annotate diamond.xml @ 6:64be1ac21109 draft

planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
author bgruening
date Thu, 27 Sep 2018 06:30:30 -0400
parents 830516f9521b
children 62c9df8382c2
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
6
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
parents: 3
diff changeset
1 <tool id="bg_diamond" name="Diamond" version="@VERSION@.0">
0
98037ef3d2a9 Imported from capsule None
bgruening
parents:
diff changeset
2 <description>alignment tool for short sequences against a protein database</description>
1
df7738595640 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit cc80b878817d052398db16574917900ebe15292e
bgruening
parents: 0
diff changeset
3 <macros>
df7738595640 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit cc80b878817d052398db16574917900ebe15292e
bgruening
parents: 0
diff changeset
4 <import>macros.xml</import>
df7738595640 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit cc80b878817d052398db16574917900ebe15292e
bgruening
parents: 0
diff changeset
5 </macros>
df7738595640 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit cc80b878817d052398db16574917900ebe15292e
bgruening
parents: 0
diff changeset
6 <expand macro="requirements" />
df7738595640 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit cc80b878817d052398db16574917900ebe15292e
bgruening
parents: 0
diff changeset
7 <expand macro="stdio" />
df7738595640 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit cc80b878817d052398db16574917900ebe15292e
bgruening
parents: 0
diff changeset
8 <expand macro="version_command" />
0
98037ef3d2a9 Imported from capsule None
bgruening
parents:
diff changeset
9 <command>
98037ef3d2a9 Imported from capsule None
bgruening
parents:
diff changeset
10 <![CDATA[
98037ef3d2a9 Imported from capsule None
bgruening
parents:
diff changeset
11
98037ef3d2a9 Imported from capsule None
bgruening
parents:
diff changeset
12 #if $ref_db_source.db_source == "history":
98037ef3d2a9 Imported from capsule None
bgruening
parents:
diff changeset
13 ln -s $ref_db_source.reference_database ./database.dmnd
98037ef3d2a9 Imported from capsule None
bgruening
parents:
diff changeset
14 #else:
98037ef3d2a9 Imported from capsule None
bgruening
parents:
diff changeset
15 ln -s ${ref_db_source.index.fields.db_path} ./database.dmnd
98037ef3d2a9 Imported from capsule None
bgruening
parents:
diff changeset
16 #end if
98037ef3d2a9 Imported from capsule None
bgruening
parents:
diff changeset
17
98037ef3d2a9 Imported from capsule None
bgruening
parents:
diff changeset
18 &&
98037ef3d2a9 Imported from capsule None
bgruening
parents:
diff changeset
19
98037ef3d2a9 Imported from capsule None
bgruening
parents:
diff changeset
20 diamond
6
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
parents: 3
diff changeset
21 $method_cond.method_select
0
98037ef3d2a9 Imported from capsule None
bgruening
parents:
diff changeset
22 --threads "\${GALAXY_SLOTS:-12}"
98037ef3d2a9 Imported from capsule None
bgruening
parents:
diff changeset
23 --db ./database
1
df7738595640 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit cc80b878817d052398db16574917900ebe15292e
bgruening
parents: 0
diff changeset
24 --query '$query'
6
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
parents: 3
diff changeset
25 #if $method_cond.method_select == "blastx"
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
parents: 3
diff changeset
26 --query-gencode '$method_cond.query_gencode'
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
parents: 3
diff changeset
27 --strand '$method_cond.query_strand'
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
parents: 3
diff changeset
28 --min-orf $method_cond.min_orf
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
parents: 3
diff changeset
29 #if $method_cond.frameshift_cond.frameshift_select == 'yes'
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
parents: 3
diff changeset
30 --frameshift $method_cond.frameshift_cond.frameshift
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
parents: 3
diff changeset
31 $method_cond.frameshift_cond.range_culling
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
parents: 3
diff changeset
32 #end if
3
830516f9521b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 0a893f1ee7f73d24004a43ec1ba6a4cc03fbfab0
bgruening
parents: 1
diff changeset
33 #end if
1
df7738595640 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit cc80b878817d052398db16574917900ebe15292e
bgruening
parents: 0
diff changeset
34
6
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
parents: 3
diff changeset
35 @OUTPUT_ARGS@
1
df7738595640 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit cc80b878817d052398db16574917900ebe15292e
bgruening
parents: 0
diff changeset
36
df7738595640 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit cc80b878817d052398db16574917900ebe15292e
bgruening
parents: 0
diff changeset
37 --compress '0'
3
830516f9521b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 0a893f1ee7f73d24004a43ec1ba6a4cc03fbfab0
bgruening
parents: 1
diff changeset
38 #if $sensitivity == "1"
830516f9521b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 0a893f1ee7f73d24004a43ec1ba6a4cc03fbfab0
bgruening
parents: 1
diff changeset
39 --sensitive
830516f9521b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 0a893f1ee7f73d24004a43ec1ba6a4cc03fbfab0
bgruening
parents: 1
diff changeset
40 #else if $sensitivity == "2"
830516f9521b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 0a893f1ee7f73d24004a43ec1ba6a4cc03fbfab0
bgruening
parents: 1
diff changeset
41 --more-sensitive
830516f9521b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 0a893f1ee7f73d24004a43ec1ba6a4cc03fbfab0
bgruening
parents: 1
diff changeset
42 #end if
830516f9521b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 0a893f1ee7f73d24004a43ec1ba6a4cc03fbfab0
bgruening
parents: 1
diff changeset
43
6
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
parents: 3
diff changeset
44 #if str($gapopen) != "":
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
parents: 3
diff changeset
45 --gapopen '$gapopen'
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
parents: 3
diff changeset
46 #end if
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
parents: 3
diff changeset
47 #if str($gapextend) != "":
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
parents: 3
diff changeset
48 --gapextend '$gapextend'
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
parents: 3
diff changeset
49 #end if
1
df7738595640 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit cc80b878817d052398db16574917900ebe15292e
bgruening
parents: 0
diff changeset
50 --matrix '$matrix'
6
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
parents: 3
diff changeset
51 --comp-based-stats '$comp_based_stats'
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
parents: 3
diff changeset
52 --masking '$masking'
0
98037ef3d2a9 Imported from capsule None
bgruening
parents:
diff changeset
53
6
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
parents: 3
diff changeset
54 @HITFILTER_ARGS@
0
98037ef3d2a9 Imported from capsule None
bgruening
parents:
diff changeset
55
98037ef3d2a9 Imported from capsule None
bgruening
parents:
diff changeset
56 #if str($filter_score.filter_score_select) == 'evalue':
1
df7738595640 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit cc80b878817d052398db16574917900ebe15292e
bgruening
parents: 0
diff changeset
57 --evalue '$filter_score.evalue'
0
98037ef3d2a9 Imported from capsule None
bgruening
parents:
diff changeset
58 #else:
1
df7738595640 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit cc80b878817d052398db16574917900ebe15292e
bgruening
parents: 0
diff changeset
59 --min-score '$filter_score.min_score'
0
98037ef3d2a9 Imported from capsule None
bgruening
parents:
diff changeset
60 #end if
98037ef3d2a9 Imported from capsule None
bgruening
parents:
diff changeset
61
1
df7738595640 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit cc80b878817d052398db16574917900ebe15292e
bgruening
parents: 0
diff changeset
62 --id '$id'
df7738595640 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit cc80b878817d052398db16574917900ebe15292e
bgruening
parents: 0
diff changeset
63 --query-cover '$query_cover'
6
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
parents: 3
diff changeset
64 --subject-cover '$subject_cover'
1
df7738595640 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit cc80b878817d052398db16574917900ebe15292e
bgruening
parents: 0
diff changeset
65 --block-size '$block_size'
6
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
parents: 3
diff changeset
66 #if str($unal) == '1':
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
parents: 3
diff changeset
67 --unal 1 --un '$unalqueries'
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
parents: 3
diff changeset
68 #end if
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
parents: 3
diff changeset
69 $no_self_hits
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
parents: 3
diff changeset
70 #if $tax_cond.tax_select == 'file':
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
parents: 3
diff changeset
71 --taxonlist `cat '$tax_cond.taxonlistfile' | grep -v "^#" | grep -v "^$" | tr "\n" "," | sed 's/,$//'`
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
parents: 3
diff changeset
72 #else if $tax_cond.tax_select == 'list':
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
parents: 3
diff changeset
73 --taxonlist '$tax_cond.taxonlist'
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
parents: 3
diff changeset
74 #end if
0
98037ef3d2a9 Imported from capsule None
bgruening
parents:
diff changeset
75 ]]>
98037ef3d2a9 Imported from capsule None
bgruening
parents:
diff changeset
76 </command>
98037ef3d2a9 Imported from capsule None
bgruening
parents:
diff changeset
77 <inputs>
6
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
parents: 3
diff changeset
78 <conditional name="method_cond">
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
parents: 3
diff changeset
79 <param name="method_select" type="select" label="What do you want to align?" help="(blastp/blastx)">
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
parents: 3
diff changeset
80 <option value="blastp">Align amino acid query sequences (blastp)</option>
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
parents: 3
diff changeset
81 <option value="blastx">Align DNA query sequences (blastx)</option>
3
830516f9521b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 0a893f1ee7f73d24004a43ec1ba6a4cc03fbfab0
bgruening
parents: 1
diff changeset
82 </param>
6
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
parents: 3
diff changeset
83 <when value="blastx">
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
parents: 3
diff changeset
84 <param name="query_gencode" argument="--query-gencode" type="select" label="Genetic code used for translation of query in BLASTX mode" help="">
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
parents: 3
diff changeset
85 <option value="1">The Standard Code</option>
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
parents: 3
diff changeset
86 <option value="2">The Vertebrate Mitochondrial Code</option>
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
parents: 3
diff changeset
87 <option value="3">The Yeast Mitochondrial Code</option>
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
parents: 3
diff changeset
88 <option value="4">The Mold, Protozoan, and Coelenterate Mitochondrial Code and the Mycoplasma/Spiroplasma Code</option>
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
parents: 3
diff changeset
89 <option value="5">The Invertebrate Mitochondrial Code</option>
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
parents: 3
diff changeset
90 <option value="6">The Ciliate, Dasycladacean and Hexamita Nuclear Code</option>
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
parents: 3
diff changeset
91 <option value="9">The Echinoderm and Flatworm Mitochondrial Code</option>
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
parents: 3
diff changeset
92 <option value="10">The Euplotid Nuclear Code</option>
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
parents: 3
diff changeset
93 <option value="11">The Bacterial, Archaeal and Plant Plastid Code</option>
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
parents: 3
diff changeset
94 <option value="12">The Alternative Yeast Nuclear Code</option>
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
parents: 3
diff changeset
95 <option value="13">The Ascidian Mitochondrial Code</option>
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
parents: 3
diff changeset
96 <option value="14">The Alternative Flatworm Mitochondrial Code</option>
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
parents: 3
diff changeset
97 <option value="16">Chlorophycean Mitochondrial Code</option>
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
parents: 3
diff changeset
98 <option value="21">Trematode Mitochondrial Code</option>
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
parents: 3
diff changeset
99 <option value="22">Scenedesmus obliquus Mitochondrial Code</option>
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
parents: 3
diff changeset
100 <option value="23">Thraustochytrium Mitochondrial Code</option>
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
parents: 3
diff changeset
101 <option value="24">Pterobranchia Mitochondrial Code</option>
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
parents: 3
diff changeset
102 <option value="25">Candidate Division SR1 and Gracilibacteria Code</option>
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
parents: 3
diff changeset
103 <option value="26">Pachysolen tannophilus Nuclear Code</option>
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
parents: 3
diff changeset
104 </param>
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
parents: 3
diff changeset
105 <param argument="--min-orf" name="min_orf" type="integer" value="1" label="ignore translated sequences without an open reading frame of at least this length" help="By default this feature is disabled for sequences of length below 30, set to 20 for sequences of length below 100, and set to 40 otherwise. Setting this option to 1 will disable this feature" />
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
parents: 3
diff changeset
106
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
parents: 3
diff changeset
107 <param name="query_strand" argument="--strand" type="select" label="query strands to search" help="">
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
parents: 3
diff changeset
108 <option value="both" selected="True">Both</option>
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
parents: 3
diff changeset
109 <option value="plus">Plus</option>
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
parents: 3
diff changeset
110 <option value="minus">Minus</option>
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
parents: 3
diff changeset
111 </param>
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
parents: 3
diff changeset
112 <conditional name="frameshift_cond">
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
parents: 3
diff changeset
113 <param name="frameshift_select" type="select" label="Allow for frameshifts?" help="">
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
parents: 3
diff changeset
114 <option value="yes">yes</option>
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
parents: 3
diff changeset
115 <option value="no" selected="true">no</option>
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
parents: 3
diff changeset
116 </param>
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
parents: 3
diff changeset
117 <when value="yes">
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
parents: 3
diff changeset
118 <param argument="--range-culling" name="range_culling" type="boolean" truevalue="--range-culling" falsevalue="" checked="false" label="restrict hit culling to overlapping query ranges" help="This feature is designed for long query DNA sequences that may span several genes. In these cases, the default of reporting the 25 best overall hits could cause hits to a lower scoring gene to be overshadowed. But just increasing the number of alignments reported will bloat the output size and reduce performance. Using this feature along with -k 25 (default), a hit will only be deleted if at least 50% of its query range is spanned by at least 25 higher or equal scoring hits. Using this feature along with --top 10, a hit will only be deleted if its score is more than 10% lower than that of a higher scoring hit over at least 50% of its query range. The percentage is configurable using --range-cover. Note that this feature is currently only available in frameshift alignment mode"/>
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
parents: 3
diff changeset
119 <param argument="--frameshift" type="integer" value="0" label="frame shift penalty" help="Values around 15 are reasonable for this parameter. Enabling this feature will have the aligner tolerate missing bases in DNA sequences and is most recommended for long, error-prone sequences like MinION reads. In the pairwise output format, frameshifts will be indicated by \ and / for a shift by +1 and -1 nucleotide in the direction of translation respectively." />
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
parents: 3
diff changeset
120 </when>
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
parents: 3
diff changeset
121 <when value="no"/>
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
parents: 3
diff changeset
122 </conditional>
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
parents: 3
diff changeset
123 </when>
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
parents: 3
diff changeset
124 <when value="blastp">
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
parents: 3
diff changeset
125 </when>
3
830516f9521b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 0a893f1ee7f73d24004a43ec1ba6a4cc03fbfab0
bgruening
parents: 1
diff changeset
126 </conditional>
1
df7738595640 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit cc80b878817d052398db16574917900ebe15292e
bgruening
parents: 0
diff changeset
127 <param argument="--query" type="data" format="fasta,fastq" label="Input query file in FASTA or FASTQ format" />
0
98037ef3d2a9 Imported from capsule None
bgruening
parents:
diff changeset
128 <conditional name="ref_db_source">
6
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
parents: 3
diff changeset
129 <param name="db_source" type="select" label="Will you select a reference database from your history or use a built-in index?" help="Built-ins were indexed using default options">
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
parents: 3
diff changeset
130 <option value="indexed">Use a built-in index</option>
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
parents: 3
diff changeset
131 <option value="history">Use one from the history</option>
0
98037ef3d2a9 Imported from capsule None
bgruening
parents:
diff changeset
132 </param>
6
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
parents: 3
diff changeset
133 <when value="indexed">
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
parents: 3
diff changeset
134 <param name="index" type="select" label="Select a reference database" help="If your database of interest is not listed, contact your Galaxy admin">
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
parents: 3
diff changeset
135 <options from_data_table="diamond_database">
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
parents: 3
diff changeset
136 <filter type="sort_by" column="2"/>
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
parents: 3
diff changeset
137 <validator type="no_options" message="No indexes are available for the selected input dataset"/>
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
parents: 3
diff changeset
138 </options>
1
df7738595640 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit cc80b878817d052398db16574917900ebe15292e
bgruening
parents: 0
diff changeset
139 </param>
df7738595640 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit cc80b878817d052398db16574917900ebe15292e
bgruening
parents: 0
diff changeset
140 </when>
6
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
parents: 3
diff changeset
141 <when value="history">
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
parents: 3
diff changeset
142 <param name="reference_database" type="data" format="dmnd" label="Select the reference database" />
0
98037ef3d2a9 Imported from capsule None
bgruening
parents:
diff changeset
143 </when>
98037ef3d2a9 Imported from capsule None
bgruening
parents:
diff changeset
144 </conditional>
6
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
parents: 3
diff changeset
145 <expand macro="output_type_macro" />
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
parents: 3
diff changeset
146 <param name="no_self_hits" argument="--no-self-hits" type="boolean" truevalue="--no-self-hits" falsevalue="" checked="true" label="suppress reporting of identical self hits?" help=""/>
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
parents: 3
diff changeset
147 <param name='sensitivity' type="select" label="Sensitivity Mode" help="Choose one of the sensitivity modes. The default mode is mainly designed for short read alignment, i.e. finding significant matches of >50 bits on 30-40aa fragments. The sensitive mode is a lot more sensitive than the default and generally recommended for aligning longer sequences. The more sensitive mode provides even more sensitivity. More sensitivity may increase computation time.">
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
parents: 3
diff changeset
148 <option value="0" selected="True">Default</option>
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
parents: 3
diff changeset
149 <option value="1">Sensitive</option>
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
parents: 3
diff changeset
150 <option value="2">More Sensitive</option>
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
parents: 3
diff changeset
151 </param>
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
parents: 3
diff changeset
152 <param argument="--matrix" type="select" label="Scoring matrix" help="In parentheses are the supported values for (gap open)/(gap extend). In brackets are default gap penalties">
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
parents: 3
diff changeset
153 <option value="BLOSUM45">BLOSUM45 ((10-13)/3; (12-16)/2; (16-19)/1) [14/2]</option>
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
parents: 3
diff changeset
154 <option value="BLOSUM50">BLOSUM50 ((9-13)/3; (12-16)/2; (15-19)/1) [13/2]</option>
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
parents: 3
diff changeset
155 <option value="BLOSUM62" selected="True">BLOSUM62 ((6-11)/2; (9-13)/1) [11/1]</option>
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
parents: 3
diff changeset
156 <option value="BLOSUM80">BLOSUM80 ((6-9)/2; 13/2; 25/2; (9-11)/1) [10/1]</option>
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
parents: 3
diff changeset
157 <option value="BLOSUM90">BLOSUM90 ((6-9)/2; (9-11)/1) [10/1]</option>
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
parents: 3
diff changeset
158 <option value="PAM250">PAM250 ((11-15)/3; (13-17)/2; (17-21)/1) [14/2]</option>
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
parents: 3
diff changeset
159 <option value="PAM70">PAM70 ((6-8)/2; (9-11)/1) [10/1]</option>
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
parents: 3
diff changeset
160 <option value="PAM30">PAM30 ((5-7)/2; (8-10)/1) [9/1]</option>
3
830516f9521b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 0a893f1ee7f73d24004a43ec1ba6a4cc03fbfab0
bgruening
parents: 1
diff changeset
161 </param>
6
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
parents: 3
diff changeset
162 <param argument="--gapopen" type="integer" optional="True" value="" label="Gap open penalty" help="leave empty for default (see scoring matrix)" />
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
parents: 3
diff changeset
163 <param argument="--gapextend" type="integer" optional="True" value="" label="Gap extension penalty" help="leave empty for default (see scoring matrix)" />
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
parents: 3
diff changeset
164 <param name="comp_based_stats" argument="--comp-based-stats" type="boolean" truevalue="1" falsevalue="0" checked="true" label="enable composition based statistics?" help="Compositionally biased sequences often cause false positive matches, which are effectively filtered by this algorithm in a way similar to the composition based statistics used by BLAST"/>
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
parents: 3
diff changeset
165 <param argument="--masking" type="boolean" truevalue="1" falsevalue="0" checked="true" label="enable masking of low complexity regions?" help="Masked residues appear in the output as X"/>
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
parents: 3
diff changeset
166 <conditional name="tax_cond">
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
parents: 3
diff changeset
167 <param name="tax_select" type="select" label="Restrict search taxonomically?" help="Any taxonomic rank can be used, and only reference sequences matching one of the specified taxon ids will be searched against">
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
parents: 3
diff changeset
168 <option value="no">No</option>
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
parents: 3
diff changeset
169 <option value="list">list of taxids entered manually</option>
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
parents: 3
diff changeset
170 <option value="file">list of taxids from single column tabular file</option>
1
df7738595640 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit cc80b878817d052398db16574917900ebe15292e
bgruening
parents: 0
diff changeset
171 </param>
6
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
parents: 3
diff changeset
172 <when value="no"/>
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
parents: 3
diff changeset
173 <when value="list">
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
parents: 3
diff changeset
174 <param name="taxonlist" argument="--taxonlist" type="text" value="" label="comma separated list of taxon ids" help="" />
1
df7738595640 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit cc80b878817d052398db16574917900ebe15292e
bgruening
parents: 0
diff changeset
175 </when>
6
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
parents: 3
diff changeset
176 <when value="file">
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
parents: 3
diff changeset
177 <param name="taxonlistfile" argument="--taxonlist" type="data" format="tabular" label="Keep alignments within the given percentage range of the top alignment score for a quer" help="" />
1
df7738595640 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit cc80b878817d052398db16574917900ebe15292e
bgruening
parents: 0
diff changeset
178 </when>
df7738595640 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit cc80b878817d052398db16574917900ebe15292e
bgruening
parents: 0
diff changeset
179 </conditional>
0
98037ef3d2a9 Imported from capsule None
bgruening
parents:
diff changeset
180 <conditional name="filter_score">
1
df7738595640 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit cc80b878817d052398db16574917900ebe15292e
bgruening
parents: 0
diff changeset
181 <param name="filter_score_select" type="select" label="Method to filter?" help="(--evalue/--min-score)">
0
98037ef3d2a9 Imported from capsule None
bgruening
parents:
diff changeset
182 <option value="evalue">Maximum e-value to report alignments</option>
1
df7738595640 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit cc80b878817d052398db16574917900ebe15292e
bgruening
parents: 0
diff changeset
183 <option value="min-score">Minimum bit score to report alignments</option>
0
98037ef3d2a9 Imported from capsule None
bgruening
parents:
diff changeset
184 </param>
98037ef3d2a9 Imported from capsule None
bgruening
parents:
diff changeset
185 <when value="evalue">
1
df7738595640 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit cc80b878817d052398db16574917900ebe15292e
bgruening
parents: 0
diff changeset
186 <param argument="--evalue" type="float" value="0.001" label="Maximum expected value to keep an alignment" />
0
98037ef3d2a9 Imported from capsule None
bgruening
parents:
diff changeset
187 </when>
1
df7738595640 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit cc80b878817d052398db16574917900ebe15292e
bgruening
parents: 0
diff changeset
188 <when value="min-score">
df7738595640 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit cc80b878817d052398db16574917900ebe15292e
bgruening
parents: 0
diff changeset
189 <param name="min_score" argument="--min-score" type="integer" value="0" label="Minimum bit score to keep an alignment" help="(--min-score)" />
0
98037ef3d2a9 Imported from capsule None
bgruening
parents:
diff changeset
190 </when>
98037ef3d2a9 Imported from capsule None
bgruening
parents:
diff changeset
191 </conditional>
6
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
parents: 3
diff changeset
192 <expand macro="hit_filter_macro" />
1
df7738595640 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit cc80b878817d052398db16574917900ebe15292e
bgruening
parents: 0
diff changeset
193 <param argument="--id" type="integer" value="0" label="Minimum identity percentage to report an alignment" help="" />
df7738595640 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit cc80b878817d052398db16574917900ebe15292e
bgruening
parents: 0
diff changeset
194 <param name="query_cover" argument="--query-cover" type="integer" value="0" label="Minimum query cover percentage to report an alignment" help="" />
6
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
parents: 3
diff changeset
195 <param name="subject_cover" argument="--subject-cover" type="integer" value="0" label="Minimum subject cover percentage to report an alignment" help="" />
1
df7738595640 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit cc80b878817d052398db16574917900ebe15292e
bgruening
parents: 0
diff changeset
196 <param name="block_size" argument="--block-size" type="float" value="2" label="Block size in billions of sequence letters to be processed at a time" help="" />
6
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
parents: 3
diff changeset
197 <param argument="--unal" type="boolean" truevalue="1" falsevalue="0" checked="false" label="report unaligned queries" help=""/>
1
df7738595640 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit cc80b878817d052398db16574917900ebe15292e
bgruening
parents: 0
diff changeset
198 </inputs>
0
98037ef3d2a9 Imported from capsule None
bgruening
parents:
diff changeset
199 <outputs>
6
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
parents: 3
diff changeset
200 <expand macro="output_macro" />
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
parents: 3
diff changeset
201 <data format="fasta" name="unalqueries" label="${tool.name} on ${on_string} (unaligned queries)">
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
parents: 3
diff changeset
202 <filter>unal == "1"</filter>
1
df7738595640 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit cc80b878817d052398db16574917900ebe15292e
bgruening
parents: 0
diff changeset
203 </data>
0
98037ef3d2a9 Imported from capsule None
bgruening
parents:
diff changeset
204 </outputs>
98037ef3d2a9 Imported from capsule None
bgruening
parents:
diff changeset
205 <tests>
98037ef3d2a9 Imported from capsule None
bgruening
parents:
diff changeset
206 <test>
6
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
parents: 3
diff changeset
207 <conditional name="method_cond">
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
parents: 3
diff changeset
208 <param name="method_select" value="blastp" />
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
parents: 3
diff changeset
209 </conditional>
0
98037ef3d2a9 Imported from capsule None
bgruening
parents:
diff changeset
210 <param name="query" value="protein.fasta" ftype="fasta"/>
6
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
parents: 3
diff changeset
211 <conditional name="ref_db_source">
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
parents: 3
diff changeset
212 <param name="db_source" value="history"/>
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
parents: 3
diff changeset
213 <param name="reference_database" value="db.dmnd"/>
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
parents: 3
diff changeset
214 </conditional>
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
parents: 3
diff changeset
215 <conditional name="output">
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
parents: 3
diff changeset
216 <param name="outfmt" value="6"/>
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
parents: 3
diff changeset
217 <param name="fields" value="qseqid,sseqid,pident,length,mismatch,gapopen,qstart,qend,sstart,send,evalue,bitscore"/>
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
parents: 3
diff changeset
218 </conditional>
3
830516f9521b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 0a893f1ee7f73d24004a43ec1ba6a4cc03fbfab0
bgruening
parents: 1
diff changeset
219 <param name="sensitivity" value="0"/>
1
df7738595640 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit cc80b878817d052398db16574917900ebe15292e
bgruening
parents: 0
diff changeset
220 <param name="matrix" value="BLOSUM62"/>
6
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
parents: 3
diff changeset
221 <param name="comp-based-stat" value="1"/>
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
parents: 3
diff changeset
222 <param name="masking" value="1"/>
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
parents: 3
diff changeset
223 <conditional name="hit_filter">
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
parents: 3
diff changeset
224 <param name="hit_filter_select" value="max"/>
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
parents: 3
diff changeset
225 <param name="max_target_seqs" value="25" />
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
parents: 3
diff changeset
226 </conditional>
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
parents: 3
diff changeset
227 <conditional name="filter_score">
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
parents: 3
diff changeset
228 <param name="filter_score_select" value="evalue"/>
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
parents: 3
diff changeset
229 <param name="evalue" value="0.001" />
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
parents: 3
diff changeset
230 </conditional>
1
df7738595640 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit cc80b878817d052398db16574917900ebe15292e
bgruening
parents: 0
diff changeset
231 <param name="id" value="0"/>
df7738595640 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit cc80b878817d052398db16574917900ebe15292e
bgruening
parents: 0
diff changeset
232 <param name="query_cover" value="0"/>
df7738595640 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit cc80b878817d052398db16574917900ebe15292e
bgruening
parents: 0
diff changeset
233 <param name="block_size" value="2"/>
df7738595640 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit cc80b878817d052398db16574917900ebe15292e
bgruening
parents: 0
diff changeset
234 <output name="blast_tabular" file="diamond_results.tabular"/>
0
98037ef3d2a9 Imported from capsule None
bgruening
parents:
diff changeset
235 </test>
6
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
parents: 3
diff changeset
236 <test>
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
parents: 3
diff changeset
237 <conditional name="method_cond">
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
parents: 3
diff changeset
238 <param name="method_select" value="blastp" />
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
parents: 3
diff changeset
239 </conditional>
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
parents: 3
diff changeset
240 <param name="query" value="protein.fasta" ftype="fasta"/>
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
parents: 3
diff changeset
241 <conditional name="ref_db_source">
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
parents: 3
diff changeset
242 <param name="db_source" value="history"/>
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
parents: 3
diff changeset
243 <param name="reference_database" value="db-wtax.dmnd"/>
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
parents: 3
diff changeset
244 </conditional>
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
parents: 3
diff changeset
245 <conditional name="tax_cond">
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
parents: 3
diff changeset
246 <param name="tax_select" value="list"/>
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
parents: 3
diff changeset
247 <param name="taxonlist" value="2" />
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
parents: 3
diff changeset
248 </conditional>
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
parents: 3
diff changeset
249 <conditional name="output">
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
parents: 3
diff changeset
250 <param name="outfmt" value="6"/>
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
parents: 3
diff changeset
251 <param name="fields" value="qseqid,sseqid,pident,length,mismatch,gapopen,qstart,qend,sstart,send,evalue,bitscore"/>
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
parents: 3
diff changeset
252 </conditional>
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
parents: 3
diff changeset
253 <param name="sensitivity" value="0"/>
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
parents: 3
diff changeset
254 <param name="matrix" value="BLOSUM62"/>
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
parents: 3
diff changeset
255 <param name="comp-based-stat" value="1"/>
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
parents: 3
diff changeset
256 <param name="masking" value="1"/>
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
parents: 3
diff changeset
257 <conditional name="hit_filter">
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
parents: 3
diff changeset
258 <param name="hit_filter_select" value="max"/>
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
parents: 3
diff changeset
259 <param name="max_target_seqs" value="25" />
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
parents: 3
diff changeset
260 </conditional>
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
parents: 3
diff changeset
261 <conditional name="filter_score">
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
parents: 3
diff changeset
262 <param name="filter_score_select" value="evalue"/>
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
parents: 3
diff changeset
263 <param name="evalue" value="0.001" />
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
parents: 3
diff changeset
264 </conditional>
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
parents: 3
diff changeset
265 <param name="id" value="0"/>
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
parents: 3
diff changeset
266 <param name="query_cover" value="0"/>
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
parents: 3
diff changeset
267 <param name="block_size" value="2"/>
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
parents: 3
diff changeset
268 <output name="blast_tabular" file="diamond_results.wtax.tabular"/>
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
parents: 3
diff changeset
269 </test>
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
parents: 3
diff changeset
270 <test>
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
parents: 3
diff changeset
271 <conditional name="method_cond">
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
parents: 3
diff changeset
272 <param name="method_select" value="blastx" />
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
parents: 3
diff changeset
273 <conditional name="frameshift_cond">
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
parents: 3
diff changeset
274 <param name="frameshift_select" value="yes"/>
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
parents: 3
diff changeset
275 </conditional>
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
parents: 3
diff changeset
276 </conditional>
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
parents: 3
diff changeset
277 <param name="query" value="nucleotide.fasta" ftype="fasta"/>
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
parents: 3
diff changeset
278 <conditional name="ref_db_source">
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
parents: 3
diff changeset
279 <param name="db_source" value="history"/>
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
parents: 3
diff changeset
280 <param name="reference_database" value="db.dmnd"/>
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
parents: 3
diff changeset
281 </conditional>
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
parents: 3
diff changeset
282 <conditional name="output">
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
parents: 3
diff changeset
283 <param name="outfmt" value="0"/>
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
parents: 3
diff changeset
284 </conditional>
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
parents: 3
diff changeset
285 <param name="sensitivity" value="0"/>
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
parents: 3
diff changeset
286 <param name="matrix" value="BLOSUM62"/>
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
parents: 3
diff changeset
287 <param name="comp-based-stat" value="1"/>
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
parents: 3
diff changeset
288 <param name="masking" value="1"/>
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
parents: 3
diff changeset
289 <conditional name="hit_filter">
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
parents: 3
diff changeset
290 <param name="hit_filter_select" value="top"/>
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
parents: 3
diff changeset
291 <param name="top" value="10" />
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
parents: 3
diff changeset
292 </conditional>
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
parents: 3
diff changeset
293 <conditional name="filter_score">
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
parents: 3
diff changeset
294 <param name="filter_score_select" value="score"/>
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
parents: 3
diff changeset
295 <param name="evalue" value="1" />
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
parents: 3
diff changeset
296 </conditional>
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
parents: 3
diff changeset
297 <param name="id" value="0"/>
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
parents: 3
diff changeset
298 <param name="query_cover" value="0"/>
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
parents: 3
diff changeset
299 <param name="block_size" value="2"/>
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
parents: 3
diff changeset
300 <output name="blast_tabular" file="diamond_results.pairwise"/>
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
parents: 3
diff changeset
301 </test>
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
parents: 3
diff changeset
302 <test>
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
parents: 3
diff changeset
303 <conditional name="method_cond">
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
parents: 3
diff changeset
304 <param name="method_select" value="blastp" />
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
parents: 3
diff changeset
305 </conditional>
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
parents: 3
diff changeset
306 <param name="query" value="protein.fasta" ftype="fasta"/>
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
parents: 3
diff changeset
307 <conditional name="ref_db_source">
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
parents: 3
diff changeset
308 <param name="db_source" value="history"/>
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
parents: 3
diff changeset
309 <param name="reference_database" value="db-wtax.dmnd"/>
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
parents: 3
diff changeset
310 </conditional>
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
parents: 3
diff changeset
311 <conditional name="output">
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
parents: 3
diff changeset
312 <param name="outfmt" value="100"/>
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
parents: 3
diff changeset
313 </conditional>
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
parents: 3
diff changeset
314 <output name="daa_output" file="diamond_results.daa" compare="sim_size" delta="10"/>
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
parents: 3
diff changeset
315 </test>
0
98037ef3d2a9 Imported from capsule None
bgruening
parents:
diff changeset
316 </tests>
98037ef3d2a9 Imported from capsule None
bgruening
parents:
diff changeset
317 <help>
98037ef3d2a9 Imported from capsule None
bgruening
parents:
diff changeset
318 <![CDATA[
98037ef3d2a9 Imported from capsule None
bgruening
parents:
diff changeset
319
98037ef3d2a9 Imported from capsule None
bgruening
parents:
diff changeset
320 **What it does**
98037ef3d2a9 Imported from capsule None
bgruening
parents:
diff changeset
321
98037ef3d2a9 Imported from capsule None
bgruening
parents:
diff changeset
322 DIAMOND_ is a new alignment tool for aligning short DNA sequencing reads to a protein reference database such as NCBI-NR.
98037ef3d2a9 Imported from capsule None
bgruening
parents:
diff changeset
323 On Illumina reads of length 100-150bp, in fast mode, DIAMOND is about 20,000 times faster than BLASTX, while reporting
98037ef3d2a9 Imported from capsule None
bgruening
parents:
diff changeset
324 about 80-90% of all matches that BLASTX finds, with an e-value of at most 1e-5. In sensitive mode, DIAMOND ist about 2,500
98037ef3d2a9 Imported from capsule None
bgruening
parents:
diff changeset
325 times faster than BLASTX, finding more than 94% of all matches.
98037ef3d2a9 Imported from capsule None
bgruening
parents:
diff changeset
326
3
830516f9521b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 0a893f1ee7f73d24004a43ec1ba6a4cc03fbfab0
bgruening
parents: 1
diff changeset
327 The DIAMOND algorithm is designed for the alignment of large datasets. The algorithm is not efficient for a small number of query sequences or only a single one of them, and speed will be low. BLAST is recommended for small datasets.
1
df7738595640 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit cc80b878817d052398db16574917900ebe15292e
bgruening
parents: 0
diff changeset
328
0
98037ef3d2a9 Imported from capsule None
bgruening
parents:
diff changeset
329 .. _DIAMOND: http://ab.inf.uni-tuebingen.de/software/diamond/
98037ef3d2a9 Imported from capsule None
bgruening
parents:
diff changeset
330
1
df7738595640 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit cc80b878817d052398db16574917900ebe15292e
bgruening
parents: 0
diff changeset
331 **Input**
df7738595640 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit cc80b878817d052398db16574917900ebe15292e
bgruening
parents: 0
diff changeset
332
df7738595640 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit cc80b878817d052398db16574917900ebe15292e
bgruening
parents: 0
diff changeset
333 Input data is a large protein or nucleotide sequence file.
df7738595640 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit cc80b878817d052398db16574917900ebe15292e
bgruening
parents: 0
diff changeset
334
df7738595640 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit cc80b878817d052398db16574917900ebe15292e
bgruening
parents: 0
diff changeset
335
df7738595640 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit cc80b878817d052398db16574917900ebe15292e
bgruening
parents: 0
diff changeset
336 **Output**
df7738595640 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit cc80b878817d052398db16574917900ebe15292e
bgruening
parents: 0
diff changeset
337
df7738595640 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit cc80b878817d052398db16574917900ebe15292e
bgruening
parents: 0
diff changeset
338 Diamond gives you a tabular output file with 12 columns:
df7738595640 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit cc80b878817d052398db16574917900ebe15292e
bgruening
parents: 0
diff changeset
339
df7738595640 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit cc80b878817d052398db16574917900ebe15292e
bgruening
parents: 0
diff changeset
340 Column Description
df7738595640 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit cc80b878817d052398db16574917900ebe15292e
bgruening
parents: 0
diff changeset
341 1 Query Seq-id (ID of your sequence)
df7738595640 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit cc80b878817d052398db16574917900ebe15292e
bgruening
parents: 0
diff changeset
342 2 Subject Seq-id (ID of the database hit)
df7738595640 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit cc80b878817d052398db16574917900ebe15292e
bgruening
parents: 0
diff changeset
343 3 Percentage of identical matches
df7738595640 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit cc80b878817d052398db16574917900ebe15292e
bgruening
parents: 0
diff changeset
344 4 Alignment length
df7738595640 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit cc80b878817d052398db16574917900ebe15292e
bgruening
parents: 0
diff changeset
345 5 Number of mismatches
df7738595640 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit cc80b878817d052398db16574917900ebe15292e
bgruening
parents: 0
diff changeset
346 6 Number of gap openings
df7738595640 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit cc80b878817d052398db16574917900ebe15292e
bgruening
parents: 0
diff changeset
347 7 Start of alignment in query
df7738595640 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit cc80b878817d052398db16574917900ebe15292e
bgruening
parents: 0
diff changeset
348 8 End of alignment in query
df7738595640 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit cc80b878817d052398db16574917900ebe15292e
bgruening
parents: 0
diff changeset
349 9 Start of alignment in subject (database hit)
df7738595640 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit cc80b878817d052398db16574917900ebe15292e
bgruening
parents: 0
diff changeset
350 10 End of alignment in subject (database hit)
df7738595640 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit cc80b878817d052398db16574917900ebe15292e
bgruening
parents: 0
diff changeset
351 11 Expectation value (E-value)
df7738595640 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit cc80b878817d052398db16574917900ebe15292e
bgruening
parents: 0
diff changeset
352 12 Bit score
df7738595640 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit cc80b878817d052398db16574917900ebe15292e
bgruening
parents: 0
diff changeset
353
0
98037ef3d2a9 Imported from capsule None
bgruening
parents:
diff changeset
354
98037ef3d2a9 Imported from capsule None
bgruening
parents:
diff changeset
355 Supported values for gap open and gap extend parameters depending on the selected scoring matrix.
98037ef3d2a9 Imported from capsule None
bgruening
parents:
diff changeset
356
98037ef3d2a9 Imported from capsule None
bgruening
parents:
diff changeset
357 ======== ============================================
98037ef3d2a9 Imported from capsule None
bgruening
parents:
diff changeset
358 Matrix Supported values for (gap open)/(gap extend)
98037ef3d2a9 Imported from capsule None
bgruening
parents:
diff changeset
359 ======== ============================================
98037ef3d2a9 Imported from capsule None
bgruening
parents:
diff changeset
360 BLOSUM45 (10-13)/3; (12-16)/2; (16-19)/1
98037ef3d2a9 Imported from capsule None
bgruening
parents:
diff changeset
361 BLOSUM50 (9-13)/3; (12-16)/2; (15-19)/1
98037ef3d2a9 Imported from capsule None
bgruening
parents:
diff changeset
362 BLOSUM62 (6-11)/2; (9-13)/1
98037ef3d2a9 Imported from capsule None
bgruening
parents:
diff changeset
363 BLOSUM80 (6-9)/2; 13/2; 25/2; (9-11)/1
98037ef3d2a9 Imported from capsule None
bgruening
parents:
diff changeset
364 BLOSUM90 (6-9)/2; (9-11)/1
98037ef3d2a9 Imported from capsule None
bgruening
parents:
diff changeset
365 PAM250 (11-15)/3; (13-17)/2; (17-21)/1
98037ef3d2a9 Imported from capsule None
bgruening
parents:
diff changeset
366 PAM70 (6-8)/2; (9-11)/1
98037ef3d2a9 Imported from capsule None
bgruening
parents:
diff changeset
367 PAM30 (5-7)/2; (8-10)/1
98037ef3d2a9 Imported from capsule None
bgruening
parents:
diff changeset
368 ======== ============================================
98037ef3d2a9 Imported from capsule None
bgruening
parents:
diff changeset
369
98037ef3d2a9 Imported from capsule None
bgruening
parents:
diff changeset
370
98037ef3d2a9 Imported from capsule None
bgruening
parents:
diff changeset
371 ]]>
98037ef3d2a9 Imported from capsule None
bgruening
parents:
diff changeset
372 </help>
1
df7738595640 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit cc80b878817d052398db16574917900ebe15292e
bgruening
parents: 0
diff changeset
373 <expand macro="citations" />
0
98037ef3d2a9 Imported from capsule None
bgruening
parents:
diff changeset
374 </tool>