Mercurial > repos > iuc > vsearch
changeset 2:f29e21388219 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit 64c1c4c664c6a131d897f574dc849f5668fa97d2
| author | iuc |
|---|---|
| date | Thu, 17 Dec 2015 12:53:39 -0500 |
| parents | 8c4e2933a17a |
| children | 4258854759ba |
| files | alignment.xml chimera.xml clustering.xml dereplication.xml masking.xml search.xml shuffling.xml sorting.xml vsearch_macros.xml |
| diffstat | 9 files changed, 160 insertions(+), 190 deletions(-) [+] |
line wrap: on
line diff
--- a/alignment.xml Wed Aug 26 13:34:22 2015 -0400 +++ b/alignment.xml Thu Dec 17 12:53:39 2015 -0500 @@ -1,4 +1,4 @@ -<tool id="vsearch_alignment" name="VSearch alignment" version="@VERSION@.0"> +<tool id="vsearch_alignment" name="VSearch alignment" version="@VERSION@.1"> <description></description> <macros> <import>vsearch_macros.xml</import> @@ -11,11 +11,13 @@ vsearch @GENERAL@ $acceptall - --id $id - --iddef $iddef - --allpairs_global "$infile" - --alnout $outfile - --query_cov $query_cov + --id "${id}" + --iddef "${iddef}" + --allpairs_global "${infile}" + --alnout "${outfile}" + #if str( $query_cov ): + --query_cov "${query_cov}" + #end if @USERFIELDS@ ]]> </command> @@ -55,10 +57,6 @@ @EXTERNAL_DOCUMENTATION@ -------- - -@REFERENCES@ - ]]> </help>
--- a/chimera.xml Wed Aug 26 13:34:22 2015 -0400 +++ b/chimera.xml Thu Dec 17 12:53:39 2015 -0500 @@ -1,4 +1,4 @@ -<tool id="vsearch_chimera_detection" name="VSearch chimera detection" version="@VERSION@.0"> +<tool id="vsearch_chimera_detection" name="VSearch chimera detection" version="@VERSION@.1"> <description></description> <macros> <import>vsearch_macros.xml</import> @@ -10,30 +10,30 @@ <![CDATA[ vsearch @GENERAL@ - --abskew $abskew - --chimeras $outfile - --dn $dn - --mindiffs $mindiffs - --mindiv $mindiv - --minh $minh - --xn $xn + --abskew "${abskew}" + --chimeras "${outfile}" + --dn "${dn}" + --mindiffs "${mindiffs}" + --mindiv "${mindiv}" + --minh "${minh}" + --xn "${xn}" $self_param $selfid_param #if $detection_mode.detection_mode_select == 'denovo': - --uchime_denovo $detection_mode.infile_denovo + --uchime_denovo "${detection_mode.infile_denovo}" #else: --uchime_ref $detection_mode.infile_reference - --db $detection_mode.db + --db "${detection_mode.db}" #end if - #if 'nonchimeras' in str($outputs): - --nonchimeras $nonchimeras + #if 'nonchimeras' in str($outputs).split( "," ): + --nonchimeras "${nonchimeras}" #end if - #if 'uchimealns' in str($outputs): - --uchimealns $uchimealns + #if 'uchimealns' in str($outputs).split( "," ): + --uchimealns "${uchimealns}" #end if - #if 'uchimeout' in str($outputs): - --uchimeout $uchimeout + #if 'uchimeout' in str($outputs).split( "," ): + --uchimeout "${uchimeout}" #end if ]]> @@ -79,13 +79,13 @@ <outputs> <data name="outfile" format="fasta" label="${tool.name} on ${on_string}" /> <data name="nonchimeras" format="fasta" label="${tool.name} on ${on_string}: Non Chimera"> - <filter>'nonchimeras' in outputs</filter> + <filter>outputs and 'nonchimeras' in outputs</filter> </data> <data name="uchimealns" format="fasta" label="${tool.name} on ${on_string}: Chimera Alignments"> - <filter>'uchimealns' in outputs</filter> + <filter>outputs and 'uchimealns' in outputs</filter> </data> <data name="uchimeout" format="tabular" label="${tool.name} on ${on_string}: Chimera Information"> - <filter>'uchimeout' in outputs</filter> + <filter>outputs and 'uchimeout' in outputs</filter> </data> </outputs> <tests> @@ -124,10 +124,6 @@ @EXTERNAL_DOCUMENTATION@ -------- - -@REFERENCES@ - ]]> </help>
--- a/clustering.xml Wed Aug 26 13:34:22 2015 -0400 +++ b/clustering.xml Thu Dec 17 12:53:39 2015 -0500 @@ -1,4 +1,4 @@ -<tool id="vsearch_clustering" name="VSearch clustering" version="@VERSION@.1"> +<tool id="vsearch_clustering" name="VSearch clustering" version="@VERSION@.2"> <description></description> <macros> <import>vsearch_macros.xml</import> @@ -11,54 +11,54 @@ vsearch @GENERAL@ - #if $clustering_mode.clustering_mode_select == 'cluster_fast': + #if $clustering_mode.clustering_mode_select == 'cluster_fast': --cluster_fast "$infile" - #else if $clustering_mode.clustering_mode_select == 'cluster_smallmem': + #else if $clustering_mode.clustering_mode_select == 'cluster_smallmem': --cluster_smallmem "$infile" #end if ##--clusters STRING output each cluster to a separate FASTA file #if $maxrejects: - --maxrejects $maxrejects + --maxrejects "$maxrejects" #end if #if $maxaccepts: - --maxaccepts $maxaccepts + --maxaccepts "$maxaccepts" #end if $cons_truncate - --id $id - --iddef $iddef + --id "$id" + --iddef "$iddef" - #if '--msaout' in str($outputs): - --msaout $msaout + #if '--msaout' in str($outputs).split( "," ): + --msaout "$msaout" #end if - #if '--consout' in str($outputs): - --consout $consout + #if '--consout' in str($outputs).split( "," ): + --consout "$consout" #end if - #if '--centroids' in str($outputs): - --centroids $centroids + #if '--centroids' in str($outputs).split( "," ): + --centroids "$centroids" #end if - #if '--alnout' in str($outputs): - --alnout $alnout + #if '--alnout' in str($outputs).split( "," ): + --alnout "$alnout" #end if - #if '--blast6out' in str($outputs): - --blast6out $blast6out + #if '--blast6out' in str($outputs).split( "," ): + --blast6out "$blast6out" #end if - #if '--notmatched' in str($outputs): - --notmatched $notmatched + #if '--notmatched' in str($outputs).split( "," ): + --notmatched "$notmatched" #end if - #if '--fastapairs' in str($outputs): - --fastapairs $fastapairs + #if '--fastapairs' in str($outputs).split( "," ): + --fastapairs "$fastapairs" #end if - #if '--matched' in str($outputs): - --matched $matched + #if '--matched' in str($outputs).split( "," ): + --matched "$matched" #end if - #if $qmask != 'no': - --qmask $qmask + #if str( $qmask ) != 'no': + --qmask "$qmask" #end if $sizein $sizeout - --strand $strand + --strand "$strand" $usersort #if $uc: --uc "$uc_outfile" @@ -225,10 +225,6 @@ @EXTERNAL_DOCUMENTATION@ -------- - -@REFERENCES@ - ]]> </help>
--- a/dereplication.xml Wed Aug 26 13:34:22 2015 -0400 +++ b/dereplication.xml Thu Dec 17 12:53:39 2015 -0500 @@ -1,4 +1,4 @@ -<tool id="vsearch_dereplication" name="VSearch dereplication" version="@VERSION@.1"> +<tool id="vsearch_dereplication" name="VSearch dereplication" version="@VERSION@.2"> <description></description> <macros> <import>vsearch_macros.xml</import> @@ -10,22 +10,22 @@ <![CDATA[ vsearch @GENERAL@ - --derep_fulllength $infile - #if $maxuniquesize: - --maxuniquesize $maxuniquesize + --derep_fulllength "$infile" + #if str($maxuniquesize): + --maxuniquesize "$maxuniquesize" #end if - #if $minuniquesize: - --minuniquesize $minuniquesize + #if str($minuniquesize): + --minuniquesize "$minuniquesize" #end if - --output $outfile + --output "$outfile" $sizein - $sizeout - --strand $strand - #if $topn: - --topn $topn + $sizeout + --strand "$strand" + #if str($topn): + --topn "$topn" #end if #if $uc: - --uc $uc_outfile + --uc "$uc_outfile" #end if ]]> </command> @@ -99,10 +99,6 @@ @EXTERNAL_DOCUMENTATION@ -------- - -@REFERENCES@ - ]]> </help>
--- a/masking.xml Wed Aug 26 13:34:22 2015 -0400 +++ b/masking.xml Thu Dec 17 12:53:39 2015 -0500 @@ -1,4 +1,4 @@ -<tool id="vsearch_masking" name="VSearch masking" version="@VERSION@.0"> +<tool id="vsearch_masking" name="VSearch masking" version="@VERSION@.1"> <description></description> <macros> <import>vsearch_macros.xml</import> @@ -10,12 +10,12 @@ <![CDATA[ vsearch @GENERAL@ - #if $qmask != 'no': - --qmask $qmask + #if str( $qmask ) != 'no': + --qmask "$qmask" #end if $hardmask --maskfasta "$infile" - --output $outfile + --output "$outfile" ]]> </command> @@ -68,10 +68,6 @@ @EXTERNAL_DOCUMENTATION@ -------- - -@REFERENCES@ - ]]> </help>
--- a/search.xml Wed Aug 26 13:34:22 2015 -0400 +++ b/search.xml Thu Dec 17 12:53:39 2015 -0500 @@ -1,4 +1,4 @@ -<tool id="vsearch_search" name="VSearch search" version="@VERSION@.0"> +<tool id="vsearch_search" name="VSearch search" version="@VERSION@.1"> <description></description> <macros> <import>vsearch_macros.xml</import> @@ -11,139 +11,139 @@ vsearch @GENERAL@ - --db $dbfile - --dbmask $dbmask + --db "$dbfile" + #if $dbmask: + --dbmask "$dbmask" + #end if ##--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 $iddef + --id "$id" + --iddef "$iddef" - #if $qmask != 'no': - --qmask $qmask + #if str( $qmask ) != 'no': + --qmask "$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 + $sizeout + --strand "$strand" + --usearch_global "$queryfile" - #if '--alnout' in str($outputs): - --alnout $alnout + #if '--alnout' in str($outputs).split( "," ): + --alnout "$alnout" #end if - #if '--blast6out' in str($outputs): - --blast6out $blast6out + #if '--blast6out' in str($outputs).split( "," ): + --blast6out "$blast6out" #end if - #if '--dbmatched' in str($outputs): - --dbmatched $dbmatched + #if '--dbmatched' in str($outputs).split( "," ): + --dbmatched "$dbmatched" #end if - #if '--dbnotmatched' in str($outputs): - --dbnotmatched $dbnotmatched + #if '--dbnotmatched' in str($outputs).split( "," ): + --dbnotmatched "$dbnotmatched" #end if - #if '--fastapairs' in str($outputs): - --fastapairs $fastapairs + #if '--fastapairs' in str($outputs).split( "," ): + --fastapairs "$fastapairs" #end if - #if '--notmatched' in str($outputs): - --notmatched $notmatched + #if '--notmatched' in str($outputs).split( "," ): + --notmatched "$notmatched" #end if - #if '--matched' in str($outputs): - --matched $matched + #if '--matched' in str($outputs).split( "," ): + --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 $adv_opts.query_cov + --target_cov "$adv_opts.target_cov" + --query_cov "$adv_opts.query_cov" - #if $adv_opts.maxid: - --maxid $adv_opts.maxid + #if str( $adv_opts.maxid ): + --maxid "$adv_opts.maxid" #end if - #if $adv_opts.maxqt: - --maxqt $adv_opts.maxqsize + #if str( $adv_opts.maxqt ): + --maxqt "$adv_opts.maxqsize" #end if - #if $adv_opts.maxsizeratio: - --maxsizeratio $adv_opts.maxsizeratio + #if str( $adv_opts.maxsizeratio ): + --maxsizeratio "$adv_opts.maxsizeratio" #end if - #if $adv_opts.maxsl: - --maxsl $adv_opts.maxsl + #if str( $adv_opts.maxsl ): + --maxsl "$adv_opts.maxsl" #end if - #if $adv_opts.mid: - --mid $adv_opts.mid + #if str( $adv_opts.mid ): + --mid "$adv_opts.mid" #end if - #if $adv_opts.minqt: - --minqt $adv_opts.minqt + #if str( $adv_opts.minqt ): + --minqt "$adv_opts.minqt" #end if - #if $adv_opts.minsizeratio: - --minsizeratio $adv_opts.minseqlength + #if str( $adv_opts.minsizeratio ): + --minsizeratio "$adv_opts.minseqlength" #end if - #if $adv_opts.minsl: - --minsl $adv_opts.minsl + #if str( $adv_opts.minsl ): + --minsl "$adv_opts.minsl" #end if - #if $adv_opts.mintsize: - --mintsize $adv_opts.mintsize + #if str( $adv_opts.mintsize ): + --mintsize "$adv_opts.mintsize" #end if - #if $adv_opts.mismatch: - --mismatch $adv_opts.mismatch + #if str( $adv_opts.mismatch ): + --mismatch "$adv_opts.mismatch" #end if - #if $adv_opts.maxqsize: - --maxqsize $adv_opts.maxqsize + #if str( $adv_opts.maxqsize ): + --maxqsize "$adv_opts.maxqsize" #end if - #if $adv_opts.mincols: - --mincols $adv_opts.mincols + #if str( $adv_opts.mincols ): + --mincols "$adv_opts.mincols" #end if - #if $adv_opts.maxsubs: - --maxsubs $adv_opts.maxsubs + #if str( $adv_opts.maxsubs ): + --maxsubs "$adv_opts.maxsubs" #end if - #if $adv_opts.maxrejects: - --maxrejects $adv_opts.maxrejects + #if str( $adv_opts.maxrejects ): + --maxrejects "$adv_opts.maxrejects" #end if - #if $adv_opts.maxaccepts: - --maxaccepts $adv_opts.maxaccepts + #if str( $adv_opts.maxaccepts ): + --maxaccepts "$adv_opts.maxaccepts" #end if - #if $adv_opts.maxdiffs: - --maxdiffs $adv_opts.maxdiffs + #if str( $adv_opts.maxdiffs ): + --maxdiffs "$adv_opts.maxdiffs" #end if - #if $adv_opts.maxgaps: - --maxgaps $adv_opts.maxgaps + #if str( $adv_opts.maxgaps ): + --maxgaps "$adv_opts.maxgaps" #end if - #if $adv_opts.maxhits: - --maxhits $adv_opts.maxhits + #if str( $adv_opts.maxhits ): + --maxhits "$adv_opts.maxhits" #end if - #if $adv_opts.match: - --match $adv_opts.match + #if str( $adv_opts.match ): + --match "$adv_opts.match" #end if - #if $adv_opts.idprefix: - --idprefix $adv_opts.idprefix + #if str( $adv_opts.idprefix ): + --idprefix "$adv_opts.idprefix" #end if - #if $adv_opts.idsuffix: - --idsuffix $adv_opts.idsuffix + #if str( $adv_opts.idsuffix ): + --idsuffix str( $adv_opts.idsuffix ) #end if #if $adv_opts.uclust_output.uclust_output_select == 'yes': - --uc + --uc "$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 $userout + --userout "$userout" #end if ##--weak_id REAL include aligned hits with >= id; continue search - --wordlength $adv_opts.wordlength + --wordlength "$adv_opts.wordlength" - $$adv_opts.output_no_hits + $adv_opts.output_no_hits #end if @@ -260,7 +260,7 @@ </inputs> <outputs> <data name="uc" format="fasta" label="${tool.name} on ${on_string}: UCLUST like output"> - <filter>adv_opts.uclust_output.uclust_output_select == 'yes'</filter> + <filter>adv_opts['adv_opts_selector'] == "advanced" and adv_opts['uclust_output']['uclust_output_select'] == 'yes'</filter> </data> <data name="dbnotmatched" format="fasta" label="${tool.name} on ${on_string}: Non-matched database sequences"> <filter>'--dbnotmatchedt' in outputs</filter> @@ -284,7 +284,7 @@ <filter>'--fastapairs' in outputs</filter> </data> <data name="userout" format="tabular" label="${tool.name} on ${on_string}: tabular output"> - <filter>adv_opts.userfields_output.userfields_output_select == 'yes'</filter> + <filter>adv_opts['adv_opts_selector'] == "advanced" and adv_opts['userfields_output']['userfields_output_select'] == 'yes'</filter> </data> </outputs> <tests> @@ -380,10 +380,6 @@ @EXTERNAL_DOCUMENTATION@ -------- - -@REFERENCES@ - ]]> </help>
--- a/shuffling.xml Wed Aug 26 13:34:22 2015 -0400 +++ b/shuffling.xml Thu Dec 17 12:53:39 2015 -0500 @@ -1,4 +1,4 @@ -<tool id="vsearch_shuffling" name="VSearch shuffling" version="@VERSION@.0"> +<tool id="vsearch_shuffling" name="VSearch shuffling" version="@VERSION@.1"> <description></description> <macros> <import>vsearch_macros.xml</import> @@ -10,10 +10,12 @@ <![CDATA[ vsearch @GENERAL@ - --output $outfile - --seed $seed - --shuffle $infile - --topn $topn + --output "$outfile" + --seed "$seed" + --shuffle "$infile" + #if str( $topn ): + --topn "$topn" + #end if ]]> </command> <inputs> @@ -48,10 +50,6 @@ @EXTERNAL_DOCUMENTATION@ -------- - -@REFERENCES@ - ]]> </help>
--- a/sorting.xml Wed Aug 26 13:34:22 2015 -0400 +++ b/sorting.xml Thu Dec 17 12:53:39 2015 -0500 @@ -1,4 +1,4 @@ -<tool id="vsearch_sorting" name="VSearch sorting" version="@VERSION@.1"> +<tool id="vsearch_sorting" name="VSearch sorting" version="@VERSION@.2"> <description></description> <macros> <import>vsearch_macros.xml</import> @@ -14,20 +14,20 @@ --sortbylength "$sorting_mode.infile" #else: --sortbysize "$sorting_mode.infile" - #if $sorting_mode.minsize: - --minsize $sorting_mode.minsize + #if str( $sorting_mode.minsize ): + --minsize "$sorting_mode.minsize" #end if - #if $sorting_mode.maxsize: - --maxsize $sorting_mode.maxsize + #if str( $sorting_mode.maxsize ): + --maxsize "$sorting_mode.maxsize" #end if #end if - --output $outfile + --output "$outfile" #if $relabel: --relabel "$relabel" #end if $sizeout - #if $topn: - --topn $topn + #if str( $topn ): + --topn "$topn" #end if ]]> @@ -112,10 +112,6 @@ @EXTERNAL_DOCUMENTATION@ -------- - -@REFERENCES@ - ]]> </help>