| Next changeset 1:5dc704146cc6 (2020-06-23) |
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Commit message:
"planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 90a172f1fc12b9c4d73f4c924a8c0c5a559589d0" |
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added:
positions2snv_invariant_alignment.xml test-data/expected-merged-all.fasta test-data/expected-merged.fasta test-data/expected-merged.phy test-data/positions.tsv test-data/ref1-all.fasta test-data/ref1.fasta test-data/ref2-all.fasta test-data/ref2.fasta test-data/reference.fasta |
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| diff -r 000000000000 -r bf542eece94a positions2snv_invariant_alignment.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/positions2snv_invariant_alignment.xml Tue Aug 27 12:32:37 2019 -0400 |
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| @@ -0,0 +1,91 @@ +<tool id="positions2snv_invariant_alignment" name="Positions to SNV invariant alignment" version ="1.8.2"> + <description>Create a SNV and non-variant alignment from the SNVPhyl positions table and a reference genome.</description> + <requirements> + <requirement type="package" version="1.8.2">snvphyl-tools</requirement> + </requirements> + <command detect_errors="exit_code"><![CDATA[ + positions2snv_invariant_alignment.pl -i $snv_table --reference-file $reference_genome -o outputs -f $out_format $keep_all $merge_alignment + ]]></command> + <inputs> + <param name="snv_table" type="data" label="SNV table" format="tabular"/> + <param name="reference_genome" type="data" label="Reference genome" format="fasta"/> + <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="merge_alignment" type="boolean" checked="false" label="Merge alignment to single file" + help="Merge individual sequences in reference file to single sequence in final alignment" truevalue="--merge-alignment" falsevalue="" /> + <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="" /> + </inputs> + <outputs> + <collection name="alignments" type="list" label="Alignment files"> + <discover_datasets pattern="__name_and_ext__" directory="outputs" /> + </collection> + </outputs> + <tests> + <test> + <param name="snv_table" value="positions.tsv"/> + <param name="reference_genome" value="reference.fasta"/> + <param name="out_format" value="fasta"/> + <param name="merge_alignment" value="true" /> + + <output_collection name="alignments" type="list"> + <element name="alignment_merged" file="expected-merged.fasta"/> + </output_collection> + </test> + <test> + <param name="snv_table" value="positions.tsv"/> + <param name="reference_genome" value="reference.fasta"/> + <param name="out_format" value="phylip"/> + <param name="merge_alignment" value="true" /> + + <output_collection name="alignments" type="list"> + <element name="alignment_merged" file="expected-merged.phy"/> + </output_collection> + </test> + <test> + <param name="snv_table" value="positions.tsv"/> + <param name="reference_genome" value="reference.fasta"/> + <param name="out_format" value="fasta"/> + <param name="merge_alignment" value="true" /> + <param name="keep_all" value="true" /> + + <output_collection name="alignments" type="list"> + <element name="alignment_merged" file="expected-merged-all.fasta"/> + </output_collection> + </test> + <test> + <param name="snv_table" value="positions.tsv"/> + <param name="reference_genome" value="reference.fasta"/> + <param name="out_format" value="fasta"/> + + <output_collection name="alignments" type="list"> + <element name="ref1" file="ref1.fasta"/> + <element name="ref2" file="ref2.fasta"/> + </output_collection> + </test> + <test> + <param name="snv_table" value="positions.tsv"/> + <param name="reference_genome" value="reference.fasta"/> + <param name="out_format" value="fasta"/> + <param name="keep_all" value="true" /> + + <output_collection name="alignments" type="list"> + <element name="ref1" file="ref1-all.fasta"/> + <element name="ref2" file="ref2-all.fasta"/> + </output_collection> + </test> + </tests> + + <help> +What it does +============ + +Creates a SNV and non-variant alignment from the SNVPhyl SNV positions table and a reference genome. + + </help> + + <citations> + </citations> +</tool> |
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| diff -r 000000000000 -r bf542eece94a test-data/expected-merged-all.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/expected-merged-all.fasta Tue Aug 27 12:32:37 2019 -0400 |
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| @@ -0,0 +1,6 @@ +>Reference +ATGCATGC +>v1 +AAGCATG- +>v2 +AAGCATGA |
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| diff -r 000000000000 -r bf542eece94a test-data/expected-merged.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/expected-merged.fasta Tue Aug 27 12:32:37 2019 -0400 |
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| @@ -0,0 +1,6 @@ +>Reference +ATGCATGC +>v1 +AAGCATGC +>v2 +AAGCATGC |
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| diff -r 000000000000 -r bf542eece94a test-data/expected-merged.phy --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/expected-merged.phy Tue Aug 27 12:32:37 2019 -0400 |
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| @@ -0,0 +1,5 @@ + 3 8 +'Reference' ATGCATGC + 'v1' AAGCATGC + 'v2' AAGCATGC + |
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| diff -r 000000000000 -r bf542eece94a test-data/positions.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/positions.tsv Tue Aug 27 12:32:37 2019 -0400 |
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| @@ -0,0 +1,3 @@ +#Chromosome Position Status Reference v1 v2 +ref1 2 valid T A A +ref2 4 filtered-coverage C - A |
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| diff -r 000000000000 -r bf542eece94a test-data/ref1-all.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/ref1-all.fasta Tue Aug 27 12:32:37 2019 -0400 |
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| @@ -0,0 +1,6 @@ +>Reference +ATGC +>v1 +AAGC +>v2 +AAGC |
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| diff -r 000000000000 -r bf542eece94a test-data/ref1.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/ref1.fasta Tue Aug 27 12:32:37 2019 -0400 |
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| @@ -0,0 +1,6 @@ +>Reference +ATGC +>v1 +AAGC +>v2 +AAGC |
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| diff -r 000000000000 -r bf542eece94a test-data/ref2-all.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/ref2-all.fasta Tue Aug 27 12:32:37 2019 -0400 |
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| @@ -0,0 +1,6 @@ +>Reference +ATGC +>v1 +ATG- +>v2 +ATGA |
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| diff -r 000000000000 -r bf542eece94a test-data/ref2.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/ref2.fasta Tue Aug 27 12:32:37 2019 -0400 |
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| @@ -0,0 +1,6 @@ +>Reference +ATGC +>v1 +ATGC +>v2 +ATGC |
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| diff -r 000000000000 -r bf542eece94a test-data/reference.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/reference.fasta Tue Aug 27 12:32:37 2019 -0400 |
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| @@ -0,0 +1,4 @@ +>ref1 +atgc +>ref2 +atgc |