Mercurial > repos > iuc > kc_align

comparison kc-align.xml @ 3:839c756a6950 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kc-align commit 6c793b7cf264021bc72b96fbd9b6ceeefcb967bd"
author iuc
date Tue, 31 Mar 2020 13:15:53 +0000
parents 585a32c6ac88
children 314f0466de22
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2:585a32c6ac88 3:839c756a6950
1 <tool id="kc-align" name="Kc-Align" version="0.1.3" python_template_version="3.5"> 1 <tool id="kc-align" name="Kc-Align" version="0.1.4" python_template_version="3.5">
2 <requirements> 2 <requirements>
3 <requirement type="package" version="0.5.9">kcalign</requirement> 3 <requirement type="package" version="0.5.9">kcalign</requirement>
4 <requirement type="package" version="3.2.2">kalign3</requirement> 4 <requirement type="package" version="3.2.2">kalign3</requirement>
5 </requirements> 5 </requirements>
6 <command detect_errors="exit_code"> 6 <command detect_errors="exit_code">
16 $compress 16 $compress
17 ]]></command> 17 ]]></command>
18 <inputs> 18 <inputs>
19 <param name="reference" type="data" format="fasta" label="Reference Sequence" help="Single FASTA reference sequence to be aligned" /> 19 <param name="reference" type="data" format="fasta" label="Reference Sequence" help="Single FASTA reference sequence to be aligned" />
20 <param name="reads" type="data" format="fasta" label="Reads" help="Multi-FASTA of seqeunces to be aligned with the reference" /> 20 <param name="reads" type="data" format="fasta" label="Reads" help="Multi-FASTA of seqeunces to be aligned with the reference" />
21 <param name="outname" type="text" value="out" label="Output Prefix" />
22 <conditional name="position" > 21 <conditional name="position" >
23 <param name="mode" type="select" label="Mode" > 22 <param name="mode" type="select" label="Mode" >
24 <option value="genome">Genome</option> 23 <option value="genome">Genome</option>
25 <option value="gene">Gene</option> 24 <option value="gene">Gene</option>
26 <option value="mixed">Mixed</option> 25 <option value="mixed">Mixed</option>
35 </when> 34 </when>
36 </conditional> 35 </conditional>
37 <param name="compress" type="boolean" truevalue="--compress" falsevalue="" label="Compress" help="Compress identical sequences" /> 36 <param name="compress" type="boolean" truevalue="--compress" falsevalue="" label="Compress" help="Compress identical sequences" />
38 </inputs> 37 </inputs>
39 <outputs> 38 <outputs>
40 <data name="fasta" format="fasta" from_work_dir="codon_align.fasta" label="${outname}.fasta" /> 39 <data name="fasta" format="fasta" from_work_dir="codon_align.fasta" label="${tool.name}: fasta output" />
41 <data name="clustal" format="txt" from_work_dir="codon_align.clustal" label="${outname}.clustal" /> 40 <data name="clustal" format="txt" from_work_dir="codon_align.clustal" label="${tool.name}: clustal output" />
42 </outputs> 41 </outputs>
43 <tests> 42 <tests>
44 <test> 43 <test>
45 <param name="reference" ftype="fasta" value="wuhan_ref.fasta" /> 44 <param name="reference" ftype="fasta" value="wuhan_ref.fasta" />
46 <param name="reads" ftype="fasta" value="3.fasta" /> 45 <param name="reads" ftype="fasta" value="3.fasta" />