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comparison search.xml @ 2:f29e21388219 draft

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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 fae6527990af
children 4258854759ba
comparison
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1:8c4e2933a17a 2:f29e21388219
1 <tool id="vsearch_search" name="VSearch search" version="@VERSION@.0"> 1 <tool id="vsearch_search" name="VSearch search" version="@VERSION@.1">
2 <description></description> 2 <description></description>
3 <macros> 3 <macros>
4 <import>vsearch_macros.xml</import> 4 <import>vsearch_macros.xml</import>
5 </macros> 5 </macros>
6 <expand macro="requirements" /> 6 <expand macro="requirements" />
9 <command> 9 <command>
10 <![CDATA[ 10 <![CDATA[
11 vsearch 11 vsearch
12 12
13 @GENERAL@ 13 @GENERAL@
14 --db $dbfile 14 --db "$dbfile"
15 --dbmask $dbmask 15 #if $dbmask:
16 --dbmask "$dbmask"
17 #end if
16 18
17 ##--fulldp full dynamic programming alignment (always on) 19 ##--fulldp full dynamic programming alignment (always on)
18 ##--gapext STRING penalties for gap extension (2I/1E) 20 ##--gapext STRING penalties for gap extension (2I/1E)
19 ##--gapopen STRING penalties for gap opening (20I/2E) 21 ##--gapopen STRING penalties for gap opening (20I/2E)
20 $hardmask 22 $hardmask
21 --id $id 23 --id "$id"
22 --iddef $iddef 24 --iddef "$iddef"
23 25
24 #if $qmask != 'no': 26 #if str( $qmask ) != 'no':
25 --qmask $qmask 27 --qmask "$qmask"
26 #end if 28 #end if
27 29
28 ## --rowlen INT width of alignment lines in alnout output (64) 30 ## --rowlen INT width of alignment lines in alnout output (64)
29 31
30 $self_param 32 $self_param
31 $selfid_param 33 $selfid_param
32 #if $sizeout: 34 $sizeout
33 --sizeout $sizeout 35 --strand "$strand"
34 #end if 36 --usearch_global "$queryfile"
35 --strand $strand 37
36 --usearch_global $queryfile 38 #if '--alnout' in str($outputs).split( "," ):
37 39 --alnout "$alnout"
38 #if '--alnout' in str($outputs): 40 #end if
39 --alnout $alnout 41 #if '--blast6out' in str($outputs).split( "," ):
40 #end if 42 --blast6out "$blast6out"
41 #if '--blast6out' in str($outputs): 43 #end if
42 --blast6out $blast6out 44 #if '--dbmatched' in str($outputs).split( "," ):
43 #end if 45 --dbmatched "$dbmatched"
44 #if '--dbmatched' in str($outputs): 46 #end if
45 --dbmatched $dbmatched 47 #if '--dbnotmatched' in str($outputs).split( "," ):
46 #end if 48 --dbnotmatched "$dbnotmatched"
47 #if '--dbnotmatched' in str($outputs): 49 #end if
48 --dbnotmatched $dbnotmatched 50 #if '--fastapairs' in str($outputs).split( "," ):
49 #end if 51 --fastapairs "$fastapairs"
50 #if '--fastapairs' in str($outputs): 52 #end if
51 --fastapairs $fastapairs 53 #if '--notmatched' in str($outputs).split( "," ):
52 #end if 54 --notmatched "$notmatched"
53 #if '--notmatched' in str($outputs): 55 #end if
54 --notmatched $notmatched 56 #if '--matched' in str($outputs).split( "," ):
55 #end if 57 --matched "$matched"
56 #if '--matched' in str($outputs):
57 --matched $matched
58 #end if 58 #end if
59 59
60 #if $adv_opts.adv_opts_selector == "advanced": 60 #if $adv_opts.adv_opts_selector == "advanced":
61 $adv_opts.top_hits_only 61 $adv_opts.top_hits_only
62 $adv_opts.rightjust 62 $adv_opts.rightjust
63 $adv_opts.leftjust 63 $adv_opts.leftjust
64 --target_cov $adv_opts.target_cov 64 --target_cov "$adv_opts.target_cov"
65 --query_cov $adv_opts.query_cov 65 --query_cov "$adv_opts.query_cov"
66 66
67 67
68 #if $adv_opts.maxid: 68 #if str( $adv_opts.maxid ):
69 --maxid $adv_opts.maxid 69 --maxid "$adv_opts.maxid"
70 #end if 70 #end if
71 #if $adv_opts.maxqt: 71 #if str( $adv_opts.maxqt ):
72 --maxqt $adv_opts.maxqsize 72 --maxqt "$adv_opts.maxqsize"
73 #end if 73 #end if
74 #if $adv_opts.maxsizeratio: 74 #if str( $adv_opts.maxsizeratio ):
75 --maxsizeratio $adv_opts.maxsizeratio 75 --maxsizeratio "$adv_opts.maxsizeratio"
76 #end if 76 #end if
77 #if $adv_opts.maxsl: 77 #if str( $adv_opts.maxsl ):
78 --maxsl $adv_opts.maxsl 78 --maxsl "$adv_opts.maxsl"
79 #end if 79 #end if
80 #if $adv_opts.mid: 80 #if str( $adv_opts.mid ):
81 --mid $adv_opts.mid 81 --mid "$adv_opts.mid"
82 #end if 82 #end if
83 #if $adv_opts.minqt: 83 #if str( $adv_opts.minqt ):
84 --minqt $adv_opts.minqt 84 --minqt "$adv_opts.minqt"
85 #end if 85 #end if
86 #if $adv_opts.minsizeratio: 86 #if str( $adv_opts.minsizeratio ):
87 --minsizeratio $adv_opts.minseqlength 87 --minsizeratio "$adv_opts.minseqlength"
88 #end if 88 #end if
89 #if $adv_opts.minsl: 89 #if str( $adv_opts.minsl ):
90 --minsl $adv_opts.minsl 90 --minsl "$adv_opts.minsl"
91 #end if 91 #end if
92 92
93 #if $adv_opts.mintsize: 93 #if str( $adv_opts.mintsize ):
94 --mintsize $adv_opts.mintsize 94 --mintsize "$adv_opts.mintsize"
95 #end if 95 #end if
96 #if $adv_opts.mismatch: 96 #if str( $adv_opts.mismatch ):
97 --mismatch $adv_opts.mismatch 97 --mismatch "$adv_opts.mismatch"
98 #end if 98 #end if
99 #if $adv_opts.maxqsize: 99 #if str( $adv_opts.maxqsize ):
100 --maxqsize $adv_opts.maxqsize 100 --maxqsize "$adv_opts.maxqsize"
101 #end if 101 #end if
102 #if $adv_opts.mincols: 102 #if str( $adv_opts.mincols ):
103 --mincols $adv_opts.mincols 103 --mincols "$adv_opts.mincols"
104 #end if 104 #end if
105 #if $adv_opts.maxsubs: 105 #if str( $adv_opts.maxsubs ):
106 --maxsubs $adv_opts.maxsubs 106 --maxsubs "$adv_opts.maxsubs"
107 #end if 107 #end if
108 #if $adv_opts.maxrejects: 108 #if str( $adv_opts.maxrejects ):
109 --maxrejects $adv_opts.maxrejects 109 --maxrejects "$adv_opts.maxrejects"
110 #end if 110 #end if
111 #if $adv_opts.maxaccepts: 111 #if str( $adv_opts.maxaccepts ):
112 --maxaccepts $adv_opts.maxaccepts 112 --maxaccepts "$adv_opts.maxaccepts"
113 #end if 113 #end if
114 #if $adv_opts.maxdiffs: 114 #if str( $adv_opts.maxdiffs ):
115 --maxdiffs $adv_opts.maxdiffs 115 --maxdiffs "$adv_opts.maxdiffs"
116 #end if 116 #end if
117 #if $adv_opts.maxgaps: 117 #if str( $adv_opts.maxgaps ):
118 --maxgaps $adv_opts.maxgaps 118 --maxgaps "$adv_opts.maxgaps"
119 #end if 119 #end if
120 #if $adv_opts.maxhits: 120 #if str( $adv_opts.maxhits ):
121 --maxhits $adv_opts.maxhits 121 --maxhits "$adv_opts.maxhits"
122 #end if 122 #end if
123 #if $adv_opts.match: 123 #if str( $adv_opts.match ):
124 --match $adv_opts.match 124 --match "$adv_opts.match"
125 #end if 125 #end if
126 #if $adv_opts.idprefix: 126 #if str( $adv_opts.idprefix ):
127 --idprefix $adv_opts.idprefix 127 --idprefix "$adv_opts.idprefix"
128 #end if 128 #end if
129 #if $adv_opts.idsuffix: 129 #if str( $adv_opts.idsuffix ):
130 --idsuffix $adv_opts.idsuffix 130 --idsuffix str( $adv_opts.idsuffix )
131 #end if 131 #end if
132 132
133 #if $adv_opts.uclust_output.uclust_output_select == 'yes': 133 #if $adv_opts.uclust_output.uclust_output_select == 'yes':
134 --uc 134 --uc "$uc"
135 $adv_opts.uclust_output.uc_allhits 135 $adv_opts.uclust_output.uc_allhits
136 #end if 136 #end if
137 137
138 #if $adv_opts.userfields_output.userfields_output_select == 'yes': 138 #if $adv_opts.userfields_output.userfields_output_select == 'yes':
139 --userfields '#echo '+'.join( str($adv_opts.userfields_output.userfields).split(',') )#' 139 --userfields '#echo '+'.join( str($adv_opts.userfields_output.userfields).split(',') )#'
140 --userout $userout 140 --userout "$userout"
141 #end if 141 #end if
142 142
143 ##--weak_id REAL include aligned hits with >= id; continue search 143 ##--weak_id REAL include aligned hits with >= id; continue search
144 --wordlength $adv_opts.wordlength 144 --wordlength "$adv_opts.wordlength"
145 145
146 $$adv_opts.output_no_hits 146 $adv_opts.output_no_hits
147 147
148 #end if 148 #end if
149 149
150 150
151 ]]> 151 ]]>
258 258
259 259
260 </inputs> 260 </inputs>
261 <outputs> 261 <outputs>
262 <data name="uc" format="fasta" label="${tool.name} on ${on_string}: UCLUST like output"> 262 <data name="uc" format="fasta" label="${tool.name} on ${on_string}: UCLUST like output">
263 <filter>adv_opts.uclust_output.uclust_output_select == 'yes'</filter> 263 <filter>adv_opts['adv_opts_selector'] == "advanced" and adv_opts['uclust_output']['uclust_output_select'] == 'yes'</filter>
264 </data> 264 </data>
265 <data name="dbnotmatched" format="fasta" label="${tool.name} on ${on_string}: Non-matched database sequences"> 265 <data name="dbnotmatched" format="fasta" label="${tool.name} on ${on_string}: Non-matched database sequences">
266 <filter>'--dbnotmatchedt' in outputs</filter> 266 <filter>'--dbnotmatchedt' in outputs</filter>
267 </data> 267 </data>
268 <data name="dbmatched" format="fasta" label="${tool.name} on ${on_string}: Matched database sequences"> 268 <data name="dbmatched" format="fasta" label="${tool.name} on ${on_string}: Matched database sequences">
282 </data> 282 </data>
283 <data name="fastapairs" format="fasta" label="${tool.name} on ${on_string}: Query/Target sequences"> 283 <data name="fastapairs" format="fasta" label="${tool.name} on ${on_string}: Query/Target sequences">
284 <filter>'--fastapairs' in outputs</filter> 284 <filter>'--fastapairs' in outputs</filter>
285 </data> 285 </data>
286 <data name="userout" format="tabular" label="${tool.name} on ${on_string}: tabular output"> 286 <data name="userout" format="tabular" label="${tool.name} on ${on_string}: tabular output">
287 <filter>adv_opts.userfields_output.userfields_output_select == 'yes'</filter> 287 <filter>adv_opts['adv_opts_selector'] == "advanced" and adv_opts['userfields_output']['userfields_output_select'] == 'yes'</filter>
288 </data> 288 </data>
289 </outputs> 289 </outputs>
290 <tests> 290 <tests>
291 <test> 291 <test>
292 <param name="dbfile" value="three_human_mRNA.fasta" ftype="fasta" /> 292 <param name="dbfile" value="three_human_mRNA.fasta" ftype="fasta" />
378 --weak_id REAL include aligned hits with >= id; continue search 378 --weak_id REAL include aligned hits with >= id; continue search
379 --wordlength INT length of words for database index 3-15 (8) 379 --wordlength INT length of words for database index 3-15 (8)
380 380
381 @EXTERNAL_DOCUMENTATION@ 381 @EXTERNAL_DOCUMENTATION@
382 382
383 -------
384
385 @REFERENCES@
386
387 383
388 ]]> 384 ]]>
389 </help> 385 </help>
390 <expand macro="citations" /> 386 <expand macro="citations" />
391 </tool> 387 </tool>