Mercurial > repos > nml > positions2snv_alignment
comparison positions2snv_alignment.xml @ 0:e2cec726fa79 draft
"planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 90a172f1fc12b9c4d73f4c924a8c0c5a559589d0"
| author | nml |
|---|---|
| date | Tue, 27 Aug 2019 12:32:15 -0400 |
| parents | |
| children | 1cf81ca17e9d |
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| -1:000000000000 | 0:e2cec726fa79 |
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| 1 <tool id="positions2snv_alignment" name="Positions to SNV alignment" version ="1.8.2"> | |
| 2 <description>Create a SNV-only alignment from the SNVPhyl positions table.</description> | |
| 3 <requirements> | |
| 4 <requirement type="package" version="1.8.2">snvphyl-tools</requirement> | |
| 5 </requirements> | |
| 6 <command detect_errors="exit_code"><![CDATA[ | |
| 7 positions2snv_alignment.pl -i $snv_table -o $output -f $out_format $keep_all | |
| 8 #if $reference_name: | |
| 9 --reference-name $reference_name | |
| 10 #end if | |
| 11 ]]></command> | |
| 12 <inputs> | |
| 13 <param name="snv_table" type="data" label="SNV table" format="tabular"/> | |
| 14 <param name="out_format" type="select" label="Output alignment format"> | |
| 15 <option value="phylip">Phylip alignment format</option> | |
| 16 <option value="fasta">FASTA alignment format</option> | |
| 17 </param> | |
| 18 <param name="keep_all" type="boolean" checked="false" label="Keep all positions" | |
| 19 help="Keep all positions with status 'filtered' in the SNV alignment" truevalue="--keep-all" falsevalue="" /> | |
| 20 <param name="reference_name" type="text" label="Reference genome name" value="Reference" | |
| 21 help="Name of reference genome in produced alignment" /> | |
| 22 </inputs> | |
| 23 <outputs> | |
| 24 <data format="phylip" name="output"> | |
| 25 <change_format> | |
| 26 <when input="out_format" value="phylip" format="phylip"/> | |
| 27 <when input="out_format" value="fasta" format="fasta"/> | |
| 28 </change_format> | |
| 29 </data> | |
| 30 </outputs> | |
| 31 <tests> | |
| 32 <test> | |
| 33 <param name="snv_table" value="positions.tsv"/> | |
| 34 <param name="out_format" value="phylip"/> | |
| 35 | |
| 36 <output name="output" file="expected.phy"/> | |
| 37 </test> | |
| 38 <test> | |
| 39 <param name="snv_table" value="positions.tsv"/> | |
| 40 <param name="out_format" value="fasta"/> | |
| 41 | |
| 42 <output name="output" file="expected.fasta"/> | |
| 43 </test> | |
| 44 <test> | |
| 45 <param name="snv_table" value="positions.tsv"/> | |
| 46 <param name="out_format" value="fasta"/> | |
| 47 <param name="keep_all" value="true" /> | |
| 48 | |
| 49 <output name="output" file="expected-all.fasta"/> | |
| 50 </test> | |
| 51 <test> | |
| 52 <param name="snv_table" value="positions.tsv"/> | |
| 53 <param name="out_format" value="fasta"/> | |
| 54 | |
| 55 <output name="output" file="expected.fasta"/> | |
| 56 </test> | |
| 57 <test> | |
| 58 <param name="snv_table" value="positions.tsv"/> | |
| 59 <param name="out_format" value="fasta"/> | |
| 60 <param name="reference_name" value="ChangedRefName" /> | |
| 61 | |
| 62 <output name="output" file="expected-changed-ref-name.fasta"/> | |
| 63 </test> | |
| 64 </tests> | |
| 65 | |
| 66 <help> | |
| 67 What it does | |
| 68 ============ | |
| 69 | |
| 70 Creates a SNV-only alignment from the SNVPhyl SNV positions table. | |
| 71 | |
| 72 </help> | |
| 73 | |
| 74 <citations> | |
| 75 </citations> | |
| 76 </tool> |