment (always on) + ##--gapext STRING penalties for gap extension (2I/1E) + ##--gapopen STRING penalties for gap opening (20I/2E) + $hardmask + --id $id + --iddef $iddef + + #if $qmask != 'no': + --qmask $qmask + #end if + + ## --rowlen INT width of alignment lines in alnout output (64) + + $self_param + $selfid_param + #if $sizeout: + --sizeout $sizeout + #end if + --strand $strand + --usearch_global $queryfile + + #if '--alnout' in str($outputs): + --alnout $alnout + #end if + #if '--blast6out' in str($outputs): + --blast6out $blast6out + #end if + #if '--dbmatched' in str($outputs): + --dbmatched $dbmatched + #end if + #if '--dbnotmatched' in str($outputs): + --dbnotmatched $dbnotmatched + #end if + #if '--fastapairs' in str($outputs): + --fastapairs $fastapairs + #end if + #if '--notmatched' in str($outputs): + --notmatched $notmatched + #end if + #if '--matched' in str($outputs): + --matched $matched + #end if + + #if $adv_opts.adv_opts_selector == "advanced": + $adv_opts.top_hits_only + $adv_opts.rightjust + $adv_opts.leftjust + --target_cov $adv_opts.target_cov + --query_cov $adv_opts.query_cov + + + #if $adv_opts.maxid: + --maxid $adv_opts.maxid + #end if + #if $adv_opts.maxqt: + --maxqt $adv_opts.maxqsize + #end if + #if $adv_opts.maxsizeratio: + --maxsizeratio $adv_opts.maxsizeratio + #end if + #if $adv_opts.maxsl: + --maxsl $adv_opts.maxsl + #end if + #if $adv_opts.mid: + --mid $adv_opts.mid + #end if + #if $adv_opts.minqt: + --minqt $adv_opts.minqt + #end if + #if $adv_opts.minsizeratio: + --minsizeratio $adv_opts.minseqlength + #end if + #if $adv_opts.minsl: + --minsl $adv_opts.minsl + #end if + + #if $adv_opts.mintsize: + --mintsize $adv_opts.mintsize + #end if + #if $adv_opts.mismatch: + --mismatch $adv_opts.mismatch + #end if + #if $adv_opts.maxqsize: + --maxqsize $adv_opts.maxqsize + #end if + #if $adv_opts.mincols: + --mincols $adv_opts.mincols + #end if + #if $adv_opts.maxsubs: + --maxsubs $adv_opts.maxsubs + #end if + #if $adv_opts.maxrejects: + --maxrejects $adv_opts.maxrejects + #end if + #if $adv_opts.maxaccepts: + --maxaccepts $adv_opts.maxaccepts + #end if + #if $adv_opts.maxdiffs: + --maxdiffs $adv_opts.maxdiffs + #end if + #if $adv_opts.maxgaps: + --maxgaps $adv_opts.maxgaps + #end if + #if $adv_opts.maxhits: + --maxhits $adv_opts.maxhits + #end if + #if $adv_opts.match: + --match $adv_opts.match + #end if + #if $adv_opts.idprefix: + --idprefix $adv_opts.idprefix + #end if + #if $adv_opts.idsuffix: + --idsuffix $adv_opts.idsuffix + #end if + + #if $adv_opts.uclust_output.uclust_output_select == 'yes': + --uc + $adv_opts.uclust_output.uc_allhits + #end if + + #if $adv_opts.userfields_output.userfields_output_select == 'yes': + --userfields '#echo '+'.join( str($adv_opts.userfields_output.userfields).split(',') )#' + --userout $userout + #end if + + ##--weak_id REAL include aligned hits with >= id; continue search + --wordlength $adv_opts.wordlength + + $$adv_opts.output_no_hits + + #end if + + +]]> + </command> + <inputs> + <param name="queryfile" type="data" format="fasta" label="Select your query FASTA file" help="(--usearch_global)" /> + <param name="dbfile" type="data" format="fasta" label="Select your database FASTA file" help="(--db)" /> + + <expand macro="qmask" /> + <expand macro="sizeout" /> + <expand macro="strand" /> + <expand macro="self_and_selfid" /> + <expand macro="id_and_iddef" /> + <expand macro="hardmask" /> + + <param name="dbmask" type="select" optional="True" label="Mask database sequences" help="(--dbmask)"> + <option value="none" selected="True">No masking</option> + <option value="dust" selected="True">dust</option> + <option value="soft">soft</option> + </param> + + <expand macro="general_output"> + <option value="--dbmatched">FASTA file for matching database sequences</option> + <option value="--dbnotmatched">FASTA file for non-matching database sequences</option> + <option value="--notmatched">Write non-matching query sequences to separate file</option> + <option value="--matched">Write matching query sequences to separate file</option> + </expand> + + <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="top_hits_only" type="boolean" truevalue="--top_hits_only" falsevalue="" checked="False" + label="Output only hits with identity equal to the best" help="(--top_hits_only)"/> + <param name="rightjust" type="boolean" truevalue="--rightjust" falsevalue="" checked="False" + label="Reject if terminal gaps at alignment right end" help="(--rightjust)"/> + <param name="leftjust" type="boolean" truevalue="--leftjust" falsevalue="" checked="False" + label="Reject if terminal gaps at alignment left end" help="(--leftjust)"/> + + <param name="query_cov" type="float" value="" optional="True" label="Reject if fraction of query seq. aligned lower than this value" + help="(--query_cov)"/> + <param name="target_cov" type="float" value="" optional="True" label="Reject if fraction of target seq. aligned lower than this value" + help="(--target_cov)"/> + <param name="maxid" type="float" value="" optional="True" label="Reject if identity higher than this value" + help="(--maxid)"/> + <param name="maxqt" type="float" value="" optional="True" label="Reject if query/target length ratio higher than this value" + help="(--maxqt)"/> + <param name="maxsizeratio" type="float" value="" optional="True" label="Reject if query/target abundance ratio higher than this value" + help="(--maxsizeratio)"/> + <param name="maxsl" type="float" value="" optional="True" label="Reject if shorter/longer length ratio higher than this value" + help="(--maxsl)"/> + <param name="mid" type="float" value="" optional="True" label="Reject if percent identity lower than this value, ignoring gaps" + help="(--mid)"/> + <param name="minqt" type="float" value="" optional="True" label="Reject if query/target length ratio lower than this value" + help="(--minqt)"/> + <param name="minsl" type="float" value="" optional="True" label="Reject if shorter/longer length ratio lower than this value" + help="(--minsl)"/> + <param name="minsizeratio" type="float" value="" optional="True" label="Reject if query/target abundance ratio lower than this value" + help="(--minsizeratio)"/> + + <param name="maxqsize" type="integer" value="" optional="True" label="Reject if query abundance larger than this value" + help="(--maxqsize)"/> + <param name="mincols" type="integer" value="" optional="True" label="Reject if alignment length shorter than this value" + help="(--mincols)"/> + <param name="maxsubs" type="integer" value="" optional="True" label="Reject if more substitutions than this value" + help="(--maxsubs)"/> + <expand macro="maxrejects" /> + <expand macro="maxaccepts" /> + <param name="maxdiffs" type="integer" value="" optional="True" label="Reject if more substitutions or indels than this value" + help="(--maxdiffs)"/> + <param name="maxgaps" type="integer" value="" optional="True" label="Reject if more indels than this value" + help="(--maxgaps)"/> + <param name="maxhits" type="integer" value="" optional="True" label="Maximum number of hits to show" + help="(--maxhits)"/> + <param name="match" type="integer" value="2" label="Score for match" + help="(--match)"/> + <param name="idprefix" type="integer" value="" optional="True" label="Reject if first n nucleotides do not match" + help="(--idprefix)"/> + <param name="idsuffix" type="integer" value="" optional="True" label="Reject if last n nucleotides do not match" + help="(--idsuffix)"/> + <param name="mintsize" type="integer" value="" optional="True" label="Reject if target abundance lower" + help="(--mintsize)"/> + <param name="mismatch" type="integer" value="-4" label="Score for mismatch" + help="(--mismatch)"/> + + <conditional name="uclust_output"> + <param name="uclust_output_select" type="select" label="UCLUST-like output" help="(--uc)"> + <option value="yes">Yes</option> + <option value="no" selected="True">No</option> + </param> + <when value="yes"> + <param name="uc_allhits" type="boolean" truevalue="--uc_allhits" falsevalue="" checked="False" + label="Show all, not just top hits" help="(--uc_allhits)"/> + </when> + <when value="no" /> + </conditional> + + <param name="wordlength" type="integer" value="8" min="3" max="15" label="Length of words for database index 3-15" + help="Allowed values: 3-15 (--wordlength)"/> + <param name="output_no_hits" type="boolean" truevalue="--output_no_hits" falsevalue="" checked="False" + label="Write non-matching queries to the output file" help="(--output_no_hits)"/> + + <expand macro="userfields" /> + </when> + </conditional> + + + </inputs> + <outputs> + <data name="uc" format="fasta" label="${tool.name} on ${on_string}: UCLUST like output"> + <filter>adv_opts.uclust_output.uclust_output_select == 'yes'</filter> + </data> + <data name="dbnotmatched" format="fasta" label="${tool.name} on ${on_string}: Non-matched database sequences"> + <filter>'--dbnotmatchedt' in outputs</filter> + </data> + <data name="dbmatched" format="fasta" label="${tool.name} on ${on_string}: Matched database sequences"> + <filter>'--dbmatched' in outputs</filter> + </data> + <data name="alnout" format="fasta" label="${tool.name} on ${on_string}: Alignment"> + <filter>'--alnout' in outputs</filter> + </data> + <data name="blast6out" format="tabular" label="${tool.name} on ${on_string}: BLAST like tabular"> + <filter>'--blast6out' in outputs</filter> + </data> + <data name="notmatched" format="fasta" label="${tool.name} on ${on_string}: Non-matched queries"> + <filter>'--notmatched' in outputs</filter> + </data> + <data name="matched" format="fasta" label="${tool.name} on ${on_string}: Matching query sequences"> + <filter>'--matched' in outputs</filter> + </data> + <data name="fastapairs" format="fasta" label="${tool.name} on ${on_string}: Query/Target sequences"> + <filter>'--fastapairs' in outputs</filter> + </data> + <data name="userout" format="tabular" label="${tool.name} on ${on_string}: tabular output"> + <filter>adv_opts.userfields_output.userfields_output_select == 'yes'</filter> + </data> + </outputs> + <tests> + <test> + <param name="dbfile" value="three_human_mRNA.fasta" ftype="fasta" /> + <param name="queryfile" value="query.fasta" ftype="fasta" /> + <param name="outputs" value="--blast6out,--dbmatched" /> + <param name="dbmask" value="none" /> + <param name="adv_opts_selector" value="advanced" /> + <param name="top_hits_only" value="True" /> + <output name="dbmatched" file="search_dbmatched_result1.fasta" ftype="fasta" /> + <output name="blast6out" file="search_blast6out_result1.tabular" ftype="tabular" /> + </test> + <test> + <param name="dbfile" value="three_human_mRNA.fasta" ftype="fasta" /> + <param name="queryfile" value="query.fasta" ftype="fasta" /> + <param name="outputs" value="--fastapairs,--matched" /> + <param name="dbmask" value="none" /> + <param name="adv_opts_selector" value="advanced" /> + <param name="userfields_output_select" value="yes" /> + <param name="userfields" value="query,target,evalue" /> + <param name="top_hits_only" value="True" /> + <param name="output_no_hits" value="True" /> + <output name="matched" file="search_matched_result2.fasta" ftype="fasta" /> + <output name="fastapairs" file="search_fastapairs_result2.fasta" ftype="fasta" /> + <output name="userout" file="search_userfields_result2.tabular" ftype="tabular" /> + </test> + </tests> + <help> +<![CDATA[ +**What it does** + +Sequence search based on vsearch. + +@USERFIELDS_HELP@ + +Searching options + --alnout FILENAME filename for human-readable alignment output + --blast6out FILENAME filename for blast-like tab-separated output + --db FILENAME filename for FASTA formatted database for search + --dbmask mask db with "dust", "soft" or "none" method (dust) + --dbmatched FILENAME FASTA file for matching database sequences + --dbnotmatched FILENAME FASTA file for non-matching database sequences + --fastapairs FILENAME FASTA file with pairs of query and target + --fulldp full dynamic programming alignment (always on) + --gapext STRING penalties for gap extension (2I/1E) + --gapopen STRING penalties for gap opening (20I/2E) + --hardmask mask by replacing with N instead of lower case + --id REAL reject if identity lower + --iddef INT id definition, 0-4=CD-HIT,all,int,MBL,BLAST (2) + --idprefix INT reject if first n nucleotides do not match + --idsuffix INT reject if last n nucleotides do not match + --leftjust reject if terminal gaps at alignment left end + --match INT score for match (2) + --matched FILENAME FASTA file for matching query sequences + --maxaccepts INT number of hits to accept and show per strand (1) + --maxdiffs INT reject if more substitutions or indels + --maxgaps INT reject if more indels + --maxhits INT maximum number of hits to show (unlimited) + --maxid REAL reject if identity higher + --maxqsize INT reject if query abundance larger + --maxqt REAL reject if query/target length ratio higher + --maxrejects INT number of non-matching hits to consider (32) + --maxsizeratio REAL reject if query/target abundance ratio higher + --maxsl REAL reject if shorter/longer length ratio higher + --maxsubs INT reject if more substitutions + --mid REAL reject if percent identity lower, ignoring gaps + --mincols INT reject if alignment length shorter + --minqt REAL reject if query/target length ratio lower + --minsizeratio REAL reject if query/target abundance ratio lower + --minsl REAL reject if shorter/longer length ratio lower + --mintsize INT reject if target abundance lower + --mismatch INT score for mismatch (-4) + --notmatched FILENAME FASTA file for non-matching query sequences + --output_no_hits output non-matching queries to output files + --qmask mask query with "dust", "soft" or "none" method (dust) + --query_cov REAL reject if fraction of query seq. aligned lower + --rightjust reject if terminal gaps at alignment right end + --rowlen INT width of alignment lines in alnout output (64) + --self reject if labels identical + --selfid reject if sequences identical + --sizeout write abundance annotation to output + --strand search "plus" or "both" strands (plus) + --target_cov REAL reject if fraction of target seq. aligned lower + --top_hits_only output only hits with identity equal to the best + --uc FILENAME filename for UCLUST-like output + --uc_allhits show all, not just top hit with uc output + --usearch_global FILENAME filename of queries for global alignment search + --userfields STRING fields to output in userout file + --userout FILENAME filename for user-defined tab-separated output + --weak_id REAL include aligned hits with >= id; continue search + --wordlength INT length of words for database index 3-15 (8) + +@EXTERNAL_DOCUMENTATION@ + +------- + +@REFERENCES@ + + +]]> + </help> + <expand macro="citations" /> +</tool>