| Previous changeset 1:8c4e2933a17a (2015-08-26) Next changeset 3:4258854759ba (2016-03-01) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit 64c1c4c664c6a131d897f574dc849f5668fa97d2 |
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modified:
alignment.xml chimera.xml clustering.xml dereplication.xml masking.xml search.xml shuffling.xml sorting.xml vsearch_macros.xml |
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| diff -r 8c4e2933a17a -r f29e21388219 alignment.xml --- a/alignment.xml Wed Aug 26 13:34:22 2015 -0400 +++ b/alignment.xml Thu Dec 17 12:53:39 2015 -0500 |
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| @@ -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> |
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| diff -r 8c4e2933a17a -r f29e21388219 chimera.xml --- 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> |
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| diff -r 8c4e2933a17a -r f29e21388219 clustering.xml --- a/clustering.xml Wed Aug 26 13:34:22 2015 -0400 +++ b/clustering.xml Thu Dec 17 12:53:39 2015 -0500 |
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| @@ -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> |
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| diff -r 8c4e2933a17a -r f29e21388219 dereplication.xml --- 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> |
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| diff -r 8c4e2933a17a -r f29e21388219 masking.xml --- 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> |
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| diff -r 8c4e2933a17a -r f29e21388219 search.xml --- a/search.xml Wed Aug 26 13:34:22 2015 -0400 +++ b/search.xml Thu Dec 17 12:53:39 2015 -0500 |
| [ |
| b'@@ -1,4 +1,4 @@\n-<tool id="vsearch_search" name="VSearch search" version="@VERSION@.0">\n+<tool id="vsearch_search" name="VSearch search" version="@VERSION@.1">\n <description></description>\n <macros>\n <import>vsearch_macros.xml</import>\n@@ -11,139 +11,139 @@\n vsearch\n \n @GENERAL@\n- --db $dbfile\n- --dbmask $dbmask\n+ --db "$dbfile"\n+ #if $dbmask:\n+ --dbmask "$dbmask"\n+ #end if\n \n ##--fulldp full dynamic programming alignment (always on)\n ##--gapext STRING penalties for gap extension (2I/1E)\n ##--gapopen STRING penalties for gap opening (20I/2E)\n $hardmask\n- --id $id\n- --iddef $iddef\n+ --id "$id"\n+ --iddef "$iddef"\n \n- #if $qmask != \'no\':\n- --qmask $qmask\n+ #if str( $qmask ) != \'no\':\n+ --qmask "$qmask"\n #end if\n \n ## --rowlen INT width of alignment lines in alnout output (64)\n \n $self_param\n $selfid_param\n- #if $sizeout:\n- --sizeout $sizeout\n- #end if\n- --strand $strand\n- --usearch_global $queryfile\n+ $sizeout\n+ --strand "$strand"\n+ --usearch_global "$queryfile"\n \n- #if \'--alnout\' in str($outputs):\n- --alnout $alnout\n+ #if \'--alnout\' in str($outputs).split( "," ):\n+ --alnout "$alnout"\n #end if\n- #if \'--blast6out\' in str($outputs):\n- --blast6out $blast6out\n+ #if \'--blast6out\' in str($outputs).split( "," ):\n+ --blast6out "$blast6out"\n #end if\n- #if \'--dbmatched\' in str($outputs):\n- --dbmatched $dbmatched\n+ #if \'--dbmatched\' in str($outputs).split( "," ):\n+ --dbmatched "$dbmatched"\n #end if\n- #if \'--dbnotmatched\' in str($outputs):\n- --dbnotmatched $dbnotmatched\n+ #if \'--dbnotmatched\' in str($outputs).split( "," ):\n+ --dbnotmatched "$dbnotmatched"\n #end if\n- #if \'--fastapairs\' in str($outputs):\n- --fastapairs $fastapairs\n+ #if \'--fastapairs\' in str($outputs).split( "," ):\n+ --fastapairs "$fastapairs"\n #end if\n- #if \'--notmatched\' in str($outputs):\n- --notmatched $notmatched\n+ #if \'--notmatched\' in str($outputs).split( "," ):\n+ --notmatched "$notmatched"\n #end if\n- #if \'--matched\' in str($outputs):\n- --matched $matched\n+ #if \'--matched\' in str($outputs).split( "," ):\n+ --matched "$matched"\n #end if\n \n #if $adv_opts.adv_opts_selector == "advanced":\n $adv_opts.top_hits_only\n $adv_opts.rightjust\n $adv_opts.leftjust\n- --target_cov $adv_opts.target_cov\n- --query_cov $adv_opts.query_cov\n+ --target_cov "$adv_opts.target_cov"\n+ --query_cov "$adv_opts.query_cov"\n \n \n- #if $adv_opts.maxid:\n- --maxid $adv_opts.maxid\n+ #if str( $adv_opts.maxid ):\n+ --maxid "$adv_opts.maxid"\n #end if\n- #if $adv_opts.maxqt:\n- --maxqt $adv_opts.maxqsize\n+ #if str( $adv_opts.maxqt ):\n+ --maxqt "$adv_opts.maxqsize"\n #end if\n- #if $adv_opts.maxsizeratio:\n- --maxsizeratio $adv_opts.maxsizeratio\n+ #if str( $adv_opts.maxsizeratio ):\n+ --maxsizeratio "$adv_opts.maxsizeratio"\n #end if\n- #if $adv_opts.maxsl:\n- --maxsl $adv_opts.maxsl\n+ #if str( $adv_opts.maxsl ):\n+ --maxsl "$adv_opts.maxsl"\n #end if\n- #if $adv_opts.mid:\n- --mid $adv_opts.mid\n+ #if str( $adv_opts.mid ):\n+ --mid "$adv_opts.mid"\n #end if\n- #if $adv_opts.minqt:\n- --minqt '..b'.maxqsize\n+ #if str( $adv_opts.maxqsize ):\n+ --maxqsize "$adv_opts.maxqsize"\n #end if\n- #if $adv_opts.mincols:\n- --mincols $adv_opts.mincols\n+ #if str( $adv_opts.mincols ):\n+ --mincols "$adv_opts.mincols"\n #end if\n- #if $adv_opts.maxsubs:\n- --maxsubs $adv_opts.maxsubs\n+ #if str( $adv_opts.maxsubs ):\n+ --maxsubs "$adv_opts.maxsubs"\n #end if\n- #if $adv_opts.maxrejects:\n- --maxrejects $adv_opts.maxrejects\n+ #if str( $adv_opts.maxrejects ):\n+ --maxrejects "$adv_opts.maxrejects"\n #end if\n- #if $adv_opts.maxaccepts:\n- --maxaccepts $adv_opts.maxaccepts\n+ #if str( $adv_opts.maxaccepts ):\n+ --maxaccepts "$adv_opts.maxaccepts"\n #end if\n- #if $adv_opts.maxdiffs:\n- --maxdiffs $adv_opts.maxdiffs\n+ #if str( $adv_opts.maxdiffs ):\n+ --maxdiffs "$adv_opts.maxdiffs"\n #end if\n- #if $adv_opts.maxgaps:\n- --maxgaps $adv_opts.maxgaps\n+ #if str( $adv_opts.maxgaps ):\n+ --maxgaps "$adv_opts.maxgaps"\n #end if\n- #if $adv_opts.maxhits:\n- --maxhits $adv_opts.maxhits\n+ #if str( $adv_opts.maxhits ):\n+ --maxhits "$adv_opts.maxhits"\n #end if\n- #if $adv_opts.match:\n- --match $adv_opts.match\n+ #if str( $adv_opts.match ):\n+ --match "$adv_opts.match"\n #end if\n- #if $adv_opts.idprefix:\n- --idprefix $adv_opts.idprefix\n+ #if str( $adv_opts.idprefix ):\n+ --idprefix "$adv_opts.idprefix"\n #end if\n- #if $adv_opts.idsuffix:\n- --idsuffix $adv_opts.idsuffix\n+ #if str( $adv_opts.idsuffix ):\n+ --idsuffix str( $adv_opts.idsuffix )\n #end if\n \n #if $adv_opts.uclust_output.uclust_output_select == \'yes\':\n- --uc\n+ --uc "$uc"\n $adv_opts.uclust_output.uc_allhits\n #end if\n \n #if $adv_opts.userfields_output.userfields_output_select == \'yes\':\n --userfields \'#echo \'+\'.join( str($adv_opts.userfields_output.userfields).split(\',\') )#\'\n- --userout $userout\n+ --userout "$userout"\n #end if\n \n ##--weak_id REAL include aligned hits with >= id; continue search\n- --wordlength $adv_opts.wordlength\n+ --wordlength "$adv_opts.wordlength"\n \n- $$adv_opts.output_no_hits\n+ $adv_opts.output_no_hits\n \n #end if\n \n@@ -260,7 +260,7 @@\n </inputs>\n <outputs>\n <data name="uc" format="fasta" label="${tool.name} on ${on_string}: UCLUST like output">\n- <filter>adv_opts.uclust_output.uclust_output_select == \'yes\'</filter>\n+ <filter>adv_opts[\'adv_opts_selector\'] == "advanced" and adv_opts[\'uclust_output\'][\'uclust_output_select\'] == \'yes\'</filter>\n </data>\n <data name="dbnotmatched" format="fasta" label="${tool.name} on ${on_string}: Non-matched database sequences">\n <filter>\'--dbnotmatchedt\' in outputs</filter>\n@@ -284,7 +284,7 @@\n <filter>\'--fastapairs\' in outputs</filter>\n </data>\n <data name="userout" format="tabular" label="${tool.name} on ${on_string}: tabular output">\n- <filter>adv_opts.userfields_output.userfields_output_select == \'yes\'</filter>\n+ <filter>adv_opts[\'adv_opts_selector\'] == "advanced" and adv_opts[\'userfields_output\'][\'userfields_output_select\'] == \'yes\'</filter>\n </data>\n </outputs>\n <tests>\n@@ -380,10 +380,6 @@\n \n @EXTERNAL_DOCUMENTATION@\n \n--------\n-\n-@REFERENCES@\n-\n \n ]]>\n </help>\n' |
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| diff -r 8c4e2933a17a -r f29e21388219 shuffling.xml --- 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> |
| b |
| diff -r 8c4e2933a17a -r f29e21388219 sorting.xml --- a/sorting.xml Wed Aug 26 13:34:22 2015 -0400 +++ b/sorting.xml Thu Dec 17 12:53:39 2015 -0500 |
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| @@ -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> |
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| diff -r 8c4e2933a17a -r f29e21388219 vsearch_macros.xml --- a/vsearch_macros.xml Wed Aug 26 13:34:22 2015 -0400 +++ b/vsearch_macros.xml Thu Dec 17 12:53:39 2015 -0500 |
| b |
| @@ -174,8 +174,6 @@ ]]> </token> - <token name="@REFERENCES@"> - </token> <token name="@USERFIELDS_HELP@"> **Available fields in user defined tabular output** |