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comparison lastal.xml @ 4:8705e0d74a0f draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit 6b601baaf89634bc8d110ea06e3e64c7a585f3ba"
author iuc
date Wed, 24 Mar 2021 22:36:50 +0000
parents bf30030e5265
children 19c265784f35
comparison
equal deleted inserted replaced
3:3de2195f32c0 4:8705e0d74a0f
1 <tool id="last_al" name="LASTal" version="@LAST_CONDA_VERSION@+galaxy1" profile="18.01"> 1 <tool id="last_al" name="LASTal" version="@LAST_CONDA_VERSION@+galaxy0" profile="20.01">
2 2
3 <description>finds local alignments between query sequences, and reference sequences.</description> 3 <description>finds local alignments between query sequences, and reference sequences.</description>
4 4
5 <macros> 5 <macros>
6 <import>macros_last.xml</import> 6 <import>macros_last.xml</import>
9 <requirements> 9 <requirements>
10 <requirement type="package" version="@LAST_CONDA_VERSION@">last</requirement> 10 <requirement type="package" version="@LAST_CONDA_VERSION@">last</requirement>
11 </requirements> 11 </requirements>
12 12
13 <command detect_errors="exit_code"><![CDATA[ 13 <command detect_errors="exit_code"><![CDATA[
14 set -e -o pipefail;
15
14 #if $db_opts.db_opts_input == 'lastdb' 16 #if $db_opts.db_opts_input == 'lastdb'
15 ln -s '$db_opts.lastdatabase.extra_files_path' './db_files' && 17 ln -s '$db_opts.lastdatabase.extra_files_path' './db_files' &&
16 #end if 18 #end if
17 19
18 lastal 20 #if $query_seq.ext.endswith('.gz')
19 21 zcat
20 #if $query_seq.ext == 'fasta' 22 #else
23 cat
24 #end if
25 '$query_seq' | lastal
26
27 #if $query_seq.ext.startswith('fasta')
21 -Q 0 28 -Q 0
22 #else if $query_seq.ext == 'fastqsanger' 29 #else if $query_seq.ext.startswith('fastqsanger')
23 -Q 1 30 -Q 1
24 #else if $query_seq.ext == 'fastqsolexa' 31 #else if $query_seq.ext.startswith('fastqsolexa')
25 -Q 2 32 -Q 2
26 #else if $query_seq.ext == 'fastqillumina' 33 #else if $query_seq.ext.startswith('fastqillumina')
27 -Q 3 34 -Q 3
28 #else if $query_seq.ext == 'pssm' 35 #else if $query_seq.ext.startswith('pssm')
29 -Q 5 36 -Q 5
30 #end if 37 #end if
31 38
32 -f $lastal.f 39 -f $lastal.f
33 -j $lastal.j 40 -j $lastal.j
77 '${"'" "'".join(str($db_opts.database.fields.path).split(","))}' 84 '${"'" "'".join(str($db_opts.database.fields.path).split(","))}'
78 #else if $db_opts.db_opts_input == 'lastdb' 85 #else if $db_opts.db_opts_input == 'lastdb'
79 'db_files/lastdb' 86 'db_files/lastdb'
80 #end if 87 #end if
81 88
82 '$query_seq'
83
84 >'$outfile' 89 >'$outfile'
85 ]]></command> 90 ]]></command>
86 91
87 <inputs> 92 <inputs>
88 <expand macro="input_db"/> 93 <expand macro="input_db"/>
89 <param name="query_seq" type="data" format="fasta,fastqsanger,fastqsolexa,fastqillumina,tabular" label="Query sequences"/> 94 <param name="query_seq" type="data" format="fasta,fasta.gz,fastq,fastq.gz,tabular" label="Query sequences"/>
90 95
91 <section name="lastal" title="Lastal arguments" expanded="true"> 96 <section name="lastal" title="Lastal arguments" expanded="true">
92 <param argument="-f" type="select" multiple="false" label="Output format"> 97 <param argument="-f" type="select" multiple="false" label="Output format">
93 <option value="MAF" selected="true">MAF</option> 98 <option value="MAF" selected="true">MAF</option>
94 <option value="TAB">TAB</option> 99 <option value="TAB">TAB</option>
346 <test> 351 <test>
347 <conditional name="db_opts"> 352 <conditional name="db_opts">
348 <param name="db_opts_input" value="db"/> 353 <param name="db_opts_input" value="db"/>
349 <param name="database" value="humdb"/> 354 <param name="database" value="humdb"/>
350 </conditional> 355 </conditional>
351 <param name="query_seq" value="fuguMito.fa" ftype="fasta"/> 356 <param name="query_seq" value="fuguMito.fa.gz" ftype="fasta.gz"/>
352 <output name="outfile" ftype="maf" file="last_align_gen.maf" lines_diff="2"/> 357 <output name="outfile" ftype="maf" file="last_align_gen.maf" lines_diff="2"/>
353 </test> 358 </test>
354 <test> 359 <test>
355 <conditional name="db_opts"> 360 <conditional name="db_opts">
356 <param name="db_opts_input" value="db"/> 361 <param name="db_opts_input" value="db"/>
367 <test> 372 <test>
368 <conditional name="db_opts"> 373 <conditional name="db_opts">
369 <param name="db_opts_input" value="db"/> 374 <param name="db_opts_input" value="db"/>
370 <param name="database" value="humdb-sanger"/> 375 <param name="database" value="humdb-sanger"/>
371 </conditional> 376 </conditional>
372 <param name="query_seq" value="fuguMito.fq" ftype="fastqsanger"/> 377 <param name="query_seq" value="fuguMito.fq.gz" ftype="fastqsanger.gz"/>
373 <section name="lastal"> 378 <section name="lastal">
374 <param name="Q" value="1"/> 379 <param name="Q" value="1"/>
375 </section> 380 </section>
376 <output name="outfile" ftype="maf" file="last_align_fastq.maf" lines_diff="2"/> 381 <output name="outfile" ftype="maf" file="last_align_fastq.maf" lines_diff="2"/>
377 </test> 382 </test>