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comparison diamond.xml @ 6:64be1ac21109 draft

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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
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5:3c6b132b154a 6:64be1ac21109
1 <tool id="bg_diamond" name="Diamond" version="@VERSION@.1"> 1 <tool id="bg_diamond" name="Diamond" version="@VERSION@.0">
2 <description>alignment tool for short sequences against a protein database</description> 2 <description>alignment tool for short sequences against a protein database</description>
3 <macros> 3 <macros>
4 <import>macros.xml</import> 4 <import>macros.xml</import>
5 </macros> 5 </macros>
6 <expand macro="requirements" /> 6 <expand macro="requirements" />
16 #end if 16 #end if
17 17
18 && 18 &&
19 19
20 diamond 20 diamond
21 $method_select.method_select 21 $method_cond.method_select
22 --threads "\${GALAXY_SLOTS:-12}" 22 --threads "\${GALAXY_SLOTS:-12}"
23 --db ./database 23 --db ./database
24 --query '$query' 24 --query '$query'
25 #if $method_select.method_select == "blastx" 25 #if $method_cond.method_select == "blastx"
26 --query-gencode '$query_gencode' 26 --query-gencode '$method_cond.query_gencode'
27 #end if 27 --strand '$method_cond.query_strand'
28 28 --min-orf $method_cond.min_orf
29 #if $output.outfmt == "5" 29 #if $method_cond.frameshift_cond.frameshift_select == 'yes'
30 --outfmt '5' 30 --frameshift $method_cond.frameshift_cond.frameshift
31 --out '$blast_xml' 31 $method_cond.frameshift_cond.range_culling
32 $output.salltitles 32 #end if
33 #else if $output.outfmt == "6" 33 #end if
34 --outfmt '6' #echo ' '.join(str($output.fields).split(',')) 34
35 --out '$blast_tabular' 35 @OUTPUT_ARGS@
36 #else if $output.outfmt == "101"
37 --outfmt '101'
38 --out '$sam_output'
39 $output.salltitles
40 #end if
41 36
42 --compress '0' 37 --compress '0'
43 #if $sensitivity == "1" 38 #if $sensitivity == "1"
44 --sensitive 39 --sensitive
45 #else if $sensitivity == "2" 40 #else if $sensitivity == "2"
46 --more-sensitive 41 --more-sensitive
47 #end if 42 #end if
48 43
49 --gapopen '$gapopen' 44 #if str($gapopen) != "":
50 --gapextend '$gapextend' 45 --gapopen '$gapopen'
46 #end if
47 #if str($gapextend) != "":
48 --gapextend '$gapextend'
49 #end if
51 --matrix '$matrix' 50 --matrix '$matrix'
52 --seg '$seg' 51 --comp-based-stats '$comp_based_stats'
53 52 --masking '$masking'
54 #if str($hit_filter.hit_filter_select) == 'max': 53
55 --max-target-seqs '$hit_filter.max_target_seqs' 54 @HITFILTER_ARGS@
56 #else:
57 --top '$hit_filter.top'
58 #end if
59 55
60 #if str($filter_score.filter_score_select) == 'evalue': 56 #if str($filter_score.filter_score_select) == 'evalue':
61 --evalue '$filter_score.evalue' 57 --evalue '$filter_score.evalue'
62 #else: 58 #else:
63 --min-score '$filter_score.min_score' 59 --min-score '$filter_score.min_score'
64 #end if 60 #end if
65 61
66 --id '$id' 62 --id '$id'
67 --query-cover '$query_cover' 63 --query-cover '$query_cover'
64 --subject-cover '$subject_cover'
68 --block-size '$block_size' 65 --block-size '$block_size'
66 #if str($unal) == '1':
67 --unal 1 --un '$unalqueries'
68 #end if
69 $no_self_hits
70 #if $tax_cond.tax_select == 'file':
71 --taxonlist `cat '$tax_cond.taxonlistfile' | grep -v "^#" | grep -v "^$" | tr "\n" "," | sed 's/,$//'`
72 #else if $tax_cond.tax_select == 'list':
73 --taxonlist '$tax_cond.taxonlist'
74 #end if
69 ]]> 75 ]]>
70 </command> 76 </command>
71
72 <inputs> 77 <inputs>
73 <conditional name="method_select"> 78 <conditional name="method_cond">
74 <param name="method_select" type="select" label="What do you want to align?" help="(--blastp/--blastx)"> 79 <param name="method_select" type="select" label="What do you want to align?" help="(blastp/blastx)">
75 <option value="blastp">Align amino acid query sequences (blastp)</option> 80 <option value="blastp">Align amino acid query sequences (blastp)</option>
76 <option value="blastx">Align DNA query sequences (blastx)</option> 81 <option value="blastx">Align DNA query sequences (blastx)</option>
77 </param>
78 <when value="blastx">
79 <param name="query_gencode" argument="--query-gencode" type="select" label="Genetic code used for translation of query in BLASTX mode" help="">
80 <option value="1">The Standard Code</option>
81 <option value="2">The Vertebrate Mitochondrial Code</option>
82 <option value="3">The Yeast Mitochondrial Code</option>
83 <option value="4">The Mold, Protozoan, and Coelenterate Mitochondrial Code and the Mycoplasma/Spiroplasma Code</option>
84 <option value="5">The Invertebrate Mitochondrial Code</option>
85 <option value="6">The Ciliate, Dasycladacean and Hexamita Nuclear Code</option>
86 <option value="9">The Echinoderm and Flatworm Mitochondrial Code</option>
87 <option value="10">The Euplotid Nuclear Code</option>
88 <option value="11">The Bacterial, Archaeal and Plant Plastid Code</option>
89 <option value="12">The Alternative Yeast Nuclear Code</option>
90 <option value="13">The Ascidian Mitochondrial Code</option>
91 <option value="14">The Alternative Flatworm Mitochondrial Code</option>
92 <option value="16">Chlorophycean Mitochondrial Code</option>
93 <option value="21">Trematode Mitochondrial Code</option>
94 <option value="22">Scenedesmus obliquus Mitochondrial Code</option>
95 <option value="23">Thraustochytrium Mitochondrial Code</option>
96 <option value="24">Pterobranchia Mitochondrial Code</option>
97 <option value="5">Candidate Division SR1 and Gracilibacteria Code</option>
98 <option value="26">Pachysolen tannophilus Nuclear Code</option>
99 </param> 82 </param>
100 </when> 83 <when value="blastx">
101 <when value="blastp"> 84 <param name="query_gencode" argument="--query-gencode" type="select" label="Genetic code used for translation of query in BLASTX mode" help="">
102 </when> 85 <option value="1">The Standard Code</option>
86 <option value="2">The Vertebrate Mitochondrial Code</option>
87 <option value="3">The Yeast Mitochondrial Code</option>
88 <option value="4">The Mold, Protozoan, and Coelenterate Mitochondrial Code and the Mycoplasma/Spiroplasma Code</option>
89 <option value="5">The Invertebrate Mitochondrial Code</option>
90 <option value="6">The Ciliate, Dasycladacean and Hexamita Nuclear Code</option>
91 <option value="9">The Echinoderm and Flatworm Mitochondrial Code</option>
92 <option value="10">The Euplotid Nuclear Code</option>
93 <option value="11">The Bacterial, Archaeal and Plant Plastid Code</option>
94 <option value="12">The Alternative Yeast Nuclear Code</option>
95 <option value="13">The Ascidian Mitochondrial Code</option>
96 <option value="14">The Alternative Flatworm Mitochondrial Code</option>
97 <option value="16">Chlorophycean Mitochondrial Code</option>
98 <option value="21">Trematode Mitochondrial Code</option>
99 <option value="22">Scenedesmus obliquus Mitochondrial Code</option>
100 <option value="23">Thraustochytrium Mitochondrial Code</option>
101 <option value="24">Pterobranchia Mitochondrial Code</option>
102 <option value="25">Candidate Division SR1 and Gracilibacteria Code</option>
103 <option value="26">Pachysolen tannophilus Nuclear Code</option>
104 </param>
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" />
106
107 <param name="query_strand" argument="--strand" type="select" label="query strands to search" help="">
108 <option value="both" selected="True">Both</option>
109 <option value="plus">Plus</option>
110 <option value="minus">Minus</option>
111 </param>
112 <conditional name="frameshift_cond">
113 <param name="frameshift_select" type="select" label="Allow for frameshifts?" help="">
114 <option value="yes">yes</option>
115 <option value="no" selected="true">no</option>
116 </param>
117 <when value="yes">
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"/>
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." />
120 </when>
121 <when value="no"/>
122 </conditional>
123 </when>
124 <when value="blastp">
125 </when>
103 </conditional> 126 </conditional>
104 <param argument="--query" type="data" format="fasta,fastq" label="Input query file in FASTA or FASTQ format" /> 127 <param argument="--query" type="data" format="fasta,fastq" label="Input query file in FASTA or FASTQ format" />
105 <conditional name="ref_db_source"> 128 <conditional name="ref_db_source">
106 <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"> 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">
107 <option value="indexed">Use a built-in index</option> 130 <option value="indexed">Use a built-in index</option>
108 <option value="history">Use one from the history</option> 131 <option value="history">Use one from the history</option>
109 </param>
110 <when value="indexed">
111 <param name="index" type="select" label="Select a reference database" help="If your database of interest is not listed, contact your Galaxy admin">
112 <options from_data_table="diamond_database">
113 <filter type="sort_by" column="2"/>
114 <validator type="no_options" message="No indexes are available for the selected input dataset"/>
115 </options>
116 </param> 132 </param>
117 </when> 133 <when value="indexed">
118 <when value="history"> 134 <param name="index" type="select" label="Select a reference database" help="If your database of interest is not listed, contact your Galaxy admin">
119 <param name="reference_database" type="data" format="dmnd" label="Select the reference database" /> 135 <options from_data_table="diamond_database">
120 </when> 136 <filter type="sort_by" column="2"/>
137 <validator type="no_options" message="No indexes are available for the selected input dataset"/>
138 </options>
139 </param>
140 </when>
141 <when value="history">
142 <param name="reference_database" type="data" format="dmnd" label="Select the reference database" />
143 </when>
121 </conditional> 144 </conditional>
122 <conditional name="output"> 145 <expand macro="output_type_macro" />
123 <param argument="--outfmt" type="select" label="Format of output file " help=""> 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=""/>
124 <option value="5">BLAST XML</option> 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.">
125 <option value="6">BLAST tabular</option> 148 <option value="0" selected="True">Default</option>
126 <option value="101">SAM</option> 149 <option value="1">Sensitive</option>
150 <option value="2">More Sensitive</option>
151 </param>
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">
153 <option value="BLOSUM45">BLOSUM45 ((10-13)/3; (12-16)/2; (16-19)/1) [14/2]</option>
154 <option value="BLOSUM50">BLOSUM50 ((9-13)/3; (12-16)/2; (15-19)/1) [13/2]</option>
155 <option value="BLOSUM62" selected="True">BLOSUM62 ((6-11)/2; (9-13)/1) [11/1]</option>
156 <option value="BLOSUM80">BLOSUM80 ((6-9)/2; 13/2; 25/2; (9-11)/1) [10/1]</option>
157 <option value="BLOSUM90">BLOSUM90 ((6-9)/2; (9-11)/1) [10/1]</option>
158 <option value="PAM250">PAM250 ((11-15)/3; (13-17)/2; (17-21)/1) [14/2]</option>
159 <option value="PAM70">PAM70 ((6-8)/2; (9-11)/1) [10/1]</option>
160 <option value="PAM30">PAM30 ((5-7)/2; (8-10)/1) [9/1]</option>
161 </param>
162 <param argument="--gapopen" type="integer" optional="True" value="" label="Gap open penalty" help="leave empty for default (see scoring matrix)" />
163 <param argument="--gapextend" type="integer" optional="True" value="" label="Gap extension penalty" help="leave empty for default (see scoring matrix)" />
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"/>
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"/>
166 <conditional name="tax_cond">
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">
168 <option value="no">No</option>
169 <option value="list">list of taxids entered manually</option>
170 <option value="file">list of taxids from single column tabular file</option>
127 </param> 171 </param>
128 <when value="5"> 172 <when value="no"/>
129 <param argument="--salltitles" type="boolean" truevalue="--salltitles" falsevalue="" checked="true" label="Include full length subject titles in output?" help=""/> 173 <when value="list">
130 </when> 174 <param name="taxonlist" argument="--taxonlist" type="text" value="" label="comma separated list of taxon ids" help="" />
131 <when value="6"> 175 </when>
132 <param name="fields" type="select" label="Tabular fields" help="" multiple="true"> 176 <when value="file">
133 <option value="qseqid" selected="true">Query Seq - id</option> 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="" />
134 <option value="sseqid" selected="true">Subject Seq - id</option>
135 <option value="sallseqid">All subject Seq - id(s)</option>
136 <option value="qlen">Query sequence length</option>
137 <option value="slen">Subject sequence length</option>
138 <option value="pident" selected="true">Percentage of identical matches</option>
139 <option value="length" selected="true">Alignment length</option>
140 <option value="nident">Number of identical matches</option>
141 <option value="mismatch" selected="true">Number of mismatches</option>
142 <option value="positive">Number of positive - scoring matches</option>
143 <option value="gapopen" selected="true">Number of gap openings</option>
144 <option value="gaps">Total number of gaps</option>
145 <option value="ppos">Percentage of positive - scoring matches</option>
146 <option value="qstart" selected="true">Start of alignment in query</option>
147 <option value="qend" selected="true">End of alignment in query</option>
148 <option value="sstart" selected="true">Start of alignment in subject</option>
149 <option value="send" selected="true">End of alignment in subject</option>
150 <option value="qseq">Aligned part of query sequence</option>
151 <option value="sseq">Aligned part of subject sequence</option>
152 <option value="evalue" selected="true">Expect value</option>
153 <option value="bitscore" selected="true">Bit score</option>
154 <option value="score">Raw score</option>
155 <option value="qframe">Query frame</option>
156 <option value="stitle">Subject Title</option>
157 <option value="salltitles">All Subject Title(s)</option>
158 <option value="qcovhsp">Query Coverage Per HSP</option>
159 </param>
160 </when>
161 <when value="101">
162 <param argument="--salltitles" type="boolean" truevalue="--salltitles" falsevalue="" checked="true" label="Include full length subject titles in output?" help=""/>
163 </when>
164 </conditional>
165 <param name='sensitivity' type="select" label="Sensitivity Mode" help="Choose one of the sensitivity modes. More sensitivity may increase computation time">
166 <option value="0" selected="True">Default</option>
167 <option value="1">Sensitive</option>
168 <option value="2">More Sensitive</option>
169 </param>
170 <param argument="--gapopen" type="integer" value="11" label="Gap open penalty" help="" />
171 <param argument="--gapextend" type="integer" value="1" label="Gap extension penalty" help="" />
172 <param argument="--matrix" type="select" label="Scoring matrix" help="In brackets are the supported values for (gap open)/(gap extend)">
173 <option value="BLOSUM45">BLOSUM45 ((10-13)/3; (12-16)/2; (16-19)/1)</option>
174 <option value="BLOSUM50">BLOSUM50 ((9-13)/3; (12-16)/2; (15-19)/1)</option>
175 <option value="BLOSUM62" selected="True">BLOSUM62 ((6-11)/2; (9-13)/1)</option>
176 <option value="BLOSUM80">BLOSUM80 ((6-9)/2; 13/2; 25/2; (9-11)/1)</option>
177 <option value="BLOSUM90">BLOSUM90 ((6-9)/2; (9-11)/1)</option>
178 <option value="PAM250">PAM250 ((11-15)/3; (13-17)/2; (17-21)/1)</option>
179 <option value="PAM70">PAM70 ((6-8)/2; (9-11)/1)</option>
180 <option value="PAM30">PAM30 ((5-7)/2; (8-10)/1)</option>
181 </param>
182 <param argument="--seg" type="boolean" truevalue="yes" falsevalue="no" checked="true" label="Enable SEG masking of low complexity segments in the query?" help=""/>
183 <conditional name="hit_filter">
184 <param name="hit_filter_select" type="select" label="Method to restrict the number of hits?">
185 <option value="max">Maximum number of target sequences</option>
186 <option value="top">Percentage of top alignment score</option>
187 </param>
188 <when value="max">
189 <param name="max_target_seqs" argument="--max-target-seqs" type="integer" value="25" label="The maximum number of target sequences per query to keep alignments for" help="" />
190 </when>
191 <when value="top">
192 <param argument="--top" type="integer" value="0" label="Keep alignments within the given percentage range of the top alignment score for a quer" help="" />
193 </when> 178 </when>
194 </conditional> 179 </conditional>
195 <conditional name="filter_score"> 180 <conditional name="filter_score">
196 <param name="filter_score_select" type="select" label="Method to filter?" help="(--evalue/--min-score)"> 181 <param name="filter_score_select" type="select" label="Method to filter?" help="(--evalue/--min-score)">
197 <option value="evalue">Maximum e-value to report alignments</option> 182 <option value="evalue">Maximum e-value to report alignments</option>
202 </when> 187 </when>
203 <when value="min-score"> 188 <when value="min-score">
204 <param name="min_score" argument="--min-score" type="integer" value="0" label="Minimum bit score to keep an alignment" help="(--min-score)" /> 189 <param name="min_score" argument="--min-score" type="integer" value="0" label="Minimum bit score to keep an alignment" help="(--min-score)" />
205 </when> 190 </when>
206 </conditional> 191 </conditional>
192 <expand macro="hit_filter_macro" />
207 <param argument="--id" type="integer" value="0" label="Minimum identity percentage to report an alignment" help="" /> 193 <param argument="--id" type="integer" value="0" label="Minimum identity percentage to report an alignment" help="" />
208 <param name="query_cover" argument="--query-cover" type="integer" value="0" label="Minimum query cover percentage to report an alignment" help="" /> 194 <param name="query_cover" argument="--query-cover" type="integer" value="0" label="Minimum query cover percentage to report an alignment" help="" />
195 <param name="subject_cover" argument="--subject-cover" type="integer" value="0" label="Minimum subject cover percentage to report an alignment" help="" />
209 <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="" /> 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="" />
197 <param argument="--unal" type="boolean" truevalue="1" falsevalue="0" checked="false" label="report unaligned queries" help=""/>
210 </inputs> 198 </inputs>
211
212 <outputs> 199 <outputs>
213 <data format="xml" name="blast_xml" label="${tool.name} on ${on_string}"> 200 <expand macro="output_macro" />
214 <filter>output["outfmt"] == "5"</filter> 201 <data format="fasta" name="unalqueries" label="${tool.name} on ${on_string} (unaligned queries)">
215 </data> 202 <filter>unal == "1"</filter>
216 <data format="tabular" name="blast_tabular" label="${tool.name} on ${on_string}">
217 <filter>output["outfmt"] == "6"</filter>
218 </data>
219 <data format="sam" name="sam_output" label="${tool.name} on ${on_string}">
220 <filter>output["outfmt"] == "101"</filter>
221 </data> 203 </data>
222 </outputs> 204 </outputs>
223
224 <tests> 205 <tests>
225 <test> 206 <test>
226 <param name="method_select" value="blastp" /> 207 <conditional name="method_cond">
208 <param name="method_select" value="blastp" />
209 </conditional>
227 <param name="query" value="protein.fasta" ftype="fasta"/> 210 <param name="query" value="protein.fasta" ftype="fasta"/>
228 <param name="db_source" value="history"/> 211 <conditional name="ref_db_source">
229 <param name="reference_database" value="db.dmnd"/> 212 <param name="db_source" value="history"/>
230 <param name="outfmt" value="6"/> 213 <param name="reference_database" value="db.dmnd"/>
231 <param name="fields" value="qseqid,sseqid,pident,length,mismatch,gapopen,qstart,qend,sstart,send,evalue,bitscore"/> 214 </conditional>
215 <conditional name="output">
216 <param name="outfmt" value="6"/>
217 <param name="fields" value="qseqid,sseqid,pident,length,mismatch,gapopen,qstart,qend,sstart,send,evalue,bitscore"/>
218 </conditional>
232 <param name="sensitivity" value="0"/> 219 <param name="sensitivity" value="0"/>
233 <param name="gapopen" value="11"/>
234 <param name="gapextend" value="1"/>
235 <param name="matrix" value="BLOSUM62"/> 220 <param name="matrix" value="BLOSUM62"/>
236 <param name="seg" value="yes"/> 221 <param name="comp-based-stat" value="1"/>
237 <param name="hit_filter_select" value="max"/> 222 <param name="masking" value="1"/>
238 <param name="max_target_seqs" value="25" /> 223 <conditional name="hit_filter">
239 <param name="filter_score_select" value="evalue"/> 224 <param name="hit_filter_select" value="max"/>
240 <param name="evalue" value="0.001" /> 225 <param name="max_target_seqs" value="25" />
226 </conditional>
227 <conditional name="filter_score">
228 <param name="filter_score_select" value="evalue"/>
229 <param name="evalue" value="0.001" />
230 </conditional>
241 <param name="id" value="0"/> 231 <param name="id" value="0"/>
242 <param name="query_cover" value="0"/> 232 <param name="query_cover" value="0"/>
243 <param name="block_size" value="2"/> 233 <param name="block_size" value="2"/>
244 <output name="blast_tabular" file="diamond_results.tabular"/> 234 <output name="blast_tabular" file="diamond_results.tabular"/>
245 </test> 235 </test>
236 <test>
237 <conditional name="method_cond">
238 <param name="method_select" value="blastp" />
239 </conditional>
240 <param name="query" value="protein.fasta" ftype="fasta"/>
241 <conditional name="ref_db_source">
242 <param name="db_source" value="history"/>
243 <param name="reference_database" value="db-wtax.dmnd"/>
244 </conditional>
245 <conditional name="tax_cond">
246 <param name="tax_select" value="list"/>
247 <param name="taxonlist" value="2" />
248 </conditional>
249 <conditional name="output">
250 <param name="outfmt" value="6"/>
251 <param name="fields" value="qseqid,sseqid,pident,length,mismatch,gapopen,qstart,qend,sstart,send,evalue,bitscore"/>
252 </conditional>
253 <param name="sensitivity" value="0"/>
254 <param name="matrix" value="BLOSUM62"/>
255 <param name="comp-based-stat" value="1"/>
256 <param name="masking" value="1"/>
257 <conditional name="hit_filter">
258 <param name="hit_filter_select" value="max"/>
259 <param name="max_target_seqs" value="25" />
260 </conditional>
261 <conditional name="filter_score">
262 <param name="filter_score_select" value="evalue"/>
263 <param name="evalue" value="0.001" />
264 </conditional>
265 <param name="id" value="0"/>
266 <param name="query_cover" value="0"/>
267 <param name="block_size" value="2"/>
268 <output name="blast_tabular" file="diamond_results.wtax.tabular"/>
269 </test>
270 <test>
271 <conditional name="method_cond">
272 <param name="method_select" value="blastx" />
273 <conditional name="frameshift_cond">
274 <param name="frameshift_select" value="yes"/>
275 </conditional>
276 </conditional>
277 <param name="query" value="nucleotide.fasta" ftype="fasta"/>
278 <conditional name="ref_db_source">
279 <param name="db_source" value="history"/>
280 <param name="reference_database" value="db.dmnd"/>
281 </conditional>
282 <conditional name="output">
283 <param name="outfmt" value="0"/>
284 </conditional>
285 <param name="sensitivity" value="0"/>
286 <param name="matrix" value="BLOSUM62"/>
287 <param name="comp-based-stat" value="1"/>
288 <param name="masking" value="1"/>
289 <conditional name="hit_filter">
290 <param name="hit_filter_select" value="top"/>
291 <param name="top" value="10" />
292 </conditional>
293 <conditional name="filter_score">
294 <param name="filter_score_select" value="score"/>
295 <param name="evalue" value="1" />
296 </conditional>
297 <param name="id" value="0"/>
298 <param name="query_cover" value="0"/>
299 <param name="block_size" value="2"/>
300 <output name="blast_tabular" file="diamond_results.pairwise"/>
301 </test>
302 <test>
303 <conditional name="method_cond">
304 <param name="method_select" value="blastp" />
305 </conditional>
306 <param name="query" value="protein.fasta" ftype="fasta"/>
307 <conditional name="ref_db_source">
308 <param name="db_source" value="history"/>
309 <param name="reference_database" value="db-wtax.dmnd"/>
310 </conditional>
311 <conditional name="output">
312 <param name="outfmt" value="100"/>
313 </conditional>
314 <output name="daa_output" file="diamond_results.daa" compare="sim_size" delta="10"/>
315 </test>
246 </tests> 316 </tests>
247
248 <help> 317 <help>
249 <![CDATA[ 318 <![CDATA[
250 319
251 **What it does** 320 **What it does**
252 321