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comparison snp-dists.xml @ 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
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1 <tool id="snp_dists" name="SNP distance matrix" version="@TOOL_VERSION@+galaxy0" python_template_version="3.5">
2 <macros>
3 <token name="@TOOL_VERSION@">0.6.3</token>
4 </macros>
5 <description>Compute distance in SNPs between all sequences in a FASTA file</description>
6 <requirements>
7 <requirement type="package" version="@TOOL_VERSION@">snp-dists</requirement>
8 </requirements>
9 <command detect_errors="exit_code"><![CDATA[
10 snp-dists -q
11 $a
12 $k
13 $b
14 '$input' > '$output'
15 ]]></command>
16 <inputs>
17 <param name="input" type="data" format="fasta,fasta.gz" label="FASTA multiple sequence alignment"
18 help="Provide a multiple sequence alignment containing sequences of equal length" />
19 <param argument="-a" type="boolean" truevalue="-a" falsevalue="" label="Count all differences, not just ACTG" />
20 <param argument="-k" type="boolean" truevalue="-k" falsevalue="" label="Keep case, don't uppercase all letters" />
21 <param argument="-b" type="boolean" truevalue="-b" falsevalue="" label="Blank top left corner cell" />
22 </inputs>
23 <outputs>
24 <data format="tabular" name="output" label="${tool.name} on ${on_string}" />
25 </outputs>
26 <tests>
27 <test>
28 <param name="input" ftype="fasta" value="input1.fasta" />
29 <output name="output" value="output_default1.tabular" ftype="tabular" />
30 </test>
31 <test>
32 <param name="input" ftype="fasta" value="input1.fasta" />
33 <param name="a" value="True" />
34 <output name="output" value="output_all_diffs1.tabular" ftype="tabular" />
35 </test>
36 <test>
37 <param name="input" ftype="fasta" value="input1.fasta" />
38 <param name="k" value="True" />
39 <output name="output" value="output_keep_case1.tabular" ftype="tabular" />
40 </test>
41 <test>
42 <param name="input" ftype="fasta" value="input1.fasta" />
43 <param name="b" value="True" />
44 <output name="output" value="output_blank_cell1.tabular" ftype="tabular" />
45 </test>
46 </tests>
47 <help><![CDATA[
48 **snp-dists**
49
50 This tool computes a SNP distance matrix from a multiple sequence alignment (MSA) of
51 sequences (all of the same length). Such distance matrices are often used as in
52 studies of disease outbreaks.
53
54 The output is a tabular file, for example this matrix describing four M. tuberculosis isolates
55 and their relationship to the inferred ancestral reference sequence:
56
57 =============== ======= ========= ========= ========= =========
58 snp-dists 0.6.3 MTB_anc ERR550641 ERR550671 ERR550691 ERR550703
59 --------------- ------- --------- --------- --------- ---------
60 MTB_anc 0 746 726 772 749
61 --------------- ------- --------- --------- --------- ---------
62 ERR550641 746 0 26 44 13
63 --------------- ------- --------- --------- --------- ---------
64 ERR550671 726 26 0 64 29
65 --------------- ------- --------- --------- --------- ---------
66 ERR550691 772 44 64 0 39
67 --------------- ------- --------- --------- --------- ---------
68 ERR550703 749 13 29 39 0
69 =============== ======= ========= ========= ========= =========
70
71 ]]></help>
72 <citations>
73 <citation type="bibtex">
74 @misc{githubsnp-dists,
75 author = {Seemann, Torsten},
76 year = {2019},
77 title = {snp-dists},
78 publisher = {GitHub},
79 journal = {GitHub repository},
80 url = {https://github.com/tseemann/snp-dists},
81 }</citation>
82 </citations>
83 </tool>