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comparison kc-align.xml @ 8:1a58649eb491 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kc-align commit 000db9fd34a1056bbdd95b007acb5919873fa2b6"
author iuc
date Mon, 05 Oct 2020 20:09:34 +0000
parents cd415d9fb240
children 5392d4425402
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7:cd415d9fb240 8:1a58649eb491
1 <tool id="kc-align" name="Kc-Align" version="0.2" python_template_version="3.5"> 1 <tool id="kc-align" name="Kc-Align" version="1.0" python_template_version="3.5">
2 <requirements> 2 <requirements>
3 <requirement type="package" version="0.6.1">kcalign</requirement> 3 <requirement type="package" version="1.0.2">kcalign</requirement>
4 </requirements> 4 </requirements>
5 <command detect_errors="exit_code"> 5 <command detect_errors="exit_code">
6 <![CDATA[ 6 <![CDATA[
7 kc-align 7 kc-align
8 --mode $position.mode 8 --mode '$position.mode'
9 --reference '$reference' 9 --reference '$ref'
10 --reads '$reads' 10 --sequences '$seqs'
11 #if $position.mode == "genome": 11 #if $position.mode == "genome":
12 --start $position.start 12 --start '$position.start'
13 --end $position.end 13 --end '$position.end'
14 -d '$position.dist'
15 #end if
16 #if $position.mode == "mixed":
17 -d '$position.dist'
14 #end if 18 #end if
15 $compress 19 $compress
16 --parallel 20 -th '$threads'
21
17 ]]></command> 22 ]]></command>
18 <inputs> 23 <inputs>
19 <param name="reference" type="data" format="fasta" label="Reference Sequence" help="Single FASTA reference sequence to be aligned" /> 24 <param name="ref" 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" /> 25 <param name="seqs" type="data" format="fasta" label="Reads" help="Multi-FASTA of seqeunces to be aligned with the reference" />
21 <conditional name="position" > 26 <conditional name="position" >
22 <param name="mode" type="select" label="Mode" > 27 <param name="mode" type="select" label="Mode" >
23 <option value="genome">Genome</option> 28 <option value="genome">Genome</option>
24 <option value="gene">Gene</option> 29 <option value="gene">Gene</option>
25 <option value="mixed">Mixed</option> 30 <option value="mixed">Mixed</option>
26 </param> 31 </param>
27 <when value="genome" > 32 <when value="genome" >
28 <param name="start" type="text" value="0" label="Start Position(s)" help="The 1-indexed start position of the gene of interest in the reference sequence (For multi-segmented sequences, input each start site separated by a comma ex: 12562,12591)" /> 33 <param name="start" type="text" value="0" label="Start Position(s)" help="The 1-indexed start position of the gene of interest in the reference sequence (For multi-segmented sequences, input each start site separated by a comma ex: 12562,12591)" />
29 <param name="end" type="text" value="0" label="End Position(s)" help="The 1-indexed end position of the gene of interest in the reference sequence (For multi-segmented sequences, input each end site separated by a comma ex: 12592,13905)" /> 34 <param name="end" type="text" value="0" label="End Position(s)" help="The 1-indexed end position of the gene of interest in the reference sequence (For multi-segmented sequences, input each end site separated by a comma ex: 12592,13905)" />
35 <param name="dist" type="select" label="Homology distance limit" help="Sequences that are more than an empirically determined distance from the reference are discarded before the final alignment">
36 <option value="none">None</option>
37 <option value="very-close">Very Close</option>
38 <option value="semi-close">Semi-Close</option>
39 <option value="less-close">Less Close</option>
40 </param>
30 </when> 41 </when>
31 <when value="gene" > 42 <when value="gene" >
32 </when> 43 </when>
33 <when value="mixed" > 44 <when value="mixed" >
45 <param name="dist" type="select" label="Homology distance limit" help="Sequences that are more than an empirically determined distance from the reference are discarded before the final alignment">
46 <option value="none">None</option>
47 <option value="very-close">Very Close</option>
48 <option value="semi-close">Semi Close</option>
49 <option value="less-close">Less Close</option>
50 </param>
34 </when> 51 </when>
35 </conditional> 52 </conditional>
36 <param name="compress" type="boolean" truevalue="--compress" falsevalue="" label="Compress" help="Compress identical sequences" /> 53 <param name="compress" type="boolean" truevalue="--compress" falsevalue="" label="Compress" help="Compress identical sequences" />
54 <param name="threads" type="integer" argument="-th" value="1" label="Cores" />
37 </inputs> 55 </inputs>
38 <outputs> 56 <outputs>
39 <data name="fasta" format="fasta" from_work_dir="codon_align.fasta" label="${tool.name}: fasta output" /> 57 <data name="fasta" format="fasta" from_work_dir="codon_align.fasta" label="${tool.name}: fasta output" />
40 <data name="clustal" format="txt" from_work_dir="codon_align.clustal" label="${tool.name}: clustal output" /> 58 <data name="clustal" format="txt" from_work_dir="codon_align.clustal" label="${tool.name}: clustal output" />
41 </outputs> 59 </outputs>
42 <tests> 60 <tests>
43 <test> 61 <test>
44 <param name="reference" ftype="fasta" value="wuhan_ref.fasta" /> 62 <param name="ref" ftype="fasta" value="wuhan_ref.fasta" />
45 <param name="reads" ftype="fasta" value="3.fasta" /> 63 <param name="seqs" ftype="fasta" value="3.fasta" />
46 <param name="mode" value="genome" /> 64 <param name="mode" value="genome" />
47 <param name="start" value="21563" /> 65 <param name="start" value="21563" />
48 <param name="end" value="25384" /> 66 <param name="end" value="25384" />
49 <output name="fasta" ftype="fasta" compare="diff" value="kc-align.fasta" /> 67 <param name="threads" value="15" />
50 <output name="clustal" ftype="txt" compare="diff" value="kc-align.clustal" /> 68 <output name="fasta" ftype="fasta" compare="contains" value="kc-align.fasta" />
69 <output name="clustal" ftype="txt" compare="contains" value="kc-align.clustal" />
51 </test> 70 </test>
52 </tests> 71 </tests>
53 <help><![CDATA[ 72 <help><![CDATA[
54 73
55 ============ 74 ============