Mercurial > repos > nml > positions2snv_alignment
changeset 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 |
| files | positions2snv_alignment.xml test-data/expected-all.fasta test-data/expected-changed-ref-name.fasta test-data/expected.fasta test-data/expected.phy test-data/positions.tsv |
| diffstat | 6 files changed, 102 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/positions2snv_alignment.xml Tue Aug 27 12:32:15 2019 -0400 @@ -0,0 +1,76 @@ +<tool id="positions2snv_alignment" name="Positions to SNV alignment" version ="1.8.2"> + <description>Create a SNV-only alignment from the SNVPhyl positions table.</description> + <requirements> + <requirement type="package" version="1.8.2">snvphyl-tools</requirement> + </requirements> + <command detect_errors="exit_code"><![CDATA[ + positions2snv_alignment.pl -i $snv_table -o $output -f $out_format $keep_all + #if $reference_name: + --reference-name $reference_name + #end if + ]]></command> + <inputs> + <param name="snv_table" type="data" label="SNV table" format="tabular"/> + <param name="out_format" type="select" label="Output alignment format"> + <option value="phylip">Phylip alignment format</option> + <option value="fasta">FASTA alignment format</option> + </param> + <param name="keep_all" type="boolean" checked="false" label="Keep all positions" + help="Keep all positions with status 'filtered' in the SNV alignment" truevalue="--keep-all" falsevalue="" /> + <param name="reference_name" type="text" label="Reference genome name" value="Reference" + help="Name of reference genome in produced alignment" /> + </inputs> + <outputs> + <data format="phylip" name="output"> + <change_format> + <when input="out_format" value="phylip" format="phylip"/> + <when input="out_format" value="fasta" format="fasta"/> + </change_format> + </data> + </outputs> + <tests> + <test> + <param name="snv_table" value="positions.tsv"/> + <param name="out_format" value="phylip"/> + + <output name="output" file="expected.phy"/> + </test> + <test> + <param name="snv_table" value="positions.tsv"/> + <param name="out_format" value="fasta"/> + + <output name="output" file="expected.fasta"/> + </test> + <test> + <param name="snv_table" value="positions.tsv"/> + <param name="out_format" value="fasta"/> + <param name="keep_all" value="true" /> + + <output name="output" file="expected-all.fasta"/> + </test> + <test> + <param name="snv_table" value="positions.tsv"/> + <param name="out_format" value="fasta"/> + + <output name="output" file="expected.fasta"/> + </test> + <test> + <param name="snv_table" value="positions.tsv"/> + <param name="out_format" value="fasta"/> + <param name="reference_name" value="ChangedRefName" /> + + <output name="output" file="expected-changed-ref-name.fasta"/> + </test> + </tests> + + <help> +What it does +============ + +Creates a SNV-only alignment from the SNVPhyl SNV positions table. + + </help> + + <citations> + </citations> +</tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/expected-all.fasta Tue Aug 27 12:32:15 2019 -0400 @@ -0,0 +1,6 @@ +>Reference +TC +>v1 +AN +>v2 +AA
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/expected-changed-ref-name.fasta Tue Aug 27 12:32:15 2019 -0400 @@ -0,0 +1,6 @@ +>ChangedRefName +T +>v1 +A +>v2 +A
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/expected.fasta Tue Aug 27 12:32:15 2019 -0400 @@ -0,0 +1,6 @@ +>Reference +T +>v1 +A +>v2 +A