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comparison search.xml @ 6:9495df9dd6ef draft default tip

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit 98411bbc8c371cf56d81fc4a1402ee64efef41eb"
author iuc
date Wed, 04 Nov 2020 07:36:19 +0000
parents 4258854759ba
children
comparison
equal deleted inserted replaced
5:b3c7199d8786 6:9495df9dd6ef
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 #if $dbmask: 15 #if $dbmask:
16 --dbmask "$dbmask" 16 --dbmask "$dbmask"
17 #end if 17 #end if
18 18
19 ##--fulldp full dynamic programming alignment (always on) 19 ##--fulldp full dynamic programming alignment (always on)
31 31
32 $self_param 32 $self_param
33 $selfid_param 33 $selfid_param
34 $sizeout 34 $sizeout
35 --strand "$strand" 35 --strand "$strand"
36 --usearch_global "$queryfile" 36 --usearch_global '$queryfile'
37 37
38 #if '--alnout' in str($outputs).split( "," ): 38 #if '--alnout' in str($outputs).split( "," ):
39 --alnout "$alnout" 39 --alnout '$alnout'
40 #end if 40 #end if
41 #if '--blast6out' in str($outputs).split( "," ): 41 #if '--blast6out' in str($outputs).split( "," ):
42 --blast6out "$blast6out" 42 --blast6out '$blast6out'
43 #end if 43 #end if
44 #if '--dbmatched' in str($outputs).split( "," ): 44 #if '--dbmatched' in str($outputs).split( "," ):
45 --dbmatched "$dbmatched" 45 --dbmatched '$dbmatched'
46 #end if 46 #end if
47 #if '--dbnotmatched' in str($outputs).split( "," ): 47 #if '--dbnotmatched' in str($outputs).split( "," ):
48 --dbnotmatched "$dbnotmatched" 48 --dbnotmatched '$dbnotmatched'
49 #end if 49 #end if
50 #if '--fastapairs' in str($outputs).split( "," ): 50 #if '--fastapairs' in str($outputs).split( "," ):
51 --fastapairs "$fastapairs" 51 --fastapairs '$fastapairs'
52 #end if 52 #end if
53 #if '--notmatched' in str($outputs).split( "," ): 53 #if '--notmatched' in str($outputs).split( "," ):
54 --notmatched "$notmatched" 54 --notmatched '$notmatched'
55 #end if 55 #end if
56 #if '--matched' in str($outputs).split( "," ): 56 #if '--matched' in str($outputs).split( "," ):
57 --matched "$matched" 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
129 #if str( $adv_opts.idsuffix ): 129 #if str( $adv_opts.idsuffix ):
130 --idsuffix str( $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 $adv_opts.uclust_output.uclust_output_select == 'yes':
134 --uc "$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 "$adv_opts.wordlength"
145 145
257 </conditional> 257 </conditional>
258 258
259 259
260 </inputs> 260 </inputs>
261 <outputs> 261 <outputs>
262 <data name="uc" format="fasta" label="${tool.name} on ${on_string}: UCLUST like output"> 262 <data name="uc" format="tabular" label="${tool.name} on ${on_string}: UCLUST like output">
263 <filter>adv_opts['adv_opts_selector'] == "advanced" and adv_opts['uclust_output']['uclust_output_select'] == 'yes'</filter> 263 <filter>adv_opts['adv_opts_selector'] == "advanced" and adv_opts['uclust_output']['uclust_output_select'] == 'yes'</filter>
264 </data> 264 </data>
265 <data name="dbnotmatched" format="fasta" label="${tool.name} on ${on_string}: Non-matched database sequences"> 265 <data name="dbnotmatched" format="fasta" label="${tool.name} on ${on_string}: Non-matched database sequences">
266 <filter>'--dbnotmatchedt' in outputs</filter> 266 <filter>'--dbnotmatchedt' in outputs</filter>
267 </data> 267 </data>
286 <data name="userout" format="tabular" label="${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['adv_opts_selector'] == "advanced" and 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 expect_num_outputs="2">
292 <param name="dbfile" value="three_human_mRNA.fasta" ftype="fasta" /> 292 <param name="dbfile" value="three_human_mRNA.fasta" ftype="fasta" />
293 <param name="queryfile" value="query.fasta" ftype="fasta" /> 293 <param name="queryfile" value="query.fasta" ftype="fasta" />
294 <param name="outputs" value="--blast6out,--dbmatched" /> 294 <param name="outputs" value="--blast6out,--dbmatched" />
295 <param name="dbmask" value="none" /> 295 <param name="dbmask" value="none" />
296 <param name="adv_opts_selector" value="advanced" /> 296 <param name="adv_opts_selector" value="advanced" />
297 <param name="top_hits_only" value="True" /> 297 <param name="top_hits_only" value="True" />
298 <output name="dbmatched" file="search_dbmatched_result1.fasta" ftype="fasta" /> 298 <output name="dbmatched" file="search_dbmatched_result1.fasta" ftype="fasta" />
299 <output name="blast6out" file="search_blast6out_result1.tabular" ftype="tabular" /> 299 <output name="blast6out" file="search_blast6out_result1.tabular" ftype="tabular" />
300 </test> 300 </test>
301 <test> 301 <test expect_num_outputs="4">
302 <param name="dbfile" value="three_human_mRNA.fasta" ftype="fasta" /> 302 <param name="dbfile" value="three_human_mRNA.fasta" ftype="fasta" />
303 <param name="queryfile" value="query.fasta" ftype="fasta" /> 303 <param name="queryfile" value="query.fasta" ftype="fasta" />
304 <param name="outputs" value="--fastapairs,--matched" /> 304 <param name="outputs" value="--fastapairs,--matched" />
305 <param name="dbmask" value="none" /> 305 <param name="dbmask" value="none" />
306 <param name="adv_opts_selector" value="advanced" /> 306 <param name="adv_opts_selector" value="advanced" />
307 <param name="userfields_output_select" value="yes" /> 307 <param name="userfields_output_select" value="yes" />
308 <param name="userfields" value="query,target,evalue" /> 308 <param name="userfields" value="query,target,evalue" />
309 <param name="top_hits_only" value="True" /> 309 <param name="top_hits_only" value="True" />
310 <param name="output_no_hits" value="True" /> 310 <param name="output_no_hits" value="True" />
311 <param name="uclust_output_select" value="yes" />
312 <output name="uc" file="search_dbmatched_uc.tsv" ftype="tabular" />
311 <output name="matched" file="search_matched_result2.fasta" ftype="fasta" /> 313 <output name="matched" file="search_matched_result2.fasta" ftype="fasta" />
312 <output name="fastapairs" file="search_fastapairs_result2.fasta" ftype="fasta" /> 314 <output name="fastapairs" file="search_fastapairs_result2.fasta" ftype="fasta" />
313 <output name="userout" file="search_userfields_result2.tabular" ftype="tabular" /> 315 <output name="userout" file="search_userfields_result2.tabular" ftype="tabular" />
314 </test> 316 </test>
315 </tests> 317 </tests>