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comparison lastal.xml @ 0:7f7e48d3b85d draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8"
author iuc
date Wed, 17 Jun 2020 10:20:20 +0000
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children 036d64816c8b
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-1:000000000000 0:7f7e48d3b85d
1 <tool id="last_al" name="LASTal" version="@LAST_CONDA_VERSION@+galaxy0" profile="18.01">
2
3 <description>finds local alignments between query sequences, and reference sequences.</description>
4
5 <macros>
6 <import>macros_last.xml</import>
7 </macros>
8
9 <requirements>
10 <requirement type="package" version="@LAST_CONDA_VERSION@">last</requirement>
11 </requirements>
12
13 <command detect_errors="exit_code"><![CDATA[
14 #if $db_opts.db_opts_input == 'lastdb'
15 ln -s '$db_opts.lastdatabase.extra_files_path' './db_files' &&
16 #end if
17
18 lastal
19
20 -Q $lastal.Q
21 -f $lastal.f
22 -j $lastal.j
23
24 -R $lastal.repeats_misc.uppercase_misc$lastal.repeats_misc.simple_repeat_misc
25
26 #if $lastal.isprotein.schoring_schemes.score_matrix != 'scoreFile'
27 -p $lastal.isprotein.schoring_schemes.score_matrix
28
29 -X $lastal.isprotein.schoring_schemes.score_opt.X
30 -x $lastal.isprotein.schoring_schemes.score_opt.x
31 -y $lastal.isprotein.schoring_schemes.score_opt.y
32 -z $lastal.isprotein.schoring_schemes.score_opt.z
33 -d $lastal.isprotein.schoring_schemes.score_opt.d
34 -e $lastal.isprotein.schoring_schemes.score_opt.e
35
36 -a $lastal.isprotein.schoring_schemes.cost_opt.a
37 -b $lastal.isprotein.schoring_schemes.cost_opt.b
38 -A $lastal.isprotein.schoring_schemes.cost_opt.A
39 -B $lastal.isprotein.schoring_schemes.cost_opt.B
40
41 -s $lastal.isprotein.s
42 #else if $lastal.isprotein.schoring_schemes.score_matrix == 'scoreFile'
43 -p $lastal.isprotein.schoring_schemes.scoreMatrixFile
44 #end if
45
46 -D $lastal.evalue_opt.D
47
48 -m $lastal.init_match_opt.m
49 -l $lastal.init_match_opt.l
50 -L $lastal.init_match_opt.L
51 -k $lastal.init_match_opt.k
52 -W $lastal.init_match_opt.W
53
54 -S $lastal.misc_opt.S
55 -K $lastal.misc_opt.K
56 -C $lastal.misc_opt.C
57 -T $lastal.misc_opt.T
58 -n $lastal.misc_opt.n
59 -w $lastal.misc_opt.w
60 -u $lastal.misc_opt.u
61 -g $lastal.misc_opt.g
62
63 -P \${GALAXY_SLOTS:-1}
64
65 #if $db_opts.db_opts_input == 'db'
66 '${"'" "'".join(str($db_opts.database.fields.path).split(","))}'
67 #else if $db_opts.db_opts_input == 'lastdb'
68 'db_files/lastdb'
69 #end if
70
71 '$query_fasta'
72
73 >'$outfile'
74 ]]></command>
75
76 <inputs>
77 <expand macro="input_db"/>
78 <param name="query_fasta" type="data" format="FASTA" label="Queries fasta file"/>
79
80 <section name="lastal" title="Lastal arguments" expanded="true">
81 <param argument="-Q" type="select" multiple="false" label="Input format">
82 <option value="0" selected="true">fasta or fastq-ignore</option>
83 <option value="1">fastq-sanger</option>
84 <option value="2">fastq-solexa</option>
85 <option value="3">fastq-illumina</option>
86 <option value="4">prb</option>
87 <option value="5">PSSM</option>
88 </param>
89 <param argument="-f" type="select" multiple="false" label="Output format">
90 <option value="MAF" selected="true">MAF</option>
91 <option value="TAB">TAB</option>
92 <option value="BlastTab">BlastTab</option>
93 <option value="BlastTab+">BlastTab+</option>
94 </param>
95 <param argument="-j" type="select" multiple="false" label="Output type">
96 <option value="0">Match counts</option>
97 <option value="1">Gapless</option>
98 <option value="2">Redundant gapped</option>
99 <option value="3" selected="true">Gapped</option>
100 <option value="4">Column ambiguity estimates</option>
101 <option value="5">Gamma-centroid</option>
102 <option value="6">LAMA</option>
103 <option value="7">Expected counts</option>
104 </param>
105
106 <conditional name="isprotein">
107 <param name="lastal_protein" type="select" multiple="false" label="The sequences are :">
108 <option value="dna" selected="true">DNA</option>
109 <option value="prot">Proteins (-p)</option>
110 </param>
111 <when value="dna">
112 <conditional name="schoring_schemes">
113 <param name="score_matrix" argument="-p" type="select" multiple="false" label="Match/mismatch score matrix.">
114 <option value="AT77">AT77</option>
115 <option value="ATMAP">ATMAP</option>
116 <option value="BISF">BISF</option>
117 <option value="BISR">BISR</option>
118 <option value="BL62">BLOSUM62</option>
119 <option value="BL80" selected="true">BLOSUM80</option>
120 <option value="HOXD70">HOXD70</option>
121 <option value="MIQS">MIQS</option>
122 <option value="PAM10">PAM10</option>
123 <option value="PAM30">PAM30</option>
124 <option value="scoreFile">Other score matrix</option>
125 </param>
126 <when value="AT77">
127 <expand macro="score_macro"/>
128 <expand macro="cost_macro" a="15" b="2"/>
129 </when>
130 <when value="ATMAP">
131 <expand macro="score_macro"/>
132 <expand macro="cost_macro" a="24" b="6"/>
133 </when>
134 <when value="BISF">
135 <expand macro="score_macro"/>
136 <expand macro="cost_macro" a="21" b="9"/>
137 </when>
138 <when value="BISR">
139 <expand macro="score_macro"/>
140 <expand macro="cost_macro" a="21" b="9"/>
141 </when>
142 <when value="BL62">
143 <expand macro="score_macro"/>
144 <expand macro="cost_macro" a="11" b="2"/>
145 </when>
146 <when value="BL80">
147 <expand macro="score_macro"/>
148 <expand macro="cost_macro" a="7" b="1"/>
149 </when>
150 <when value="HOXD70">
151 <expand macro="score_macro"/>
152 <expand macro="cost_macro" a="400" b="30"/>
153 </when>
154 <when value="MIQS">
155 <expand macro="score_macro"/>
156 <expand macro="cost_macro" a="13" b="2"/>
157 </when>
158 <when value="PAM10">
159 <expand macro="score_macro"/>
160 <expand macro="cost_macro" a="20" b="3"/>
161 </when>
162 <when value="PAM30">
163 <expand macro="score_macro"/>
164 <expand macro="cost_macro" a="13" b="3"/>
165 </when>
166 <when value="scoreFile">
167 <param name="scoreMatrixFile" type="data" format="txt" label="Score matrix file" />
168 </when>
169 </conditional>
170 <param argument="-s" type="select" multiple="false" label="Strand">
171 <option value="0">Reverse</option>
172 <option value="1">Forward</option>
173 <option value="2" selected="true">Both</option>
174 </param>
175 </when>
176 <when value="prot">
177 <conditional name="schoring_schemes">
178 <param name="score_matrix" argument="-p" type="select" multiple="false" label="Match/mismatch score matrix.">
179 <option value="AT77">AT77</option>
180 <option value="ATMAP">ATMAP</option>
181 <option value="BISF">BISF</option>
182 <option value="BISR">BISR</option>
183 <option value="BL62" selected="true">BLOSUM62</option>
184 <option value="BL80">BLOSUM80</option>
185 <option value="HOXD70">HOXD70</option>
186 <option value="MIQS">MIQS</option>
187 <option value="PAM10">PAM10</option>
188 <option value="PAM30">PAM30</option>
189 <option value="scoreFile">Other score matrix</option>
190 </param>
191 <when value="AT77">
192 <expand macro="score_macro"/>
193 <expand macro="cost_macro" a="15" b="2"/>
194 </when>
195 <when value="ATMAP">
196 <expand macro="score_macro"/>
197 <expand macro="cost_macro" a="24" b="6"/>
198 </when>
199 <when value="BISF">
200 <expand macro="score_macro"/>
201 <expand macro="cost_macro" a="21" b="9"/>
202 </when>
203 <when value="BISR">
204 <expand macro="score_macro"/>
205 <expand macro="cost_macro" a="21" b="9"/>
206 </when>
207 <when value="BL62">
208 <expand macro="score_macro"/>
209 <expand macro="cost_macro" a="11" b="2"/>
210 </when>
211 <when value="BL80">
212 <expand macro="score_macro"/>
213 <expand macro="cost_macro" a="7" b="1"/>
214 </when>
215 <when value="HOXD70">
216 <expand macro="score_macro"/>
217 <expand macro="cost_macro" a="400" b="30"/>
218 </when>
219 <when value="MIQS">
220 <expand macro="score_macro"/>
221 <expand macro="cost_macro" a="13" b="2"/>
222 </when>
223 <when value="PAM10">
224 <expand macro="score_macro"/>
225 <expand macro="cost_macro" a="20" b="3"/>
226 </when>
227 <when value="PAM30">
228 <expand macro="score_macro"/>
229 <expand macro="cost_macro" a="13" b="3"/>
230 </when>
231 <when value="scoreFile">
232 <param name="scoreMatrixFile" type="data" format="txt" label="Score matrix file" />
233 </when>
234 </conditional>
235 <param argument="-s" type="select" multiple="false" label="Strand">
236 <option value="0">Reverse</option>
237 <option value="1" selected="true">Forward</option>
238 <option value="2">Both</option>
239 </param>
240 </when>
241 </conditional>
242
243 <section name="repeats_misc" title="Specify lowercase-marking of repeats. (-R)" expanded="false">
244 <param name="uppercase_misc" type="select" multiple="false" label="Input sequences to uppercase.">
245 <option value="0">Convert the input sequences to uppercase while reading them.(0)</option>
246 <option value="1" selected="true">Keep any lowercase in the input sequences.(1)</option>
247 </param>
248 <param name="simple_repeat_misc" type="select" multiple="false" label="Check for simple repeats.">
249 <option value="0" selected="true">Do not check for simple repeats.(0)</option>
250 <option value="1">Convert simple repeats to lowercase.(1)</option>
251 <option value="2">Convert simple DNA repeats to lowercase.(2)</option>
252 </param>
253 </section>
254
255 <section name="evalue_opt" title="E-value options" expanded="false">
256 <param argument="-D" type="integer" value="1000000" label="Query letters per random alignment (-D)"/>
257 <!--<param argument="-E" type="integer" value="1e+18" label="Maximum expected alignments per square giga"/>-->
258 </section>
259
260 <section name="init_match_opt" title="Initial-match options" expanded="false">
261 <param argument="-m" type="integer" value="10" min="1" label="Maximum initial matches per query position"/>
262 <param argument="-l" type="integer" value="1" min="1" label="Minimum length for initial matches"/>
263 <!-- Infinity -->
264 <param argument="-L" type="integer" value="999999999" min="1" label="Maximum length for initial matches"/>
265 <param argument="-k" type="integer" value="1" min="1" label="Use initial matches starting at every k-th position in each query"/>
266 <param argument="-W" type="integer" value="1" min="1" label="Use minimum positions in sliding windows of W consecutive positions"/>
267 </section>
268
269 <section name="misc_opt" title="Miscellaneous options" expanded="false">
270 <param argument="-S" type="select" multiple="false" label="Score matrix applies to forward strand of :">
271 <option value="0" selected="true">Reference</option>
272 <option value="1">Query</option>
273 </param>
274 <param argument="-K" type="integer" value="0" min="0" label="Omit alignments whose query range lies in >= K others with > score"/>
275 <param argument="-C" type="integer" value="0" min="0" label="Omit gapless alignments in >= C others with > score-per-length"/>
276 <!--<param name="omit_gap" argument="-M" type="integer" value="" label="Find minimum-difference alignments (faster but cruder)"/>-->
277
278 <param argument="-T" type="select" multiple="false" label="Type of alignment">
279 <option value="0" selected="true">Local</option>
280 <option value="1">Overlap</option>
281 </param>
282 <param argument="-n" type="integer" value="10" min="0" label="Maximum gapless alignments per query position" help="Infinity if m=0"/>
283 <!--<param name="max_gap_align" argument="-N" type="integer" value="0" label="Stop after the first N alignments per query strand"/>-->
284
285 <!-- Condition lastdb : 2 if lastdb -c and Q<5 -->
286 <param argument="-u" type="select" multiple="false" label="Mask lowercase during extensions.">
287 <option value="0" selected="true">Never.(0)</option>
288 <option value="1">Gapless.(1)</option>
289 <option value="2">Gapless+postmask.(2)</option>
290 <option value="3">Always.(3)</option>
291 </param>
292 <param argument="-w" type="integer" value="1000" min="0" label="Suppress repeats inside exact matches, offset by less or equal this distance. Use 0 to set this off" help="Use 0 to turn this off"/>
293
294 <!-- https://www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi -->
295 <!-- Condition if ADN vs prot and -F -->
296 <param argument="-G" type="select" multiple="false" label="Genetic code.">
297 <option value="1" selected="true">Standard Code</option>
298 <option value="2">Vertebrate Mitochondrial Code</option>
299 <option value="3">Yeast Mitochondrial Code</option>
300 <option value="4">Mold, Protozoan, and Coelenterate Mitochondrial Code and the Mycoplasma/Spiroplasma</option>
301 <option value="5">Invertebrate Mitochondrial Code</option>
302 <option value="6">Ciliate, Dasycladacean and Hexamita Nuclear Code</option>
303 <option value="9">Echinoderm and Flatworm Mitochondrial Code</option>
304 <option value="10">Euplotid Nuclear Code</option>
305 <option value="11">Bacterial, Archaeal and Plant Plastid Code</option>
306 <option value="12">Alternative Yeast Nuclear Code</option>
307 <option value="13">Ascidian Mitochondrial Code</option>
308 <option value="14">Alternative Flatworm Mitochondrial Code</option>
309 <option value="16">Chlorophycean Mitochondrial Code</option>
310 <option value="21">Trematode Mitochondrial Code</option>
311 <option value="22">Scenedesmus obliquus Mitochondrial Code</option>
312 <option value="23">Thraustochytrium Mitochondrial Code</option>
313 <option value="24">Pterabranchia Mitochondrial Code</option>
314 <option value="25">Candidate Division SR1 and Gracilibacteria Code</option>
315 <option value="26">Pachysolen tannophilus Nuclear Code</option>
316 <option value="27">Karyorelict Nuclear Code</option>
317 <option value="28">Condylostoma Nuclear Code</option>
318 <option value="29">Mesodinium Nuclear Code</option>
319 <option value="30">Peritrich Nuclear Code</option>
320 <option value="31">Blastocrithidia Nuclear Code</option>
321 <option value="33">Cephalodiscidae Mitochondrial UAA-Tyr Code</option>
322 <!-- Add filename option with <repeat> -->
323 </param>
324
325 <!--<param name="temperature" argument="-t" type="integer" value="1/lambda" label="Temperature for calculating probabilities"/>-->
326 <param argument="-g" type="integer" value="1" min="0" label="Gamma parameter for gamma-centroid and LAMA"/>
327 </section>
328 </section>
329 </inputs>
330
331 <outputs>
332 <data name="outfile" format="maf" label="LAST align from ${on_string}" />
333 </outputs>
334
335 <tests>
336 <test>
337 <conditional name="db_opts">
338 <param name="db_opts_input" value="db"/>
339 <param name="database" value="humdb"/>
340 </conditional>
341 <param name="query_fasta" value="fuguMito.fa" ftype="fasta"/>
342 <output name="outfile" ftype="maf" file="last_align_gen.maf" lines_diff="2"/>
343 </test>
344 <test>
345 <conditional name="db_opts">
346 <param name="db_opts_input" value="db"/>
347 <param name="database" value="hedgdb"/>
348 </conditional>
349 <section name="lastal">
350 <conditional name="isprotein">
351 <param name="lastal_protein" value="prot"/>
352 </conditional>
353 </section>
354 <param name="query_fasta" value="hedgehog_prot_drosophila.fa" ftype="fasta"/>
355 <output name="outfile" ftype="maf" file="last_align_prot.maf" lines_diff="2"/>
356 </test>
357 </tests>
358
359 <help>@LAST_HELP@</help>
360 <citations><expand macro="citations"/></citations>
361 </tool>