Mercurial > repos > iuc > snp_dists

annotate snp-dists.xml @ 1:f78492521996 draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snp-dists commit 6c633d56b703fb77beb12dbe93cdd67d01b83920"
author iuc
date Fri, 08 Oct 2021 07:15:59 +0000
parents 1959cc43b414
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
1959cc43b414 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snp-dists commit d47295a437bdca2a1d248e8210dddea530bb6d12"
iuc
parents:
diff changeset
1 <tool id="snp_dists" name="SNP distance matrix" version="@TOOL_VERSION@+galaxy0" python_template_version="3.5">
1959cc43b414 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snp-dists commit d47295a437bdca2a1d248e8210dddea530bb6d12"
iuc
parents:
diff changeset
2 <macros>
1
f78492521996 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snp-dists commit 6c633d56b703fb77beb12dbe93cdd67d01b83920"
iuc
parents: 0
diff changeset
3 <token name="@TOOL_VERSION@">0.8.2</token>
0
1959cc43b414 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snp-dists commit d47295a437bdca2a1d248e8210dddea530bb6d12"
iuc
parents:
diff changeset
4 </macros>
1959cc43b414 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snp-dists commit d47295a437bdca2a1d248e8210dddea530bb6d12"
iuc
parents:
diff changeset
5 <description>Compute distance in SNPs between all sequences in a FASTA file</description>
1959cc43b414 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snp-dists commit d47295a437bdca2a1d248e8210dddea530bb6d12"
iuc
parents:
diff changeset
6 <requirements>
1959cc43b414 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snp-dists commit d47295a437bdca2a1d248e8210dddea530bb6d12"
iuc
parents:
diff changeset
7 <requirement type="package" version="@TOOL_VERSION@">snp-dists</requirement>
1959cc43b414 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snp-dists commit d47295a437bdca2a1d248e8210dddea530bb6d12"
iuc
parents:
diff changeset
8 </requirements>
1959cc43b414 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snp-dists commit d47295a437bdca2a1d248e8210dddea530bb6d12"
iuc
parents:
diff changeset
9 <command detect_errors="exit_code"><![CDATA[
1959cc43b414 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snp-dists commit d47295a437bdca2a1d248e8210dddea530bb6d12"
iuc
parents:
diff changeset
10 snp-dists -q
1959cc43b414 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snp-dists commit d47295a437bdca2a1d248e8210dddea530bb6d12"
iuc
parents:
diff changeset
11 $a
1959cc43b414 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snp-dists commit d47295a437bdca2a1d248e8210dddea530bb6d12"
iuc
parents:
diff changeset
12 $k
1959cc43b414 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snp-dists commit d47295a437bdca2a1d248e8210dddea530bb6d12"
iuc
parents:
diff changeset
13 $b
1
f78492521996 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snp-dists commit 6c633d56b703fb77beb12dbe93cdd67d01b83920"
iuc
parents: 0
diff changeset
14 -j \${GALAXY_SLOTS:-4}
0
1959cc43b414 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snp-dists commit d47295a437bdca2a1d248e8210dddea530bb6d12"
iuc
parents:
diff changeset
15 '$input' > '$output'
1959cc43b414 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snp-dists commit d47295a437bdca2a1d248e8210dddea530bb6d12"
iuc
parents:
diff changeset
16 ]]></command>
1959cc43b414 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snp-dists commit d47295a437bdca2a1d248e8210dddea530bb6d12"
iuc
parents:
diff changeset
17 <inputs>
1959cc43b414 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snp-dists commit d47295a437bdca2a1d248e8210dddea530bb6d12"
iuc
parents:
diff changeset
18 <param name="input" type="data" format="fasta,fasta.gz" label="FASTA multiple sequence alignment"
1959cc43b414 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snp-dists commit d47295a437bdca2a1d248e8210dddea530bb6d12"
iuc
parents:
diff changeset
19 help="Provide a multiple sequence alignment containing sequences of equal length" />
1959cc43b414 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snp-dists commit d47295a437bdca2a1d248e8210dddea530bb6d12"
iuc
parents:
diff changeset
20 <param argument="-a" type="boolean" truevalue="-a" falsevalue="" label="Count all differences, not just ACTG" />
1959cc43b414 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snp-dists commit d47295a437bdca2a1d248e8210dddea530bb6d12"
iuc
parents:
diff changeset
21 <param argument="-k" type="boolean" truevalue="-k" falsevalue="" label="Keep case, don't uppercase all letters" />
1959cc43b414 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snp-dists commit d47295a437bdca2a1d248e8210dddea530bb6d12"
iuc
parents:
diff changeset
22 <param argument="-b" type="boolean" truevalue="-b" falsevalue="" label="Blank top left corner cell" />
1959cc43b414 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snp-dists commit d47295a437bdca2a1d248e8210dddea530bb6d12"
iuc
parents:
diff changeset
23 </inputs>
1959cc43b414 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snp-dists commit d47295a437bdca2a1d248e8210dddea530bb6d12"
iuc
parents:
diff changeset
24 <outputs>
1959cc43b414 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snp-dists commit d47295a437bdca2a1d248e8210dddea530bb6d12"
iuc
parents:
diff changeset
25 <data format="tabular" name="output" label="${tool.name} on ${on_string}" />
1959cc43b414 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snp-dists commit d47295a437bdca2a1d248e8210dddea530bb6d12"
iuc
parents:
diff changeset
26 </outputs>
1959cc43b414 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snp-dists commit d47295a437bdca2a1d248e8210dddea530bb6d12"
iuc
parents:
diff changeset
27 <tests>
1959cc43b414 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snp-dists commit d47295a437bdca2a1d248e8210dddea530bb6d12"
iuc
parents:
diff changeset
28 <test>
1959cc43b414 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snp-dists commit d47295a437bdca2a1d248e8210dddea530bb6d12"
iuc
parents:
diff changeset
29 <param name="input" ftype="fasta" value="input1.fasta" />
1959cc43b414 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snp-dists commit d47295a437bdca2a1d248e8210dddea530bb6d12"
iuc
parents:
diff changeset
30 <output name="output" value="output_default1.tabular" ftype="tabular" />
1959cc43b414 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snp-dists commit d47295a437bdca2a1d248e8210dddea530bb6d12"
iuc
parents:
diff changeset
31 </test>
1959cc43b414 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snp-dists commit d47295a437bdca2a1d248e8210dddea530bb6d12"
iuc
parents:
diff changeset
32 <test>
1959cc43b414 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snp-dists commit d47295a437bdca2a1d248e8210dddea530bb6d12"
iuc
parents:
diff changeset
33 <param name="input" ftype="fasta" value="input1.fasta" />
1959cc43b414 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snp-dists commit d47295a437bdca2a1d248e8210dddea530bb6d12"
iuc
parents:
diff changeset
34 <param name="a" value="True" />
1959cc43b414 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snp-dists commit d47295a437bdca2a1d248e8210dddea530bb6d12"
iuc
parents:
diff changeset
35 <output name="output" value="output_all_diffs1.tabular" ftype="tabular" />
1959cc43b414 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snp-dists commit d47295a437bdca2a1d248e8210dddea530bb6d12"
iuc
parents:
diff changeset
36 </test>
1959cc43b414 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snp-dists commit d47295a437bdca2a1d248e8210dddea530bb6d12"
iuc
parents:
diff changeset
37 <test>
1959cc43b414 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snp-dists commit d47295a437bdca2a1d248e8210dddea530bb6d12"
iuc
parents:
diff changeset
38 <param name="input" ftype="fasta" value="input1.fasta" />
1959cc43b414 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snp-dists commit d47295a437bdca2a1d248e8210dddea530bb6d12"
iuc
parents:
diff changeset
39 <param name="k" value="True" />
1959cc43b414 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snp-dists commit d47295a437bdca2a1d248e8210dddea530bb6d12"
iuc
parents:
diff changeset
40 <output name="output" value="output_keep_case1.tabular" ftype="tabular" />
1959cc43b414 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snp-dists commit d47295a437bdca2a1d248e8210dddea530bb6d12"
iuc
parents:
diff changeset
41 </test>
1959cc43b414 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snp-dists commit d47295a437bdca2a1d248e8210dddea530bb6d12"
iuc
parents:
diff changeset
42 <test>
1959cc43b414 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snp-dists commit d47295a437bdca2a1d248e8210dddea530bb6d12"
iuc
parents:
diff changeset
43 <param name="input" ftype="fasta" value="input1.fasta" />
1959cc43b414 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snp-dists commit d47295a437bdca2a1d248e8210dddea530bb6d12"
iuc
parents:
diff changeset
44 <param name="b" value="True" />
1959cc43b414 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snp-dists commit d47295a437bdca2a1d248e8210dddea530bb6d12"
iuc
parents:
diff changeset
45 <output name="output" value="output_blank_cell1.tabular" ftype="tabular" />
1959cc43b414 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snp-dists commit d47295a437bdca2a1d248e8210dddea530bb6d12"
iuc
parents:
diff changeset
46 </test>
1959cc43b414 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snp-dists commit d47295a437bdca2a1d248e8210dddea530bb6d12"
iuc
parents:
diff changeset
47 </tests>
1959cc43b414 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snp-dists commit d47295a437bdca2a1d248e8210dddea530bb6d12"
iuc
parents:
diff changeset
48 <help><![CDATA[
1959cc43b414 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snp-dists commit d47295a437bdca2a1d248e8210dddea530bb6d12"
iuc
parents:
diff changeset
49 **snp-dists**
1959cc43b414 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snp-dists commit d47295a437bdca2a1d248e8210dddea530bb6d12"
iuc
parents:
diff changeset
50
1959cc43b414 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snp-dists commit d47295a437bdca2a1d248e8210dddea530bb6d12"
iuc
parents:
diff changeset
51 This tool computes a SNP distance matrix from a multiple sequence alignment (MSA) of
1959cc43b414 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snp-dists commit d47295a437bdca2a1d248e8210dddea530bb6d12"
iuc
parents:
diff changeset
52 sequences (all of the same length). Such distance matrices are often used as in
1959cc43b414 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snp-dists commit d47295a437bdca2a1d248e8210dddea530bb6d12"
iuc
parents:
diff changeset
53 studies of disease outbreaks.
1959cc43b414 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snp-dists commit d47295a437bdca2a1d248e8210dddea530bb6d12"
iuc
parents:
diff changeset
54
1959cc43b414 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snp-dists commit d47295a437bdca2a1d248e8210dddea530bb6d12"
iuc
parents:
diff changeset
55 The output is a tabular file, for example this matrix describing four M. tuberculosis isolates
1959cc43b414 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snp-dists commit d47295a437bdca2a1d248e8210dddea530bb6d12"
iuc
parents:
diff changeset
56 and their relationship to the inferred ancestral reference sequence:
1959cc43b414 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snp-dists commit d47295a437bdca2a1d248e8210dddea530bb6d12"
iuc
parents:
diff changeset
57
1959cc43b414 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snp-dists commit d47295a437bdca2a1d248e8210dddea530bb6d12"
iuc
parents:
diff changeset
58 =============== ======= ========= ========= ========= =========
1959cc43b414 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snp-dists commit d47295a437bdca2a1d248e8210dddea530bb6d12"
iuc
parents:
diff changeset
59 snp-dists 0.6.3 MTB_anc ERR550641 ERR550671 ERR550691 ERR550703
1959cc43b414 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snp-dists commit d47295a437bdca2a1d248e8210dddea530bb6d12"
iuc
parents:
diff changeset
60 --------------- ------- --------- --------- --------- ---------
1959cc43b414 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snp-dists commit d47295a437bdca2a1d248e8210dddea530bb6d12"
iuc
parents:
diff changeset
61 MTB_anc 0 746 726 772 749
1959cc43b414 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snp-dists commit d47295a437bdca2a1d248e8210dddea530bb6d12"
iuc
parents:
diff changeset
62 --------------- ------- --------- --------- --------- ---------
1959cc43b414 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snp-dists commit d47295a437bdca2a1d248e8210dddea530bb6d12"
iuc
parents:
diff changeset
63 ERR550641 746 0 26 44 13
1959cc43b414 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snp-dists commit d47295a437bdca2a1d248e8210dddea530bb6d12"
iuc
parents:
diff changeset
64 --------------- ------- --------- --------- --------- ---------
1959cc43b414 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snp-dists commit d47295a437bdca2a1d248e8210dddea530bb6d12"
iuc
parents:
diff changeset
65 ERR550671 726 26 0 64 29
1959cc43b414 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snp-dists commit d47295a437bdca2a1d248e8210dddea530bb6d12"
iuc
parents:
diff changeset
66 --------------- ------- --------- --------- --------- ---------
1959cc43b414 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snp-dists commit d47295a437bdca2a1d248e8210dddea530bb6d12"
iuc
parents:
diff changeset
67 ERR550691 772 44 64 0 39
1959cc43b414 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snp-dists commit d47295a437bdca2a1d248e8210dddea530bb6d12"
iuc
parents:
diff changeset
68 --------------- ------- --------- --------- --------- ---------
1959cc43b414 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snp-dists commit d47295a437bdca2a1d248e8210dddea530bb6d12"
iuc
parents:
diff changeset
69 ERR550703 749 13 29 39 0
1959cc43b414 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snp-dists commit d47295a437bdca2a1d248e8210dddea530bb6d12"
iuc
parents:
diff changeset
70 =============== ======= ========= ========= ========= =========
1959cc43b414 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snp-dists commit d47295a437bdca2a1d248e8210dddea530bb6d12"
iuc
parents:
diff changeset
71
1959cc43b414 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snp-dists commit d47295a437bdca2a1d248e8210dddea530bb6d12"
iuc
parents:
diff changeset
72 ]]></help>
1959cc43b414 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snp-dists commit d47295a437bdca2a1d248e8210dddea530bb6d12"
iuc
parents:
diff changeset
73 <citations>
1959cc43b414 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snp-dists commit d47295a437bdca2a1d248e8210dddea530bb6d12"
iuc
parents:
diff changeset
74 <citation type="bibtex">
1959cc43b414 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snp-dists commit d47295a437bdca2a1d248e8210dddea530bb6d12"
iuc
parents:
diff changeset
75 @misc{githubsnp-dists,
1959cc43b414 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snp-dists commit d47295a437bdca2a1d248e8210dddea530bb6d12"
iuc
parents:
diff changeset
76 author = {Seemann, Torsten},
1959cc43b414 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snp-dists commit d47295a437bdca2a1d248e8210dddea530bb6d12"
iuc
parents:
diff changeset
77 year = {2019},
1959cc43b414 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snp-dists commit d47295a437bdca2a1d248e8210dddea530bb6d12"
iuc
parents:
diff changeset
78 title = {snp-dists},
1959cc43b414 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snp-dists commit d47295a437bdca2a1d248e8210dddea530bb6d12"
iuc
parents:
diff changeset
79 publisher = {GitHub},
1959cc43b414 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snp-dists commit d47295a437bdca2a1d248e8210dddea530bb6d12"
iuc
parents:
diff changeset
80 journal = {GitHub repository},
1959cc43b414 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snp-dists commit d47295a437bdca2a1d248e8210dddea530bb6d12"
iuc
parents:
diff changeset
81 url = {https://github.com/tseemann/snp-dists},
1959cc43b414 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snp-dists commit d47295a437bdca2a1d248e8210dddea530bb6d12"
iuc
parents:
diff changeset
82 }</citation>
1959cc43b414 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snp-dists commit d47295a437bdca2a1d248e8210dddea530bb6d12"
iuc
parents:
diff changeset
83 </citations>
1959cc43b414 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snp-dists commit d47295a437bdca2a1d248e8210dddea530bb6d12"
iuc
parents:
diff changeset
84 </tool>