Mercurial > repos > iuc > vsearch
comparison search.xml @ 6:9495df9dd6ef draft default tip
"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 |
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| 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> |