annotate screen.seqs.xml @ 10:63b74bfc8052 draft default tip

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit dfdd4c590370ecb3a9806314d43eb5668e36a01a"
author iuc
date Fri, 22 Jan 2021 01:26:14 +0000
parents c1feef4d5e34
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
9
c1feef4d5e34 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4c950508328589b5215b6c96868659a03f9dead8"
iuc
parents: 3
diff changeset
1 <tool profile="16.07" id="mothur_screen_seqs" name="Screen.seqs" version="@WRAPPER_VERSION@.1">
0
125a6ae65887 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff changeset
2 <description>Screen sequences</description>
125a6ae65887 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff changeset
3 <macros>
125a6ae65887 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff changeset
4 <import>macros.xml</import>
125a6ae65887 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff changeset
5 </macros>
125a6ae65887 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff changeset
6 <expand macro="requirements"/>
125a6ae65887 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff changeset
7 <expand macro="stdio"/>
125a6ae65887 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff changeset
8 <expand macro="version_command"/>
125a6ae65887 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff changeset
9 <command><![CDATA[
3
6202ff80199f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
parents: 2
diff changeset
10 @SHELL_OPTIONS@
0
125a6ae65887 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff changeset
11
3
6202ff80199f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
parents: 2
diff changeset
12 ## create symlinks to input datasets
6202ff80199f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
parents: 2
diff changeset
13 ln -s '$fasta' fasta.dat &&
6202ff80199f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
parents: 2
diff changeset
14 ln -s '$names' names.dat &&
6202ff80199f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
parents: 2
diff changeset
15 ln -s '$groups' groups.dat &&
6202ff80199f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
parents: 2
diff changeset
16 ln -s '$qfile' qfile.dat &&
6202ff80199f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
parents: 2
diff changeset
17 ln -s '$count' count.dat &&
6202ff80199f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
parents: 2
diff changeset
18 ln -s '$taxonomy' taxonomy.dat &&
6202ff80199f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
parents: 2
diff changeset
19 ln -s '$summary' summary.dat &&
6202ff80199f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
parents: 2
diff changeset
20 #if $contigsrep.usecontigs == "yes":
6202ff80199f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
parents: 2
diff changeset
21 ln -s '$contigsrep.contigsreport' contigsreport.dat &&
6202ff80199f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
parents: 2
diff changeset
22 #end if
6202ff80199f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
parents: 2
diff changeset
23 #if $alignrep.usealign == "yes":
6202ff80199f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
parents: 2
diff changeset
24 ln -s '$alignrep.alignreport' alignreport.dat &&
6202ff80199f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
parents: 2
diff changeset
25 #end if
0
125a6ae65887 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff changeset
26
3
6202ff80199f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
parents: 2
diff changeset
27 echo 'screen.seqs(
6202ff80199f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
parents: 2
diff changeset
28 fasta=fasta.dat
6202ff80199f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
parents: 2
diff changeset
29 #if int($start) > -1:
6202ff80199f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
parents: 2
diff changeset
30 ,start=$start
6202ff80199f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
parents: 2
diff changeset
31 #end if
6202ff80199f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
parents: 2
diff changeset
32 #if int($end) > -1:
6202ff80199f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
parents: 2
diff changeset
33 ,end=$end
6202ff80199f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
parents: 2
diff changeset
34 #end if
6202ff80199f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
parents: 2
diff changeset
35 #if int($minlength) > -1:
6202ff80199f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
parents: 2
diff changeset
36 ,minlength=$minlength
6202ff80199f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
parents: 2
diff changeset
37 #end if
6202ff80199f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
parents: 2
diff changeset
38 #if int($maxlength) > -1:
6202ff80199f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
parents: 2
diff changeset
39 ,maxlength=$maxlength
6202ff80199f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
parents: 2
diff changeset
40 #end if
6202ff80199f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
parents: 2
diff changeset
41 #if int($maxambig) > -1:
6202ff80199f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
parents: 2
diff changeset
42 ,maxambig=$maxambig
6202ff80199f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
parents: 2
diff changeset
43 #end if
6202ff80199f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
parents: 2
diff changeset
44 #if int($maxhomop) > -1:
6202ff80199f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
parents: 2
diff changeset
45 ,maxhomop=$maxhomop
6202ff80199f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
parents: 2
diff changeset
46 #end if
6202ff80199f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
parents: 2
diff changeset
47 #if int($criteria) > -1:
6202ff80199f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
parents: 2
diff changeset
48 ,criteria=$criteria
6202ff80199f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
parents: 2
diff changeset
49 #end if
6202ff80199f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
parents: 2
diff changeset
50 #if $optimize:
9
c1feef4d5e34 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4c950508328589b5215b6c96868659a03f9dead8"
iuc
parents: 3
diff changeset
51 ,optimize=#echo str($optimize).replace(',','-') #
3
6202ff80199f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
parents: 2
diff changeset
52 #end if
6202ff80199f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
parents: 2
diff changeset
53 #if $qfile:
6202ff80199f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
parents: 2
diff changeset
54 ,qfile=qfile.dat
6202ff80199f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
parents: 2
diff changeset
55 #end if
6202ff80199f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
parents: 2
diff changeset
56 #if $names:
6202ff80199f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
parents: 2
diff changeset
57 ,name=names.dat
6202ff80199f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
parents: 2
diff changeset
58 #end if
6202ff80199f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
parents: 2
diff changeset
59 #if $groups:
6202ff80199f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
parents: 2
diff changeset
60 ,group=groups.dat
6202ff80199f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
parents: 2
diff changeset
61 #end if
6202ff80199f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
parents: 2
diff changeset
62 #if $taxonomy:
6202ff80199f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
parents: 2
diff changeset
63 ,taxonomy=taxonomy.dat
6202ff80199f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
parents: 2
diff changeset
64 #end if
6202ff80199f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
parents: 2
diff changeset
65 #if $count:
6202ff80199f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
parents: 2
diff changeset
66 ,count=count.dat
6202ff80199f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
parents: 2
diff changeset
67 #end if
6202ff80199f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
parents: 2
diff changeset
68 #if $summary:
6202ff80199f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
parents: 2
diff changeset
69 ,summary=summary.dat
6202ff80199f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
parents: 2
diff changeset
70 #end if
6202ff80199f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
parents: 2
diff changeset
71 #if $contigsrep.usecontigs == "yes":
6202ff80199f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
parents: 2
diff changeset
72 ,contigsreport=contigsreport.dat
6202ff80199f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
parents: 2
diff changeset
73 ,minoverlap=$contigsrep.minoverlap
6202ff80199f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
parents: 2
diff changeset
74 ,ostart=$contigsrep.ostart
6202ff80199f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
parents: 2
diff changeset
75 ,oend=$contigsrep.oend
6202ff80199f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
parents: 2
diff changeset
76 ,mismatches=$contigsrep.mismatches
6202ff80199f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
parents: 2
diff changeset
77 #end if
6202ff80199f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
parents: 2
diff changeset
78 #if $alignrep.usealign == "yes":
6202ff80199f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
parents: 2
diff changeset
79 ,alignreport=alignreport.dat
6202ff80199f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
parents: 2
diff changeset
80 ,minsim=$alignrep.minsim
6202ff80199f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
parents: 2
diff changeset
81 ,minscore=$alignrep.minscore
6202ff80199f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
parents: 2
diff changeset
82 ,maxinsert=$alignrep.maxinsert
6202ff80199f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
parents: 2
diff changeset
83 #end if
6202ff80199f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
parents: 2
diff changeset
84 ,processors='"\${GALAXY_SLOTS:-8}"'
6202ff80199f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
parents: 2
diff changeset
85 )'
6202ff80199f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
parents: 2
diff changeset
86 | sed 's/ //g' ## mothur trips over whitespace
6202ff80199f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
parents: 2
diff changeset
87 | mothur
6202ff80199f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
parents: 2
diff changeset
88 | tee mothur.out.log
0
125a6ae65887 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff changeset
89 ]]></command>
125a6ae65887 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff changeset
90 <inputs>
3
6202ff80199f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
parents: 2
diff changeset
91 <param argument="fasta" type="data" format="fasta,mothur.align" label="fasta - Fasta to screen"/>
6202ff80199f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
parents: 2
diff changeset
92 <param argument="start" type="integer" value="-1" label="start - Remove sequences that start after position (ignored when negative)"/>
6202ff80199f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
parents: 2
diff changeset
93 <param argument="end" type="integer" value="-1" label="end - Remove sequences that end before position (ignored when negative)"/>
6202ff80199f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
parents: 2
diff changeset
94 <param argument="minlength" type="integer" value="10" label="minlength - Remove sequences shorter than (ignored when negative)"/>
6202ff80199f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
parents: 2
diff changeset
95 <param argument="maxlength" type="integer" value="-1" label="maxlength - Remove sequences longer than (ignored when negative)"/>
6202ff80199f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
parents: 2
diff changeset
96 <param argument="maxambig" type="integer" value="-1" label="maxambig - Remove sequences with ambiguous bases greater than (ignored when negative)"/>
6202ff80199f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
parents: 2
diff changeset
97 <param argument="maxhomop" type="integer" value="-1" label="maxhomop - Remove sequences with homopolymers greater than (ignored when negative)"/>
6202ff80199f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
parents: 2
diff changeset
98 <param argument="criteria" type="integer" value="-1" label="criteria - Percent of sequences that an optimize value must match to be retained (ignored when negative)"/>
6202ff80199f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
parents: 2
diff changeset
99 <param argument="optimize" type="select" multiple="true" display="checkboxes" label="optimize - Optimize selected paramenters">
0
125a6ae65887 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff changeset
100 <option value="start">start</option>
125a6ae65887 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff changeset
101 <option value="end">end</option>
125a6ae65887 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff changeset
102 <option value="minlength">minlength</option>
125a6ae65887 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff changeset
103 <option value="maxlength">maxlength</option>
125a6ae65887 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff changeset
104 <option value="maxambig">maxambig</option>
125a6ae65887 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff changeset
105 <option value="maxhomop">maxhomop</option>
125a6ae65887 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff changeset
106 </param>
3
6202ff80199f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
parents: 2
diff changeset
107 <param argument="qfile" type="data" format="qual" optional="true" label="qfile - Sequence Quality file to screen"/>
6202ff80199f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
parents: 2
diff changeset
108 <param argument="names" type="data" format="mothur.names" optional="true" label="name - Sequence Names to screen"/>
6202ff80199f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
parents: 2
diff changeset
109 <param argument="groups" type="data" format="mothur.groups" optional="true" label="group - Groups to screen"/>
6202ff80199f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
parents: 2
diff changeset
110 <param argument="summary" type="data" format="mothur.summary" optional="true" label="summary file - as created by summary.seqs"
6202ff80199f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
parents: 2
diff changeset
111 help="saves processing time when screening with parameters in the summary file"/>
6202ff80199f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
parents: 2
diff changeset
112 <param argument="taxonomy" type="data" format="taxonomy" optional="true" label="taxonomy - Taxonomy to screen"/>
6202ff80199f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
parents: 2
diff changeset
113 <param argument="count" type="data" format="mothur.count_table" optional="true" label="count - a count_table" help="generated by count.seqs"/>
6202ff80199f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
parents: 2
diff changeset
114 <conditional name="alignrep">
6202ff80199f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
parents: 2
diff changeset
115 <param name="usealign" type="select" label="Perform screening using an alignment report?" help="An alignment report is created by the align.seqs tool.
6202ff80199f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
parents: 2
diff changeset
116 If you provide the alignment report file you can screen your sequences using the following parameters: minsim, minscore, and maxinsert">
6202ff80199f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
parents: 2
diff changeset
117 <option value="yes">Yes</option>
6202ff80199f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
parents: 2
diff changeset
118 <option value="no" selected="true">No</option>
6202ff80199f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
parents: 2
diff changeset
119 </param>
6202ff80199f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
parents: 2
diff changeset
120 <when value="yes">
6202ff80199f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
parents: 2
diff changeset
121 <param argument="alignreport" type="data" format="mothur.align.report" label="alignreport - Align Report to screen with"/>
6202ff80199f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
parents: 2
diff changeset
122 <param argument="minsim" type="integer" value="-1" min="-1" label="minsim - Minimum similarity to template sequences during alignment"/>
6202ff80199f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
parents: 2
diff changeset
123 <param argument="minscore" type="integer" value="-1" min="-1" label="minscore - Minimum search score during alignment (ignored when negative)"/>
6202ff80199f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
parents: 2
diff changeset
124 <param argument="maxinsert" type="integer" value="-1" min="-1" label="maxinsert - Maximum number of insertions during alignment (ignored when negative)"/>
6202ff80199f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
parents: 2
diff changeset
125 </when>
6202ff80199f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
parents: 2
diff changeset
126 <when value="no"/>
6202ff80199f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
parents: 2
diff changeset
127 </conditional>
6202ff80199f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
parents: 2
diff changeset
128 <conditional name="contigsrep">
6202ff80199f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
parents: 2
diff changeset
129 <param name="usecontigs" type="select" label="Perform screening using a contigsreport?" help="A contigsreport is created by the make.contigs tool.
6202ff80199f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
parents: 2
diff changeset
130 If you provide the contigs report file you can screen your sequences using the following parameters: minoverlap, ostart, oend and mismatches">
6202ff80199f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
parents: 2
diff changeset
131 <option value="yes">Yes</option>
6202ff80199f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
parents: 2
diff changeset
132 <option value="no" selected="true">No</option>
6202ff80199f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
parents: 2
diff changeset
133 </param>
6202ff80199f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
parents: 2
diff changeset
134 <when value="yes">
6202ff80199f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
parents: 2
diff changeset
135 <param argument="contigsreport" type="data" format="tabular" label="contigsreport - Contigs Report to screen with"
6202ff80199f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
parents: 2
diff changeset
136 help="this file is created by the make.contigs command"/>
6202ff80199f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
parents: 2
diff changeset
137 <param argument="minoverlap" type="integer" value="-1" min="-1" label="minoverlap - Minimum overlap length (ignored when negative)"/>
6202ff80199f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
parents: 2
diff changeset
138 <param argument="ostart" type="integer" value="-1" min="-1" label="ostart - Position the overlap must start by (ignored when negative)"/>
6202ff80199f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
parents: 2
diff changeset
139 <param argument="oend" type="integer" value="-1" min="-1" label="oend - Position the overlap must end after (ignored when negative)"/>
6202ff80199f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
parents: 2
diff changeset
140 <param argument="mismatches" type="integer" value="-1" min="-1" label="mismatches - Maximum number of mismatches (ignored when negative)"/>
6202ff80199f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
parents: 2
diff changeset
141 </when>
6202ff80199f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
parents: 2
diff changeset
142 <when value="no"/>
6202ff80199f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
parents: 2
diff changeset
143 </conditional>
6202ff80199f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
parents: 2
diff changeset
144 <expand macro="param-savelog"/>
0
125a6ae65887 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff changeset
145 </inputs>
125a6ae65887 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff changeset
146 <outputs>
125a6ae65887 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff changeset
147 <expand macro="logfile-output"/>
3
6202ff80199f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
parents: 2
diff changeset
148 <data name="fasta_out" format_source="fasta" from_work_dir="fasta*.good.dat" label="${tool.name} on ${on_string}: good.${fasta.datatype.file_ext}"/>
6202ff80199f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
parents: 2
diff changeset
149 <data name="bad_accnos" format="mothur.accnos" from_work_dir="fasta*.bad.accnos" label="${tool.name} on ${on_string}: bad.accnos"/>
6202ff80199f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
parents: 2
diff changeset
150 <data name="qfile_out" format_source="qfile" from_work_dir="qfile*.good.dat" label="${tool.name} on ${on_string}: qfile">
6202ff80199f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
parents: 2
diff changeset
151 <filter>qfile</filter>
0
125a6ae65887 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff changeset
152 </data>
3
6202ff80199f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
parents: 2
diff changeset
153 <data name="names_out" format="mothur.names" from_work_dir="names*.good.dat" label="${tool.name} on ${on_string}: names">
6202ff80199f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
parents: 2
diff changeset
154 <filter>names</filter>
0
125a6ae65887 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff changeset
155 </data>
3
6202ff80199f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
parents: 2
diff changeset
156 <data name="groups_out" format="mothur.groups" from_work_dir="groups*.good.dat" label="${tool.name} on ${on_string}: groups">
6202ff80199f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
parents: 2
diff changeset
157 <filter>groups</filter>
6202ff80199f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
parents: 2
diff changeset
158 </data>
6202ff80199f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
parents: 2
diff changeset
159 <data name="alignreport_out" format="mothur.align.report" from_work_dir="alignreport.good.align.report" label="${tool.name} on ${on_string}: align.report">
6202ff80199f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
parents: 2
diff changeset
160 <filter>alignrep.alignreport</filter>
0
125a6ae65887 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff changeset
161 </data>
3
6202ff80199f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
parents: 2
diff changeset
162 <data name="contigsreport_out" format="tabular" from_work_dir="contigsreport.good.contigs.report" label="${tool.name} on ${on_string}: contigs.report">
6202ff80199f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
parents: 2
diff changeset
163 <filter>contigsrep.contigsreport</filter>
0
125a6ae65887 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff changeset
164 </data>
3
6202ff80199f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
parents: 2
diff changeset
165 <data name="count_out" format="mothur.count_table" from_work_dir="count*.good.dat" label="${tool.name} on ${on_string}: count">
6202ff80199f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
parents: 2
diff changeset
166 <filter>count</filter>
0
125a6ae65887 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff changeset
167 </data>
125a6ae65887 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff changeset
168 </outputs>
125a6ae65887 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff changeset
169 <tests>
125a6ae65887 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff changeset
170 <test>
3
6202ff80199f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
parents: 2
diff changeset
171 <param name="fasta" value="Mock_S280_L001_R1_001_small.trim.contigs.fasta" ftype="fasta"/>
0
125a6ae65887 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff changeset
172 <param name="maxambig" value="0"/>
125a6ae65887 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff changeset
173 <param name="maxlength" value="275"/>
125a6ae65887 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff changeset
174 <output name="fasta_out" file="Mock_S280_L001_R1_001_small.trim.contigs.good.fasta" ftype="fasta"/>
125a6ae65887 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff changeset
175 <output name="bad_accnos" file="Mock_S280_L001_R1_001_small.trim.contigs.bad.accnos" ftype="mothur.accnos"/>
3
6202ff80199f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
parents: 2
diff changeset
176 <param name="savelog" value="true"/>
6202ff80199f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
parents: 2
diff changeset
177 <expand macro="logfile-test"/>
6202ff80199f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
parents: 2
diff changeset
178 </test>
9
c1feef4d5e34 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4c950508328589b5215b6c96868659a03f9dead8"
iuc
parents: 3
diff changeset
179 <test><!-- test for multiple optimize options minlenght, maxlength, maxhomop -->
c1feef4d5e34 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4c950508328589b5215b6c96868659a03f9dead8"
iuc
parents: 3
diff changeset
180 <param name="fasta" value="Mock_S280_L001_R1_001_small.trim.contigs.fasta" ftype="fasta"/>
c1feef4d5e34 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4c950508328589b5215b6c96868659a03f9dead8"
iuc
parents: 3
diff changeset
181 <param name="criteria" value="50"/>
c1feef4d5e34 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4c950508328589b5215b6c96868659a03f9dead8"
iuc
parents: 3
diff changeset
182 <param name="optimize" value="minlength,maxlength,maxhomop"/>
c1feef4d5e34 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4c950508328589b5215b6c96868659a03f9dead8"
iuc
parents: 3
diff changeset
183 <output name="fasta_out" file="Mock_S280_L001_R1_001_small.trim.contigs.optimize.minlength.maxlength.maxhomop.good.fasta" ftype="fasta"/>
c1feef4d5e34 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4c950508328589b5215b6c96868659a03f9dead8"
iuc
parents: 3
diff changeset
184 <output name="bad_accnos" file="Mock_S280_L001_R1_001_small.trim.contigs.optimize.minlength.maxlength.maxhomop.bad.accnos" ftype="mothur.accnos"/>
c1feef4d5e34 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4c950508328589b5215b6c96868659a03f9dead8"
iuc
parents: 3
diff changeset
185 <param name="savelog" value="true"/>
c1feef4d5e34 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4c950508328589b5215b6c96868659a03f9dead8"
iuc
parents: 3
diff changeset
186 <expand macro="logfile-test"/>
c1feef4d5e34 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4c950508328589b5215b6c96868659a03f9dead8"
iuc
parents: 3
diff changeset
187 </test>
c1feef4d5e34 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4c950508328589b5215b6c96868659a03f9dead8"
iuc
parents: 3
diff changeset
188 <test><!-- test for multiple optimize options end, maxambig -->
c1feef4d5e34 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4c950508328589b5215b6c96868659a03f9dead8"
iuc
parents: 3
diff changeset
189 <param name="fasta" value="Mock_S280_L001_R1_001_small.trim.contigs.fasta" ftype="fasta"/>
c1feef4d5e34 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4c950508328589b5215b6c96868659a03f9dead8"
iuc
parents: 3
diff changeset
190 <param name="criteria" value="50"/>
c1feef4d5e34 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4c950508328589b5215b6c96868659a03f9dead8"
iuc
parents: 3
diff changeset
191 <param name="optimize" value="end,maxambig"/>
c1feef4d5e34 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4c950508328589b5215b6c96868659a03f9dead8"
iuc
parents: 3
diff changeset
192 <output name="fasta_out" file="Mock_S280_L001_R1_001_small.trim.contigs.optimize.end.maxambig.good.fasta" ftype="fasta"/>
c1feef4d5e34 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4c950508328589b5215b6c96868659a03f9dead8"
iuc
parents: 3
diff changeset
193 <output name="bad_accnos" file="Mock_S280_L001_R1_001_small.trim.contigs.optimize.end.maxambig.bad.accnos" ftype="mothur.accnos"/>
c1feef4d5e34 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4c950508328589b5215b6c96868659a03f9dead8"
iuc
parents: 3
diff changeset
194 <param name="savelog" value="true"/>
c1feef4d5e34 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4c950508328589b5215b6c96868659a03f9dead8"
iuc
parents: 3
diff changeset
195 <expand macro="logfile-test"/>
c1feef4d5e34 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4c950508328589b5215b6c96868659a03f9dead8"
iuc
parents: 3
diff changeset
196 </test>
3
6202ff80199f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
parents: 2
diff changeset
197 <test><!-- test with count table -->
6202ff80199f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
parents: 2
diff changeset
198 <param name="fasta" value="amazon.fasta" ftype="mothur.align"/>
6202ff80199f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
parents: 2
diff changeset
199 <param name="count" value="amazon1.count_table"/>
6202ff80199f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
parents: 2
diff changeset
200 <param name="maxambig" value="0"/>
6202ff80199f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
parents: 2
diff changeset
201 <param name="maxlength" value="500"/>
6202ff80199f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
parents: 2
diff changeset
202 <output name="fasta_out" ftype="mothur.align">
6202ff80199f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
parents: 2
diff changeset
203 <assert_contents>
6202ff80199f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
parents: 2
diff changeset
204 <expand macro="test-fasta-format"/>
6202ff80199f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
parents: 2
diff changeset
205 <has_text text="U68638"/>
6202ff80199f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
parents: 2
diff changeset
206 <not_has_text text="U68589"/>
6202ff80199f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
parents: 2
diff changeset
207 </assert_contents>
6202ff80199f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
parents: 2
diff changeset
208 </output>
6202ff80199f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
parents: 2
diff changeset
209 <output name="count_out" ftype="mothur.count_table">
6202ff80199f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
parents: 2
diff changeset
210 <assert_contents>
6202ff80199f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
parents: 2
diff changeset
211 <expand macro="test-count-format"/>
6202ff80199f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
parents: 2
diff changeset
212 <has_text text="U68638"/>
6202ff80199f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
parents: 2
diff changeset
213 <not_has_text text="U68589"/>
6202ff80199f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
parents: 2
diff changeset
214 </assert_contents>
6202ff80199f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
parents: 2
diff changeset
215 </output>
6202ff80199f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
parents: 2
diff changeset
216 <output name="bad_accnos" ftype="mothur.accnos">
6202ff80199f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
parents: 2
diff changeset
217 <assert_contents>
6202ff80199f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
parents: 2
diff changeset
218 <expand macro="test-accnos-format"/>
6202ff80199f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
parents: 2
diff changeset
219 <not_has_text text="U68638"/>
6202ff80199f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
parents: 2
diff changeset
220 <has_text text="U68589"/>
6202ff80199f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
parents: 2
diff changeset
221 <has_text text="ambig"/>
6202ff80199f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
parents: 2
diff changeset
222 <has_text text="length"/>
6202ff80199f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
parents: 2
diff changeset
223 </assert_contents>
6202ff80199f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
parents: 2
diff changeset
224 </output>
6202ff80199f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
parents: 2
diff changeset
225 <param name="savelog" value="true"/>
0
125a6ae65887 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff changeset
226 <expand macro="logfile-test"/>
125a6ae65887 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff changeset
227 </test>
3
6202ff80199f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
parents: 2
diff changeset
228 <test><!-- test screening with contigsreport -->
6202ff80199f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
parents: 2
diff changeset
229 <param name="fasta" value="Mock_S280_L001_R1_001_small.trim.contigs.fasta" ftype="fasta"/>
0
125a6ae65887 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff changeset
230 <param name="maxambig" value="0"/>
125a6ae65887 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff changeset
231 <param name="maxlength" value="275"/>
3
6202ff80199f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
parents: 2
diff changeset
232 <param name="usecontigs" value="yes"/>
6202ff80199f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
parents: 2
diff changeset
233 <param name="contigsreport" value="Mock_S280_L001_R1_001_small.contigs.report"/>
6202ff80199f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
parents: 2
diff changeset
234 <param name="mismatches" value="18"/>
6202ff80199f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
parents: 2
diff changeset
235 <output name="fasta_out" file="Mock_S280_L001_R1_001_small.trim.contigs.good.fasta" ftype="fasta"/>
6202ff80199f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
parents: 2
diff changeset
236 <output name="bad_accnos" ftype="mothur.accnos">
6202ff80199f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
parents: 2
diff changeset
237 <assert_contents>
6202ff80199f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
parents: 2
diff changeset
238 <expand macro="test-accnos-format"/>
6202ff80199f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
parents: 2
diff changeset
239 <has_text text="mismatches"/>
6202ff80199f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
parents: 2
diff changeset
240 <has_text text="ambig"/>
6202ff80199f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
parents: 2
diff changeset
241 </assert_contents>
6202ff80199f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
parents: 2
diff changeset
242 </output>
6202ff80199f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
parents: 2
diff changeset
243 <output name="contigsreport_out" ftype="tabular">
6202ff80199f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
parents: 2
diff changeset
244 <assert_contents>
6202ff80199f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
parents: 2
diff changeset
245 <expand macro="test-contigsreport-format"/>
6202ff80199f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
parents: 2
diff changeset
246 <not_has_text text="M00967_43_000000000-A3JHG_1_1101_22487_4260"/>
6202ff80199f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
parents: 2
diff changeset
247 <has_text text="M00967_43_000000000-A3JHG_1_1101_15923_3823"/>
6202ff80199f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
parents: 2
diff changeset
248 </assert_contents>
6202ff80199f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
parents: 2
diff changeset
249 </output>
6202ff80199f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
parents: 2
diff changeset
250 <param name="savelog" value="true"/>
6202ff80199f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
parents: 2
diff changeset
251 <expand macro="logfile-test"/>
6202ff80199f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
parents: 2
diff changeset
252 </test>
6202ff80199f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
parents: 2
diff changeset
253 <test><!-- test screening with alignment report -->
6202ff80199f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
parents: 2
diff changeset
254 <param name="fasta" value="Mock_S280_L001_R1_001_small.trim.contigs.good.fasta" ftype="fasta"/>
6202ff80199f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
parents: 2
diff changeset
255 <param name="maxambig" value="0"/>
6202ff80199f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
parents: 2
diff changeset
256 <param name="maxlength" value="275"/>
6202ff80199f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
parents: 2
diff changeset
257 <param name="usealign" value="yes"/>
6202ff80199f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
parents: 2
diff changeset
258 <param name="alignreport" value="Mock_S280_L001_R1_001_small.trim.contigs.good.align.report"/>
6202ff80199f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
parents: 2
diff changeset
259 <param name="minscore" value="100"/>
6202ff80199f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
parents: 2
diff changeset
260 <output name="fasta_out" ftype="fasta">
6202ff80199f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
parents: 2
diff changeset
261 <assert_contents>
6202ff80199f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
parents: 2
diff changeset
262 <expand macro="test-fasta-format"/>
6202ff80199f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
parents: 2
diff changeset
263 <not_has_text text="M00967_43_000000000-A3JHG_1_1101_14010_4122"/>
6202ff80199f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
parents: 2
diff changeset
264 <has_text text="M00967_43_000000000-A3JHG_1_1101_19936_3208"/>
6202ff80199f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
parents: 2
diff changeset
265 </assert_contents>
6202ff80199f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
parents: 2
diff changeset
266 </output>
6202ff80199f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
parents: 2
diff changeset
267 <output name="bad_accnos" ftype="mothur.accnos">
6202ff80199f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
parents: 2
diff changeset
268 <assert_contents>
6202ff80199f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
parents: 2
diff changeset
269 <expand macro="test-accnos-format"/>
6202ff80199f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
parents: 2
diff changeset
270 <has_text text="score"/>
6202ff80199f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
parents: 2
diff changeset
271 </assert_contents>
6202ff80199f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
parents: 2
diff changeset
272 </output>
6202ff80199f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
parents: 2
diff changeset
273 <output name="alignreport_out" ftype="mothur.align.report">
6202ff80199f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
parents: 2
diff changeset
274 <assert_contents>
6202ff80199f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
parents: 2
diff changeset
275 <expand macro="test-alignreport-format"/>
6202ff80199f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
parents: 2
diff changeset
276 <not_has_text text="M00967_43_000000000-A3JHG_1_1101_14010_4122"/>
6202ff80199f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
parents: 2
diff changeset
277 <has_text text="M00967_43_000000000-A3JHG_1_1101_19936_3208"/>
6202ff80199f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
parents: 2
diff changeset
278 </assert_contents>
6202ff80199f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
parents: 2
diff changeset
279 </output>
6202ff80199f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
parents: 2
diff changeset
280 <param name="savelog" value="true"/>
0
125a6ae65887 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff changeset
281 <expand macro="logfile-test"/>
125a6ae65887 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff changeset
282 </test>
125a6ae65887 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff changeset
283 </tests>
3
6202ff80199f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
parents: 2
diff changeset
284 <help><![CDATA[
0
125a6ae65887 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff changeset
285
125a6ae65887 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff changeset
286 @MOTHUR_OVERVIEW@
125a6ae65887 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff changeset
287
125a6ae65887 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff changeset
288 **Command Documentation**
125a6ae65887 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff changeset
289
125a6ae65887 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff changeset
290 The screen.seqs_ command enables you to keep sequences that fulfill certain user defined criteria. Furthermore, it enables you to cull those sequences not meeting the criteria from a name_, group_, or align.report_ file.
125a6ae65887 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff changeset
291
125a6ae65887 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff changeset
292 .. _name: https://www.mothur.org/wiki/Name_file
125a6ae65887 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff changeset
293 .. _group: https://www.mothur.org/wiki/Group_file
125a6ae65887 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff changeset
294 .. _align.report: https://www.mothur.org/wiki/Align.seqs
125a6ae65887 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff changeset
295 .. _screen.seqs: https://www.mothur.org/wiki/Screen.seqs
125a6ae65887 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff changeset
296
3
6202ff80199f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
parents: 2
diff changeset
297 ]]></help>
0
125a6ae65887 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff changeset
298 <expand macro="citations"/>
125a6ae65887 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff changeset
299 </tool>