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changeset 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 b3c7199d8786
children
files search.xml test-data/search_dbmatched_uc.tsv
diffstat 2 files changed, 18 insertions(+), 15 deletions(-) [+]
line wrap: on
line diff
--- 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" />
--- /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
@@ -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.