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comparison kc-align.xml @ 2:20bef04b5272 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kc-align commit 03afe9e2a97f86f13041214639112a80e9765a71"
author iuc
date Mon, 30 Mar 2020 10:01:40 -0400
parents 60ed1c94f584
children 0243407479f1
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1:60ed1c94f584 2:20bef04b5272
1 <tool id="kc-align" name="Kc-Align" version="0.1.2" python_template_version="3.5"> 1 <tool id="kc-align" name="Kc-Align" version="0.1.3" python_template_version="3.5">
2 <requirements> 2 <requirements>
3 <requirement type="package" version="0.5.8">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">
7 <![CDATA[ 7 <![CDATA[
8 kc-align 8 kc-align
11 --reads '$reads' 11 --reads '$reads'
12 #if $position.mode == "genome": 12 #if $position.mode == "genome":
13 --start $position.start 13 --start $position.start
14 --end $position.end 14 --end $position.end
15 #end if 15 #end if
16 $compress
16 ]]></command> 17 ]]></command>
17 <inputs> 18 <inputs>
18 <param name="reference" type="data" format="fasta" label="Reference Sequence" help="Single FASTA reference sequence to be aligned" /> 19 <param name="reference" type="data" format="fasta" label="Reference Sequence" help="Single FASTA reference sequence to be aligned" />
19 <param name="reads" type="data" format="fasta" label="Reads" help="Multi-FASTA of seqeunces to be aligned with the reference" /> 20 <param name="reads" type="data" format="fasta" label="Reads" help="Multi-FASTA of seqeunces to be aligned with the reference" />
20 <param name="outname" type="text" value="out" label="Output Prefix" /> 21 <param name="outname" type="text" value="out" label="Output Prefix" />
31 <when value="gene" > 32 <when value="gene" >
32 </when> 33 </when>
33 <when value="mixed" > 34 <when value="mixed" >
34 </when> 35 </when>
35 </conditional> 36 </conditional>
37 <param name="compress" type="boolean" truevalue="--compress" falsevalue="" label="Compress" help="Compress identical sequences" />
36 </inputs> 38 </inputs>
37 <outputs> 39 <outputs>
38 <data name="fasta" format="fasta" from_work_dir="codon_align.fasta" label="${outname}.fasta" /> 40 <data name="fasta" format="fasta" from_work_dir="codon_align.fasta" label="${outname}.fasta" />
39 <data name="clustal" format="txt" from_work_dir="codon_align.clustal" label="${outname}.clustal" /> 41 <data name="clustal" format="txt" from_work_dir="codon_align.clustal" label="${outname}.clustal" />
40 </outputs> 42 </outputs>