| Next changeset 1:f78492521996 (2021-10-08) |
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Commit message:
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snp-dists commit d47295a437bdca2a1d248e8210dddea530bb6d12" |
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added:
snp-dists.xml test-data/input1.fasta test-data/output_all_diffs1.tabular test-data/output_blank_cell1.tabular test-data/output_default1.tabular test-data/output_keep_case1.tabular |
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| diff -r 000000000000 -r 1959cc43b414 snp-dists.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/snp-dists.xml Sat Oct 19 05:08:45 2019 -0400 |
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| @@ -0,0 +1,83 @@ +<tool id="snp_dists" name="SNP distance matrix" version="@TOOL_VERSION@+galaxy0" python_template_version="3.5"> + <macros> + <token name="@TOOL_VERSION@">0.6.3</token> + </macros> + <description>Compute distance in SNPs between all sequences in a FASTA file</description> + <requirements> + <requirement type="package" version="@TOOL_VERSION@">snp-dists</requirement> + </requirements> + <command detect_errors="exit_code"><![CDATA[ + snp-dists -q + $a + $k + $b + '$input' > '$output' + ]]></command> + <inputs> + <param name="input" type="data" format="fasta,fasta.gz" label="FASTA multiple sequence alignment" + help="Provide a multiple sequence alignment containing sequences of equal length" /> + <param argument="-a" type="boolean" truevalue="-a" falsevalue="" label="Count all differences, not just ACTG" /> + <param argument="-k" type="boolean" truevalue="-k" falsevalue="" label="Keep case, don't uppercase all letters" /> + <param argument="-b" type="boolean" truevalue="-b" falsevalue="" label="Blank top left corner cell" /> + </inputs> + <outputs> + <data format="tabular" name="output" label="${tool.name} on ${on_string}" /> + </outputs> + <tests> + <test> + <param name="input" ftype="fasta" value="input1.fasta" /> + <output name="output" value="output_default1.tabular" ftype="tabular" /> + </test> + <test> + <param name="input" ftype="fasta" value="input1.fasta" /> + <param name="a" value="True" /> + <output name="output" value="output_all_diffs1.tabular" ftype="tabular" /> + </test> + <test> + <param name="input" ftype="fasta" value="input1.fasta" /> + <param name="k" value="True" /> + <output name="output" value="output_keep_case1.tabular" ftype="tabular" /> + </test> + <test> + <param name="input" ftype="fasta" value="input1.fasta" /> + <param name="b" value="True" /> + <output name="output" value="output_blank_cell1.tabular" ftype="tabular" /> + </test> + </tests> + <help><![CDATA[ + **snp-dists** + + This tool computes a SNP distance matrix from a multiple sequence alignment (MSA) of + sequences (all of the same length). Such distance matrices are often used as in + studies of disease outbreaks. + + The output is a tabular file, for example this matrix describing four M. tuberculosis isolates + and their relationship to the inferred ancestral reference sequence: + +=============== ======= ========= ========= ========= ========= +snp-dists 0.6.3 MTB_anc ERR550641 ERR550671 ERR550691 ERR550703 +--------------- ------- --------- --------- --------- --------- +MTB_anc 0 746 726 772 749 +--------------- ------- --------- --------- --------- --------- +ERR550641 746 0 26 44 13 +--------------- ------- --------- --------- --------- --------- +ERR550671 726 26 0 64 29 +--------------- ------- --------- --------- --------- --------- +ERR550691 772 44 64 0 39 +--------------- ------- --------- --------- --------- --------- +ERR550703 749 13 29 39 0 +=============== ======= ========= ========= ========= ========= + + ]]></help> + <citations> + <citation type="bibtex"> +@misc{githubsnp-dists, + author = {Seemann, Torsten}, + year = {2019}, + title = {snp-dists}, + publisher = {GitHub}, + journal = {GitHub repository}, + url = {https://github.com/tseemann/snp-dists}, +}</citation> + </citations> +</tool> |
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| diff -r 000000000000 -r 1959cc43b414 test-data/input1.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/input1.fasta Sat Oct 19 05:08:45 2019 -0400 |
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| @@ -0,0 +1,75 @@ +>MTB_anc foo +ccccNGGAGCCCGGTAGGCCGTCGGATGCGTCCCGCCCGGCGCGCCGTCCGCCACTCGGT +CGCACGCCCGGCCGGCCCCTAATGTTCGGCCACACCGAGCGGGCGAGAGGGGTGACTCGG +AGTCCCGGAGGCCGCCCCGGCCGAGTGCGTCGCCCACGCCGCGGCTTCCATGTGACATGC +TGGCCGAGCAGACAGAAGACGGGACGATCGCCCTCACGCGCGGGGGACCCGTGTGCAGGT +CCGGGGCCCGCAAGGCGACATGCCAACGGGCTTACACCCAATCTCCGCTGCTGTCCGCCA +ACACACGGTATTCCCCGGCGCGCCAGCCACGGGCTCTGGAGAACACCCATGACGGGGCGC +CCCGGCGCCCCCCCACGGAGAGGTACCGCCGCGGGAGCTCAGGGGGGCAGTTCTGGCCCT +ACGGAGGGCGGCTGTAGCCCGCCCTCTGCCCGAGCGGAGTCTCGGGGGCGGCGGGGACCT +CCGGATGCGTCTCTGAGGAGGTCTCGCGCCGCGTAGTTTGGTCTCAGCGCGACTGCGCCC +GGGCGGAGTACAAGAGGGCGGGAGGGGTCGGGCCCCGCGTCGCGGAGCGGCGGGGCGGTG +CCGGCCGGTTGGGTGGCCGCTGGGGCAGGCTCGCCGGGGGGATCGGGGCAAGACGACTGG +ACGAAACCCGCTACAGGCGCAAGCTGCCCGCCGGCGAGGAGCTCCCACTACGGGGTGTTT +CGGGCCTCGGGGACTGCACGAGGGCCGTGTGGTGGACGAGCAACGCAGGCCCGGCCGGCC +GCGCGC +>ERR550641 +TTATAACCATTTAAATAATTAGTAAGGATACTTTATTTACTTTATTCCAGATTGTGTAAC +TATGGAATGCATTCTTTTTGGCCGCTCGAAGGGTTGAGGTATACCCATGAAAGTGTGGAA +AACATTCTGAATTATATTAATTAGTATTGCCGTTAGTCTTCTCTACATTAGCGACTCGAT +GAACTTGAAGCGCGAGTTGACTTGGAGGAAGTAGTGACTAGATAAACTTTATCGATCTGC +ATATAAGGTGGGCCTTAGTGGCTTGCAAAATCCGTCTAAGGCAGTGTACATCTCATGAGG +GTCTGAAACAGTGTTGAAACTTGTCGCTGGAACTGTCCAGTGGCCTTGTCAGTTACATAG +TGAGATATCGTTAATTACGACAAGCTTCTTAACAAGATGTTCAGATAGGACCTGACTTCG +GGACGATTTGATGACGAATCATTTGTCTTTAAGATATCCGTCTATAAAAACTAAAACTTG +TTAAGGACACTGACACCAGAAGTTAAAATTATAGGAGCCAACTGAGCTCTACGCCTATGA +TAATTACGCGTGCACAAATAAACAACCCGAAATATTTTAGTAATAGAGAATACCAGACCA +TTTAAGACCCCATCATATAGCCAAATGGCTCAAATAAACGAGCTAAATTGCCGTGGATGA +CTAGGCGTTATGGAGAAGCGGCCTGATGTATTAAAACTTGATCTTTCTCCGAATACACCC +AAAAATGGCCAACTCCAGGCGATATTACAGCTCCCGTCGAGCCAAACAAGTGACTTGATG +ACAGTT +>ERR550671 +TTATAGCCATTTAAATAATTAGTAAGGATACTTTATTTACTTTATTCCAGATTGTGTGAC +TGTGGAATGCATTCTTTCTGGCCGCTCGAAGGGTTGAGGTATACCCATGAAAGTATGGAA +AACATTCTGAATTATATTAATTAGTATTGTCGTTAGTGTTCTCTACATTAGCGACTCGAT +GAACTTGAAGCGCGAGTTGACTTGGAGGAAGTAGTGACTAGATAGACTTTATCGATCTGC +CTATAAGGTAGACCTTAGTGGCTTGCAAAATCCGTCTACAGCAGTGTACATCTCATGAGG +GTCTGAAACATTGTTGAAACTTCTCGCTGGAACTGTCCAGTGGCCTTGTCAGTTACATAG +TGAAATATCGTTAATTACGACAAGCTTCTTAACAAGATGTTCAGATAGGACCTGACTTCG +GGACGATTTGATGACGAATTATTTGTCTTTAAGATGTCGGTCTATAAAAACTAAAAATTG +TTAAGGACACTGACACCAGAAGTTAAAACTATAGGAGCCAACTGAGCTCTACGCCTATGA +TAATTACGCGTGCACAAATAAACAACCCGAAATATTTTAGTAATAGAGAACACCACACCA +TTTAAGACCCCATCATATAGCCAAATGGCTCAAATAAACGAGCTAAATTGCCGTGGATGA +CTAGGCGTTATGGAGAAGCGGCCTGATCTATTAAAACTTAATCTTTCTCCGAATACACCC +AAAAATGGCCAACCCCAGGCGATATTACAGCTCCCGTCGAGCCAAACAAGTGACTTGATG +ACAGTT +>ERR550691 +TTATAACCATTTAAATAATTAGTAAGGATACTTTATTTACTTTATTCCAGACTGTGTAAC +TATGGAATGCATTCTTTTTGGCCCCCTTAAGGGTTGAGTTATATCCATAAAAGTGTGGAA +CACATTCTGAATTATATTAATTAGTATTACTATTAGTCTTCTCTACATTCGCGACTCGAT +GAAATTGAAGCGGGAGTTGACTTGGAGGAAGTAGTGACTAGATAAACTTTACCGATCTAC +ATATAAGGTGGGCCTTAGTGGCTTGCAAAATCCGTCTAAAGCAGTCGACATCTCATCAGG +GTCTGAAACCTGGTTGAAAGTTGTCTTTGGAACTGTCCAGTGGTCTTGTCAGTTACATAG +TGAGGTATTGTTAATTACGACAAGCTTCTTAACAAGATGTTCAAATAGGACCTGACTTAG +GGACGATTTAATGACGAATCATTTGTCTTTAAGATATCCGTCTATAAAAACTAAAACTTG +TTAAGGACACTGACACCAGAAGTCAAAATTATAGGAGCCAACTGAGCTCTACGCCTATGA +TAATTACACGTGCACAAATAAACAACCCGAAATATTTTAGTAATAGAGAATACCACACCA +TTTAAGACCCCATCATATAGCCAGATGACTCAAATAAACAAGCTAAATTGCCGTAGAAAA +CTAGGCGTTATGGAGAAGCGGCCTGATGTATTAAAACTTGATCTTTCTCCGAATACACCC +AAAAATGGCCAACTCCAGGCGATATTACAGCTCCCGTCGAGCCAAACAAGTGACTTAATG +ATAGTT +>ERR550703 +TTATAACCATTTAAATAATTAGTAAGGATACTTTATTTACTTTATTCCAGATTGTGTAAC +TATGGAATGCATTCTTTTTGGCCGCTTGAAGGGTTGAGGTATATCCATGAAAGTGTGGAA +AACATTCTGAATTATATTAATTAGTATTGCTGTTAGTCTTCTCTACATTAGCGACTCGAT +GAACTTGAAGCGCGAGTTGACTTGGAGGAAGTAGTGACTAGATAGACTTTATCGATCTAC +ATATAAGGTGGGCCTTAGTGGCTTGCAAAATCCGTCTACAGCAGTGTACATCTCATGAGG +GTCTGAAACATTGTTGAAACTTGTCGTTGGAACTGTCCAGTGGCCTTGTCAGTTACATAG +TGAGATATCGTTAATTACGACAAGCTTCTTAACAAGATGTTCAGATAGGACCTGACTTCG +GGACGATTTGATGACGAATCATTTGTCTTTAAGATATCCGTCTATAAAAACTAAAACTTG +TTAAGGATACTGACACCAGAAGTTAAAACTATAGGAGCCAACTGAGCTCTACGCCTATGA +TAATTACGCGTGCACAAATAAACAACCCGAAATATTTTAGTAATAGAGAATACCAGACCA +TTTAAGACCCCATCATATAGCCAAATGGCTCAAATAAACAAGCTAAATTGCCGTGGAAGA +CTAGGCGTTATGGAGAAGCGGCCTGATGTATTAAAACTTGATCTTTCTCCGAATACACCC +AAAAATGGCCAACTCCAGGCGATATTACAGCTCCCGTCGAGCCAAACAAGTGACTTGATG +ACAGTT |
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| diff -r 000000000000 -r 1959cc43b414 test-data/output_all_diffs1.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/output_all_diffs1.tabular Sat Oct 19 05:08:45 2019 -0400 |
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| @@ -0,0 +1,6 @@ +snp-dists 0.6.3 MTB_anc ERR550641 ERR550671 ERR550691 ERR550703 +MTB_anc 0 747 727 773 750 +ERR550641 747 0 26 44 13 +ERR550671 727 26 0 64 29 +ERR550691 773 44 64 0 39 +ERR550703 750 13 29 39 0 |
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| diff -r 000000000000 -r 1959cc43b414 test-data/output_blank_cell1.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/output_blank_cell1.tabular Sat Oct 19 05:08:45 2019 -0400 |
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| @@ -0,0 +1,6 @@ + MTB_anc ERR550641 ERR550671 ERR550691 ERR550703 +MTB_anc 0 746 726 772 749 +ERR550641 746 0 26 44 13 +ERR550671 726 26 0 64 29 +ERR550691 772 44 64 0 39 +ERR550703 749 13 29 39 0 |
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| diff -r 000000000000 -r 1959cc43b414 test-data/output_default1.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/output_default1.tabular Sat Oct 19 05:08:45 2019 -0400 |
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| @@ -0,0 +1,6 @@ +snp-dists 0.6.3 MTB_anc ERR550641 ERR550671 ERR550691 ERR550703 +MTB_anc 0 746 726 772 749 +ERR550641 746 0 26 44 13 +ERR550671 726 26 0 64 29 +ERR550691 772 44 64 0 39 +ERR550703 749 13 29 39 0 |
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| diff -r 000000000000 -r 1959cc43b414 test-data/output_keep_case1.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/output_keep_case1.tabular Sat Oct 19 05:08:45 2019 -0400 |
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| @@ -0,0 +1,6 @@ +snp-dists 0.6.3 MTB_anc ERR550641 ERR550671 ERR550691 ERR550703 +MTB_anc 0 742 722 768 745 +ERR550641 742 0 26 44 13 +ERR550671 722 26 0 64 29 +ERR550691 768 44 64 0 39 +ERR550703 745 13 29 39 0 |