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changeset 0:1959cc43b414 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snp-dists commit d47295a437bdca2a1d248e8210dddea530bb6d12"
author iuc
date Sat, 19 Oct 2019 05:08:45 -0400
parents
children f78492521996
files 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
diffstat 6 files changed, 182 insertions(+), 0 deletions(-) [+]
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/snp-dists.xml	Sat Oct 19 05:08:45 2019 -0400
@@ -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>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/input1.fasta	Sat Oct 19 05:08:45 2019 -0400
@@ -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
--- /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
@@ -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
--- /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
@@ -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
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/output_default1.tabular	Sat Oct 19 05:08:45 2019 -0400
@@ -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
--- /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
@@ -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