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comparison diamond.xml @ 8:54f751e413f4 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit 75abf7d4b23ed7ae8abce80609d81b20bc882863"
author iuc
date Mon, 22 Mar 2021 13:21:23 +0000
parents 62c9df8382c2
children f921014aba5a
comparison
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7:62c9df8382c2 8:54f751e413f4
4 <import>macros.xml</import> 4 <import>macros.xml</import>
5 </macros> 5 </macros>
6 <expand macro="requirements" /> 6 <expand macro="requirements" />
7 <expand macro="stdio" /> 7 <expand macro="stdio" />
8 <expand macro="version_command" /> 8 <expand macro="version_command" />
9 <command> 9 <command detect_errors="aggressive">
10 <![CDATA[ 10 <![CDATA[
11 11
12 #if $ref_db_source.db_source == "history": 12 #if $ref_db_source.db_source == "history":
13 ln -s $ref_db_source.reference_database ./database.dmnd 13 ln -s $ref_db_source.reference_database ./database.dmnd
14 #else: 14 #else:
17 17
18 && 18 &&
19 19
20 diamond 20 diamond
21 $method_cond.method_select 21 $method_cond.method_select
22 --quiet
22 --threads "\${GALAXY_SLOTS:-12}" 23 --threads "\${GALAXY_SLOTS:-12}"
23 --db ./database 24 --db ./database
24 --query '$query' 25 --query '$query'
25 #if $method_cond.method_select == "blastx" 26 #if $method_cond.method_select == "blastx"
26 --query-gencode '$method_cond.query_gencode' 27 --query-gencode '$method_cond.query_gencode'
27 --strand '$method_cond.query_strand' 28 --strand '$method_cond.query_strand'
28 --min-orf $method_cond.min_orf 29 --min-orf $method_cond.min_orf
29 #if $method_cond.frameshift_cond.frameshift_select == 'yes' 30 #if $method_cond.frameshift_cond.frameshift_select == 'yes'
30 --frameshift $method_cond.frameshift_cond.frameshift 31 --frameshift $method_cond.frameshift_cond.frameshift
31 $method_cond.frameshift_cond.range_culling 32 $method_cond.frameshift_cond.range_culling
32 #end if 33 #end if
34 #else if $method_cond.method_select == "blastp"
35 $method_cond.no_self_hits
33 #end if 36 #end if
34 37
35 @OUTPUT_ARGS@ 38 @OUTPUT_ARGS@
36 39
37 --compress '0' 40 --compress '0'
38 #if $sensitivity == "1" 41 $sens_cond.sensitivity
39 --sensitive
40 #else if $sensitivity == "2"
41 --more-sensitive
42 #end if
43 42
44 #if str($gapopen) != "": 43 #if str($gapopen) != "":
45 --gapopen '$gapopen' 44 --gapopen '$gapopen'
46 #end if 45 #end if
47 #if str($gapextend) != "": 46 #if str($gapextend) != "":
48 --gapextend '$gapextend' 47 --gapextend '$gapextend'
49 #end if 48 #end if
50 --matrix '$matrix' 49 --matrix '$matrix'
51 --comp-based-stats '$comp_based_stats' 50 --comp-based-stats '$method_cond.comp_based_stats'
52 --masking '$masking' 51 --masking '$masking'
53 52
54 @HITFILTER_ARGS@ 53 @HITFILTER_ARGS@
55 54
56 #if str($filter_score.filter_score_select) == 'evalue': 55 #if str($filter_score.filter_score_select) == 'evalue':
60 #end if 59 #end if
61 60
62 --id '$id' 61 --id '$id'
63 --query-cover '$query_cover' 62 --query-cover '$query_cover'
64 --subject-cover '$subject_cover' 63 --subject-cover '$subject_cover'
65 --block-size '$block_size' 64 --block-size '$sens_cond.block_size'
66 #if str($unal) == '1': 65 #if str($unal) == '1':
67 --unal 1 --un '$unalqueries' 66 --unal 1 --un '$unalqueries'
68 #end if 67 #end if
69 $no_self_hits
70 #if $tax_cond.tax_select == 'file': 68 #if $tax_cond.tax_select == 'file':
71 --taxonlist `cat '$tax_cond.taxonlistfile' | grep -v "^#" | grep -v "^$" | tr "\n" "," | sed 's/,$//'` 69 --taxonlist `cat '$tax_cond.taxonlistfile' | grep -v "^#" | grep -v "^$" | tr "\n" "," | sed 's/,$//'`
72 #else if $tax_cond.tax_select == 'list': 70 #else if $tax_cond.tax_select == 'list':
73 --taxonlist '$tax_cond.taxonlist' 71 --taxonlist '$tax_cond.taxonlist'
74 #end if 72 #end if
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"/> 116 <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." /> 117 <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> 118 </when>
121 <when value="no"/> 119 <when value="no"/>
122 </conditional> 120 </conditional>
121
122 <param name="comp_based_stats" argument="--comp-based-stats" type="select" label="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">
123 <option value="0">Disable</option>
124 <option value="1" selected="True">Default mode (Hauser, 2016)</option>
125 </param>
123 </when> 126 </when>
124 <when value="blastp"> 127 <when value="blastp">
128 <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=""/>
129
130 <param name="comp_based_stats" argument="--comp-based-stats" type="select" label="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">
131 <option value="0">Disable</option>
132 <option value="1" selected="True">Default mode (Hauser, 2016)</option>
133 <option value="2">Compositional matrix adjust conditioned on sequence properties, simplified (Yu, 2005)</option>
134 <option value="3">Compositional matrix adjust conditioned on sequence properties (Yu, 2005)</option>
135 <option value="4">Compositional matrix adjust unconditionally (Yu, 2005)</option>
136 </param>
125 </when> 137 </when>
126 </conditional> 138 </conditional>
127 <param argument="--query" type="data" format="fasta,fastq" label="Input query file in FASTA or FASTQ format" /> 139 <param argument="--query" type="data" format="fasta,fastq" label="Input query file in FASTA or FASTQ format" />
128 <conditional name="ref_db_source"> 140 <conditional name="ref_db_source">
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"> 141 <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">
137 <validator type="no_options" message="No indexes are available for the selected input dataset"/> 149 <validator type="no_options" message="No indexes are available for the selected input dataset"/>
138 </options> 150 </options>
139 </param> 151 </param>
140 </when> 152 </when>
141 <when value="history"> 153 <when value="history">
142 <param name="reference_database" type="data" format="dmnd" label="Select the reference database" /> 154 <param name="reference_database" argument="--db" type="data" format="dmnd" label="Select the reference database" />
143 </when> 155 </when>
144 </conditional> 156 </conditional>
145 <expand macro="output_type_macro" /> 157 <expand macro="output_type_macro">
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=""/> 158 <!-- Taxonomy features are not supported for the DAA format (i.e.
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."> 159 can't be used in diamond view) -->
148 <option value="0" selected="True">Default</option> 160 <option value="staxids">unique Subject Taxonomy ID(s), separated by a ';' (in numerical order)</option>
149 <option value="1">Sensitive</option> 161 <option value="sskingdoms">Subject super kingdoms</option>
150 <option value="2">More Sensitive</option> 162 <option value="skingdoms">Subject kingdoms</option>
151 </param> 163 <option value="sphylums">Subject phylums</option>
164 </expand>
165 <conditional name="sens_cond">
166 <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.">
167 <option value="" selected="True">Default</option>
168 <option value="--mid-sensitive">Mid Sensitive (--mid-sensitive)</option>
169 <option value="--sensitive">Sensitive (--sensitive)</option>
170 <option value="--more-sensitive">More Sensitive (--more-sensitive)</option>
171 <option value="--very-sensitive">Very Sensitive (--very-sensitive)</option>
172 <option value="--ultra-sensitive">Ultra Sensitive (--ultra-sensitive)</option>
173 </param>
174 <when value="">
175 <expand macro="block_size_low_sens"/>
176 </when>
177 <when value="--mid-sensitive">
178 <expand macro="block_size_low_sens"/>
179 </when>
180 <when value="--sensitive">
181 <expand macro="block_size_low_sens"/>
182 </when>
183 <when value="--more-sensitive">
184 <expand macro="block_size_low_sens"/>
185 </when>
186 <when value="--very-sensitive">
187 <expand macro="block_size_hi_sens"/>
188 </when>
189 <when value="--ultra-sensitive">
190 <expand macro="block_size_hi_sens"/>
191 </when>
192 </conditional>
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"> 193 <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> 194 <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> 195 <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> 196 <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> 197 <option value="BLOSUM80">BLOSUM80 ((6-9)/2; 13/2; 25/2; (9-11)/1) [10/1]</option>
159 <option value="PAM70">PAM70 ((6-8)/2; (9-11)/1) [10/1]</option> 200 <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> 201 <option value="PAM30">PAM30 ((5-7)/2; (8-10)/1) [9/1]</option>
161 </param> 202 </param>
162 <param argument="--gapopen" type="integer" optional="True" value="" label="Gap open penalty" help="leave empty for default (see scoring matrix)" /> 203 <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)" /> 204 <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"/> 205 <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"> 206 <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"> 207 <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" selected="True">No</option> 208 <option value="no" selected="True">No</option>
169 <option value="list">list of taxids entered manually</option> 209 <option value="list">list of taxids entered manually</option>
170 <option value="file">list of taxids from single column tabular file</option> 210 <option value="file">list of taxids from single column tabular file</option>
171 </param> 211 </param>
172 <when value="no"/> 212 <when value="no"/>
173 <when value="list"> 213 <when value="list">
174 <param name="taxonlist" argument="--taxonlist" type="text" value="" label="comma separated list of taxon ids" help="" /> 214 <param name="taxonlist" argument="--taxonlist" type="text" value="" label="comma separated list of taxon ids" help="">
215 <validator type="regex" message="taxonlist needs to be a comma separated list of integers">[0-9,]*</validator>
216 <validator type="expression" message="taxon ids 0 and 1 are not allowed">not ("0" in value.split(",") or "1" in value.split(","))</validator>
217 </param>
175 </when> 218 </when>
176 <when value="file"> 219 <when value="file">
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="" /> 220 <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="" />
178 </when> 221 </when>
179 </conditional> 222 </conditional>
191 </conditional> 234 </conditional>
192 <expand macro="hit_filter_macro" /> 235 <expand macro="hit_filter_macro" />
193 <param argument="--id" type="integer" value="0" label="Minimum identity percentage to report an alignment" help="" /> 236 <param argument="--id" type="integer" value="0" label="Minimum identity 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="" /> 237 <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="" /> 238 <param name="subject_cover" argument="--subject-cover" type="integer" value="0" label="Minimum subject cover percentage to report an alignment" 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=""/> 239 <param argument="--unal" type="boolean" truevalue="1" falsevalue="0" checked="false" label="report unaligned queries" help=""/>
198 </inputs> 240 </inputs>
199 <outputs> 241 <outputs>
200 <expand macro="output_macro" /> 242 <expand macro="output_macro" />
201 <data format="fasta" name="unalqueries" label="${tool.name} on ${on_string} (unaligned queries)"> 243 <data format="fasta" name="unalqueries" label="${tool.name} on ${on_string} (unaligned queries)">
208 <param name="method_select" value="blastp" /> 250 <param name="method_select" value="blastp" />
209 </conditional> 251 </conditional>
210 <param name="query" value="protein.fasta" ftype="fasta"/> 252 <param name="query" value="protein.fasta" ftype="fasta"/>
211 <conditional name="ref_db_source"> 253 <conditional name="ref_db_source">
212 <param name="db_source" value="history"/> 254 <param name="db_source" value="history"/>
213 <param name="reference_database" value="db.dmnd"/> 255 <param name="reference_database" value="db-wtax.dmnd"/>
214 </conditional> 256 </conditional>
215 <conditional name="output"> 257 <conditional name="output">
216 <param name="outfmt" value="6"/> 258 <param name="outfmt" value="6"/>
217 <param name="fields" value="qseqid,sseqid,pident,length,mismatch,gapopen,qstart,qend,sstart,send,evalue,bitscore"/> 259 <param name="fields" value="qseqid,sseqid,pident,length,mismatch,gapopen,qstart,qend,sstart,send,evalue,bitscore,cigar,scovhsp,sskingdoms,skingdoms,sphylums"/>
218 </conditional> 260 </conditional>
219 <param name="sensitivity" value="0"/> 261 <conditional name="sens_cond">
262 <param name="sensitivity" value=""/>
263 </conditional>
220 <param name="matrix" value="BLOSUM62"/> 264 <param name="matrix" value="BLOSUM62"/>
221 <param name="comp-based-stat" value="1"/> 265 <param name="comp-based-stat" value="1"/>
222 <param name="masking" value="1"/> 266 <param name="masking" value="1"/>
223 <conditional name="hit_filter"> 267 <conditional name="hit_filter">
224 <param name="hit_filter_select" value="max"/> 268 <param name="hit_filter_select" value="max"/>
228 <param name="filter_score_select" value="evalue"/> 272 <param name="filter_score_select" value="evalue"/>
229 <param name="evalue" value="0.001" /> 273 <param name="evalue" value="0.001" />
230 </conditional> 274 </conditional>
231 <param name="id" value="0"/> 275 <param name="id" value="0"/>
232 <param name="query_cover" value="0"/> 276 <param name="query_cover" value="0"/>
233 <param name="block_size" value="2"/> 277 <conditional name="sens_cond">
278 <param name="block_size" value="2"/>
279 </conditional>
234 <output name="blast_tabular" file="diamond_results.tabular"/> 280 <output name="blast_tabular" file="diamond_results.tabular"/>
235 </test> 281 </test>
236 <test> 282 <test>
237 <conditional name="method_cond"> 283 <conditional name="method_cond">
238 <param name="method_select" value="blastp" /> 284 <param name="method_select" value="blastp" />
241 <conditional name="ref_db_source"> 287 <conditional name="ref_db_source">
242 <param name="db_source" value="history"/> 288 <param name="db_source" value="history"/>
243 <param name="reference_database" value="db-wtax.dmnd"/> 289 <param name="reference_database" value="db-wtax.dmnd"/>
244 </conditional> 290 </conditional>
245 <conditional name="tax_cond"> 291 <conditional name="tax_cond">
246 <param name="tax_select" value="list"/> 292 <param name="tax_select" value="list"/>
247 <param name="taxonlist" value="2" /> 293 <param name="taxonlist" value="2" />
248 </conditional> 294 </conditional>
249 <conditional name="output"> 295 <conditional name="output">
250 <param name="outfmt" value="6"/> 296 <param name="outfmt" value="6"/>
251 <param name="fields" value="qseqid,sseqid,pident,length,mismatch,gapopen,qstart,qend,sstart,send,evalue,bitscore"/> 297 <param name="fields" value="qseqid,sseqid,pident,length,mismatch,gapopen,qstart,qend,sstart,send,evalue,bitscore"/>
252 </conditional> 298 </conditional>
253 <param name="sensitivity" value="0"/> 299 <conditional name="sens_cond">
300 <param name="sensitivity" value=""/>
301 </conditional>
254 <param name="matrix" value="BLOSUM62"/> 302 <param name="matrix" value="BLOSUM62"/>
255 <param name="comp-based-stat" value="1"/> 303 <param name="comp-based-stat" value="1"/>
256 <param name="masking" value="1"/> 304 <param name="masking" value="1"/>
257 <conditional name="hit_filter"> 305 <conditional name="hit_filter">
258 <param name="hit_filter_select" value="max"/> 306 <param name="hit_filter_select" value="max"/>
262 <param name="filter_score_select" value="evalue"/> 310 <param name="filter_score_select" value="evalue"/>
263 <param name="evalue" value="0.001" /> 311 <param name="evalue" value="0.001" />
264 </conditional> 312 </conditional>
265 <param name="id" value="0"/> 313 <param name="id" value="0"/>
266 <param name="query_cover" value="0"/> 314 <param name="query_cover" value="0"/>
267 <param name="block_size" value="2"/> 315 <conditional name="sens_cond">
316 <param name="block_size" value="2"/>
317 </conditional>
268 <output name="blast_tabular" file="diamond_results.wtax.tabular"/> 318 <output name="blast_tabular" file="diamond_results.wtax.tabular"/>
269 </test> 319 </test>
270 <test> 320 <test>
271 <conditional name="method_cond"> 321 <conditional name="method_cond">
272 <param name="method_select" value="blastx" /> 322 <param name="method_select" value="blastx" />
280 <param name="reference_database" value="db.dmnd"/> 330 <param name="reference_database" value="db.dmnd"/>
281 </conditional> 331 </conditional>
282 <conditional name="output"> 332 <conditional name="output">
283 <param name="outfmt" value="0"/> 333 <param name="outfmt" value="0"/>
284 </conditional> 334 </conditional>
285 <param name="sensitivity" value="0"/> 335 <conditional name="sens_cond">
336 <param name="sensitivity" value=""/>
337 </conditional>
286 <param name="matrix" value="BLOSUM62"/> 338 <param name="matrix" value="BLOSUM62"/>
287 <param name="comp-based-stat" value="1"/> 339 <param name="comp-based-stat" value="1"/>
288 <param name="masking" value="1"/> 340 <param name="masking" value="1"/>
289 <conditional name="hit_filter"> 341 <conditional name="hit_filter">
290 <param name="hit_filter_select" value="top"/> 342 <param name="hit_filter_select" value="top"/>
291 <param name="top" value="10" /> 343 <param name="top" value="10" />
292 </conditional> 344 </conditional>
293 <conditional name="filter_score"> 345 <conditional name="filter_score">
294 <param name="filter_score_select" value="score"/> 346 <param name="filter_score_select" value="min-score"/>
295 <param name="evalue" value="1" /> 347 <param name="min_score" value="1" />
296 </conditional> 348 </conditional>
297 <param name="id" value="0"/> 349 <param name="id" value="0"/>
298 <param name="query_cover" value="0"/> 350 <param name="query_cover" value="0"/>
299 <param name="block_size" value="2"/> 351 <conditional name="sens_cond">
352 <param name="block_size" value="2"/>
353 </conditional>
300 <output name="blast_tabular" file="diamond_results.pairwise"/> 354 <output name="blast_tabular" file="diamond_results.pairwise"/>
301 </test> 355 </test>
302 <test> 356 <test>
303 <conditional name="method_cond"> 357 <conditional name="method_cond">
304 <param name="method_select" value="blastp" /> 358 <param name="method_select" value="blastp" />
310 </conditional> 364 </conditional>
311 <conditional name="output"> 365 <conditional name="output">
312 <param name="outfmt" value="100"/> 366 <param name="outfmt" value="100"/>
313 </conditional> 367 </conditional>
314 <output name="daa_output" file="diamond_results.daa" compare="sim_size" delta="10"/> 368 <output name="daa_output" file="diamond_results.daa" compare="sim_size" delta="10"/>
369 </test>
370 <test>
371 <conditional name="method_cond">
372 <param name="method_select" value="blastx" />
373 <conditional name="frameshift_cond">
374 <param name="frameshift_select" value="yes"/>
375 </conditional>
376 </conditional>
377 <param name="query" value="nucleotide.fasta" ftype="fasta"/>
378 <conditional name="ref_db_source">
379 <param name="db_source" value="indexed"/>
380 <param name="index" value="testDb"/>
381 </conditional>
382 <conditional name="output">
383 <param name="outfmt" value="0"/>
384 </conditional>
385 <conditional name="sens_cond">
386 <param name="sensitivity" value=""/>
387 </conditional>
388 <param name="matrix" value="BLOSUM62"/>
389 <param name="comp-based-stat" value="1"/>
390 <param name="masking" value="1"/>
391 <conditional name="hit_filter">
392 <param name="hit_filter_select" value="top"/>
393 <param name="top" value="10" />
394 </conditional>
395 <conditional name="filter_score">
396 <param name="filter_score_select" value="min-score"/>
397 <param name="min_score" value="1" />
398 </conditional>
399 <param name="id" value="0"/>
400 <param name="query_cover" value="0"/>
401 <conditional name="sens_cond">
402 <param name="block_size" value="2"/>
403 </conditional>
404 <output name="blast_tabular" file="diamond_results.pairwise"/>
315 </test> 405 </test>
316 </tests> 406 </tests>
317 <help> 407 <help>
318 <![CDATA[ 408 <![CDATA[
319 409