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comparison lastal.xml @ 2:bf30030e5265 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit d48fa8fc8724e2a1c659dde00cad9d6db3e710db"
author iuc
date Thu, 10 Sep 2020 16:08:15 +0000
parents 86206f93fb13
children 8705e0d74a0f
comparison
equal deleted inserted replaced
1:86206f93fb13 2:bf30030e5265
13 <command detect_errors="exit_code"><![CDATA[ 13 <command detect_errors="exit_code"><![CDATA[
14 #if $db_opts.db_opts_input == 'lastdb' 14 #if $db_opts.db_opts_input == 'lastdb'
15 ln -s '$db_opts.lastdatabase.extra_files_path' './db_files' && 15 ln -s '$db_opts.lastdatabase.extra_files_path' './db_files' &&
16 #end if 16 #end if
17 17
18 lastal 18 lastal
19 19
20 -Q $lastal.Q 20 #if $query_seq.ext == 'fasta'
21 -Q 0
22 #else if $query_seq.ext == 'fastqsanger'
23 -Q 1
24 #else if $query_seq.ext == 'fastqsolexa'
25 -Q 2
26 #else if $query_seq.ext == 'fastqillumina'
27 -Q 3
28 #else if $query_seq.ext == 'pssm'
29 -Q 5
30 #end if
31
21 -f $lastal.f 32 -f $lastal.f
22 -j $lastal.j 33 -j $lastal.j
23 34
24 -R $lastal.repeats_misc.uppercase_misc$lastal.repeats_misc.simple_repeat_misc 35 -R $lastal.repeats_misc.uppercase_misc$lastal.repeats_misc.simple_repeat_misc
25 36
66 '${"'" "'".join(str($db_opts.database.fields.path).split(","))}' 77 '${"'" "'".join(str($db_opts.database.fields.path).split(","))}'
67 #else if $db_opts.db_opts_input == 'lastdb' 78 #else if $db_opts.db_opts_input == 'lastdb'
68 'db_files/lastdb' 79 'db_files/lastdb'
69 #end if 80 #end if
70 81
71 '$query_fasta' 82 '$query_seq'
72 83
73 >'$outfile' 84 >'$outfile'
74 ]]></command> 85 ]]></command>
75 86
76 <inputs> 87 <inputs>
77 <expand macro="input_db"/> 88 <expand macro="input_db"/>
78 <param name="query_fasta" type="data" format="fasta,fastqsanger,fastqsolexa,fastqillumina,tabular" label="Queries FASTA file"/> 89 <param name="query_seq" type="data" format="fasta,fastqsanger,fastqsolexa,fastqillumina,tabular" label="Query sequences"/>
79 90
80 <section name="lastal" title="Lastal arguments" expanded="true"> 91 <section name="lastal" title="Lastal arguments" expanded="true">
81 <param argument="-Q" type="select" multiple="false" label="Query input format">
82 <option value="0" selected="true">FASTA</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="5">PSSM</option>
87 </param>
88 <param argument="-f" type="select" multiple="false" label="Output format"> 92 <param argument="-f" type="select" multiple="false" label="Output format">
89 <option value="MAF" selected="true">MAF</option> 93 <option value="MAF" selected="true">MAF</option>
90 <option value="TAB">TAB</option> 94 <option value="TAB">TAB</option>
91 <option value="BlastTab">BlastTab</option> 95 <option value="BlastTab">BlastTab</option>
92 <option value="BlastTab+">BlastTab+</option> 96 <option value="BlastTab+">BlastTab+</option>
326 </section> 330 </section>
327 </section> 331 </section>
328 </inputs> 332 </inputs>
329 333
330 <outputs> 334 <outputs>
331 <data name="outfile" format="maf" label="LAST align from ${on_string}" /> 335 <data name="outfile" format="maf" label="LAST align from ${on_string}" >
336 <change_format>
337 <when input="f" value="MAF" format="maf" />
338 <when input="f" value="TAB" format="tabular" />
339 <when input="f" value="BlastTab" format="tabular" />
340 <when input="f" value="BlastTab+" format="tabular" />
341 </change_format>
342 </data>
332 </outputs> 343 </outputs>
333 344
334 <tests> 345 <tests>
335 <test> 346 <test>
336 <conditional name="db_opts"> 347 <conditional name="db_opts">
337 <param name="db_opts_input" value="db"/> 348 <param name="db_opts_input" value="db"/>
338 <param name="database" value="humdb"/> 349 <param name="database" value="humdb"/>
339 </conditional> 350 </conditional>
340 <param name="query_fasta" value="fuguMito.fa" ftype="fasta"/> 351 <param name="query_seq" value="fuguMito.fa" ftype="fasta"/>
341 <output name="outfile" ftype="maf" file="last_align_gen.maf" lines_diff="2"/> 352 <output name="outfile" ftype="maf" file="last_align_gen.maf" lines_diff="2"/>
342 </test> 353 </test>
343 <test> 354 <test>
344 <conditional name="db_opts"> 355 <conditional name="db_opts">
345 <param name="db_opts_input" value="db"/> 356 <param name="db_opts_input" value="db"/>
348 <section name="lastal"> 359 <section name="lastal">
349 <conditional name="isprotein"> 360 <conditional name="isprotein">
350 <param name="lastal_protein" value="prot"/> 361 <param name="lastal_protein" value="prot"/>
351 </conditional> 362 </conditional>
352 </section> 363 </section>
353 <param name="query_fasta" value="hedgehog_prot_drosophila.fa" ftype="fasta"/> 364 <param name="query_seq" value="hedgehog_prot_drosophila.fa" ftype="fasta"/>
354 <output name="outfile" ftype="maf" file="last_align_prot.maf" lines_diff="2"/> 365 <output name="outfile" ftype="maf" file="last_align_prot.maf" lines_diff="2"/>
355 </test> 366 </test>
367 <test>
368 <conditional name="db_opts">
369 <param name="db_opts_input" value="db"/>
370 <param name="database" value="humdb-sanger"/>
371 </conditional>
372 <param name="query_seq" value="fuguMito.fq" ftype="fastqsanger"/>
373 <section name="lastal">
374 <param name="Q" value="1"/>
375 </section>
376 <output name="outfile" ftype="maf" file="last_align_fastq.maf" lines_diff="2"/>
377 </test>
356 </tests> 378 </tests>
357 379
358 <help>@LAST_HELP@</help> 380 <help>@LAST_HELP@</help>
359 <citations><expand macro="citations"/></citations> 381 <citations><expand macro="citations"/></citations>
360 </tool> 382 </tool>