| Previous changeset 5:b3c7199d8786 (2018-09-07) |
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Commit message:
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit 98411bbc8c371cf56d81fc4a1402ee64efef41eb" |
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modified:
search.xml |
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added:
test-data/search_dbmatched_uc.tsv |
| b |
| diff -r b3c7199d8786 -r 9495df9dd6ef search.xml --- a/search.xml Fri Sep 07 11:31:31 2018 -0400 +++ b/search.xml Wed Nov 04 07:36:19 2020 +0000 |
| [ |
| @@ -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> @@ -11,7 +11,7 @@ vsearch @GENERAL@ - --db "$dbfile" + --db '$dbfile' #if $dbmask: --dbmask "$dbmask" #end if @@ -33,28 +33,28 @@ $selfid_param $sizeout --strand "$strand" - --usearch_global "$queryfile" + --usearch_global '$queryfile' #if '--alnout' in str($outputs).split( "," ): - --alnout "$alnout" + --alnout '$alnout' #end if #if '--blast6out' in str($outputs).split( "," ): - --blast6out "$blast6out" + --blast6out '$blast6out' #end if #if '--dbmatched' in str($outputs).split( "," ): - --dbmatched "$dbmatched" + --dbmatched '$dbmatched' #end if #if '--dbnotmatched' in str($outputs).split( "," ): - --dbnotmatched "$dbnotmatched" + --dbnotmatched '$dbnotmatched' #end if #if '--fastapairs' in str($outputs).split( "," ): - --fastapairs "$fastapairs" + --fastapairs '$fastapairs' #end if #if '--notmatched' in str($outputs).split( "," ): - --notmatched "$notmatched" + --notmatched '$notmatched' #end if #if '--matched' in str($outputs).split( "," ): - --matched "$matched" + --matched '$matched' #end if #if $adv_opts.adv_opts_selector == "advanced": @@ -131,13 +131,13 @@ #end if #if $adv_opts.uclust_output.uclust_output_select == 'yes': - --uc "$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 @@ -259,7 +259,7 @@ </inputs> <outputs> - <data name="uc" format="fasta" label="${tool.name} on ${on_string}: UCLUST like output"> + <data name="uc" format="tabular" label="${tool.name} on ${on_string}: UCLUST like output"> <filter>adv_opts['adv_opts_selector'] == "advanced" and adv_opts['uclust_output']['uclust_output_select'] == 'yes'</filter> </data> <data name="dbnotmatched" format="fasta" label="${tool.name} on ${on_string}: Non-matched database sequences"> @@ -288,7 +288,7 @@ </data> </outputs> <tests> - <test> + <test expect_num_outputs="2"> <param name="dbfile" value="three_human_mRNA.fasta" ftype="fasta" /> <param name="queryfile" value="query.fasta" ftype="fasta" /> <param name="outputs" value="--blast6out,--dbmatched" /> @@ -298,7 +298,7 @@ <output name="dbmatched" file="search_dbmatched_result1.fasta" ftype="fasta" /> <output name="blast6out" file="search_blast6out_result1.tabular" ftype="tabular" /> </test> - <test> + <test expect_num_outputs="4"> <param name="dbfile" value="three_human_mRNA.fasta" ftype="fasta" /> <param name="queryfile" value="query.fasta" ftype="fasta" /> <param name="outputs" value="--fastapairs,--matched" /> @@ -308,6 +308,8 @@ <param name="userfields" value="query,target,evalue" /> <param name="top_hits_only" value="True" /> <param name="output_no_hits" value="True" /> + <param name="uclust_output_select" value="yes" /> + <output name="uc" file="search_dbmatched_uc.tsv" ftype="tabular" /> <output name="matched" file="search_matched_result2.fasta" ftype="fasta" /> <output name="fastapairs" file="search_fastapairs_result2.fasta" ftype="fasta" /> <output name="userout" file="search_userfields_result2.tabular" ftype="tabular" /> |
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| diff -r b3c7199d8786 -r 9495df9dd6ef test-data/search_dbmatched_uc.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/search_dbmatched_uc.tsv Wed Nov 04 07:36:19 2020 +0000 |
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| @@ -0,0 +1,1 @@ +H 0 1500 100.0 + 0 0 1500M3296I ENA|AB011145|AB011145.1 Homo sapiens mRNA for KIAA0573 protein, partial cds. ENA|AB011145|AB011145.1 Homo sapiens mRNA for KIAA0573 protein, partial cds. |