Mercurial > repos > dfornika > snippy

annotate snippy-core.xml @ 8:c441153cb4c2 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/tseemann/snippy commit 73ec6ea773b1b88f7c32a2e8bc57b644b82f7ff9-dirty
author dfornika
date Mon, 21 Jan 2019 18:26:12 -0500
parents 3f5ced130c5c
children 8a6b951f6ec2
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
0276bb8bd561 planemo upload for repository https://github.com/tseemann/snippy commit d9e4e18619d5b9378f4fcbe518856fc1fa202d73-dirty
dfornika
parents:
diff changeset
1 <tool id="snippy_core" name="snippy-core" version="@VERSION@">
0276bb8bd561 planemo upload for repository https://github.com/tseemann/snippy commit d9e4e18619d5b9378f4fcbe518856fc1fa202d73-dirty
dfornika
parents:
diff changeset
2 <description>
0276bb8bd561 planemo upload for repository https://github.com/tseemann/snippy commit d9e4e18619d5b9378f4fcbe518856fc1fa202d73-dirty
dfornika
parents:
diff changeset
3 Combine multiple Snippy outputs into a core SNP alignment
0276bb8bd561 planemo upload for repository https://github.com/tseemann/snippy commit d9e4e18619d5b9378f4fcbe518856fc1fa202d73-dirty
dfornika
parents:
diff changeset
4 </description>
0276bb8bd561 planemo upload for repository https://github.com/tseemann/snippy commit d9e4e18619d5b9378f4fcbe518856fc1fa202d73-dirty
dfornika
parents:
diff changeset
5 <macros>
0276bb8bd561 planemo upload for repository https://github.com/tseemann/snippy commit d9e4e18619d5b9378f4fcbe518856fc1fa202d73-dirty
dfornika
parents:
diff changeset
6 <import>macros.xml</import>
0276bb8bd561 planemo upload for repository https://github.com/tseemann/snippy commit d9e4e18619d5b9378f4fcbe518856fc1fa202d73-dirty
dfornika
parents:
diff changeset
7 </macros>
0276bb8bd561 planemo upload for repository https://github.com/tseemann/snippy commit d9e4e18619d5b9378f4fcbe518856fc1fa202d73-dirty
dfornika
parents:
diff changeset
8 <expand macro="requirements" />
0276bb8bd561 planemo upload for repository https://github.com/tseemann/snippy commit d9e4e18619d5b9378f4fcbe518856fc1fa202d73-dirty
dfornika
parents:
diff changeset
9 <command detect_errors="exit_code"><![CDATA[
0276bb8bd561 planemo upload for repository https://github.com/tseemann/snippy commit d9e4e18619d5b9378f4fcbe518856fc1fa202d73-dirty
dfornika
parents:
diff changeset
10
4
3f5ced130c5c planemo upload for repository https://github.com/tseemann/snippy commit 73ec6ea773b1b88f7c32a2e8bc57b644b82f7ff9-dirty
dfornika
parents: 2
diff changeset
11 python '$__tool_directory__/snippy_core_wrapper.py'
2
1a3c85497d96 planemo upload for repository https://github.com/tseemann/snippy commit 73ec6ea773b1b88f7c32a2e8bc57b644b82f7ff9-dirty
dfornika
parents: 0
diff changeset
12 --ref '$ref'
8
c441153cb4c2 planemo upload for repository https://github.com/tseemann/snippy commit 73ec6ea773b1b88f7c32a2e8bc57b644b82f7ff9-dirty
dfornika
parents: 4
diff changeset
13 --indirs '$indirs'
0
0276bb8bd561 planemo upload for repository https://github.com/tseemann/snippy commit d9e4e18619d5b9378f4fcbe518856fc1fa202d73-dirty
dfornika
parents:
diff changeset
14
0276bb8bd561 planemo upload for repository https://github.com/tseemann/snippy commit d9e4e18619d5b9378f4fcbe518856fc1fa202d73-dirty
dfornika
parents:
diff changeset
15 ]]></command>
0276bb8bd561 planemo upload for repository https://github.com/tseemann/snippy commit d9e4e18619d5b9378f4fcbe518856fc1fa202d73-dirty
dfornika
parents:
diff changeset
16
0276bb8bd561 planemo upload for repository https://github.com/tseemann/snippy commit d9e4e18619d5b9378f4fcbe518856fc1fa202d73-dirty
dfornika
parents:
diff changeset
17 <inputs>
0276bb8bd561 planemo upload for repository https://github.com/tseemann/snippy commit d9e4e18619d5b9378f4fcbe518856fc1fa202d73-dirty
dfornika
parents:
diff changeset
18 <param name="indirs" type="data" multiple="true" format="zip" label="Snippy input zipped dirs" help="Select all the snippy inputs for alignment" />
2
1a3c85497d96 planemo upload for repository https://github.com/tseemann/snippy commit 73ec6ea773b1b88f7c32a2e8bc57b644b82f7ff9-dirty
dfornika
parents: 0
diff changeset
19 <param name="ref" type="data" format="fasta,genbank" label="Reference File (either in fasta or genbank format)" help="Fasta or Genbank file to use as the reference" />
0
0276bb8bd561 planemo upload for repository https://github.com/tseemann/snippy commit d9e4e18619d5b9378f4fcbe518856fc1fa202d73-dirty
dfornika
parents:
diff changeset
20 <param name="outputs" type="select" multiple="true" display="checkboxes" label="Output selection">
0276bb8bd561 planemo upload for repository https://github.com/tseemann/snippy commit d9e4e18619d5b9378f4fcbe518856fc1fa202d73-dirty
dfornika
parents:
diff changeset
21 <option value="outaln" selected="True">A core SNP alignment in the fasta format</option>
0276bb8bd561 planemo upload for repository https://github.com/tseemann/snippy commit d9e4e18619d5b9378f4fcbe518856fc1fa202d73-dirty
dfornika
parents:
diff changeset
22 <option value="outfull" selected="False">A whole genome SNP alignment (includes invariant sites)</option>
0276bb8bd561 planemo upload for repository https://github.com/tseemann/snippy commit d9e4e18619d5b9378f4fcbe518856fc1fa202d73-dirty
dfornika
parents:
diff changeset
23 <option value="outtab" selected="False">Tab-separated columnar list of core SNP sites with alleles and annotations</option>
0276bb8bd561 planemo upload for repository https://github.com/tseemann/snippy commit d9e4e18619d5b9378f4fcbe518856fc1fa202d73-dirty
dfornika
parents:
diff changeset
24 <option value="outtxt" selected="False">Tab-separated columnar list of alignment/core-size statistics</option>
0276bb8bd561 planemo upload for repository https://github.com/tseemann/snippy commit d9e4e18619d5b9378f4fcbe518856fc1fa202d73-dirty
dfornika
parents:
diff changeset
25 </param>
0276bb8bd561 planemo upload for repository https://github.com/tseemann/snippy commit d9e4e18619d5b9378f4fcbe518856fc1fa202d73-dirty
dfornika
parents:
diff changeset
26
0276bb8bd561 planemo upload for repository https://github.com/tseemann/snippy commit d9e4e18619d5b9378f4fcbe518856fc1fa202d73-dirty
dfornika
parents:
diff changeset
27 </inputs>
0276bb8bd561 planemo upload for repository https://github.com/tseemann/snippy commit d9e4e18619d5b9378f4fcbe518856fc1fa202d73-dirty
dfornika
parents:
diff changeset
28
0276bb8bd561 planemo upload for repository https://github.com/tseemann/snippy commit d9e4e18619d5b9378f4fcbe518856fc1fa202d73-dirty
dfornika
parents:
diff changeset
29 <outputs>
0276bb8bd561 planemo upload for repository https://github.com/tseemann/snippy commit d9e4e18619d5b9378f4fcbe518856fc1fa202d73-dirty
dfornika
parents:
diff changeset
30 <data format="fasta" name="alignment_fasta" label="${tool.name} on ${on_string} core alignment fasta" from_work_dir="core.aln">
0276bb8bd561 planemo upload for repository https://github.com/tseemann/snippy commit d9e4e18619d5b9378f4fcbe518856fc1fa202d73-dirty
dfornika
parents:
diff changeset
31 <filter>outputs and 'outaln' in outputs</filter>
0276bb8bd561 planemo upload for repository https://github.com/tseemann/snippy commit d9e4e18619d5b9378f4fcbe518856fc1fa202d73-dirty
dfornika
parents:
diff changeset
32 </data>
0276bb8bd561 planemo upload for repository https://github.com/tseemann/snippy commit d9e4e18619d5b9378f4fcbe518856fc1fa202d73-dirty
dfornika
parents:
diff changeset
33 <data format="fasta" name="full_alignment_fasta" label="${tool.name} on ${on_string} full alignment fasta" from_work_dir="core.full.aln">
0276bb8bd561 planemo upload for repository https://github.com/tseemann/snippy commit d9e4e18619d5b9378f4fcbe518856fc1fa202d73-dirty
dfornika
parents:
diff changeset
34 <filter>outputs and 'outfull' in outputs</filter>
0276bb8bd561 planemo upload for repository https://github.com/tseemann/snippy commit d9e4e18619d5b9378f4fcbe518856fc1fa202d73-dirty
dfornika
parents:
diff changeset
35 </data>
0276bb8bd561 planemo upload for repository https://github.com/tseemann/snippy commit d9e4e18619d5b9378f4fcbe518856fc1fa202d73-dirty
dfornika
parents:
diff changeset
36 <data format="tabular" name="alignment_table" label="${tool.name} on ${on_string} core alignment table" from_work_dir="core.tab">
0276bb8bd561 planemo upload for repository https://github.com/tseemann/snippy commit d9e4e18619d5b9378f4fcbe518856fc1fa202d73-dirty
dfornika
parents:
diff changeset
37 <filter>outputs and 'outtab' in outputs</filter>
0276bb8bd561 planemo upload for repository https://github.com/tseemann/snippy commit d9e4e18619d5b9378f4fcbe518856fc1fa202d73-dirty
dfornika
parents:
diff changeset
38 </data>
0276bb8bd561 planemo upload for repository https://github.com/tseemann/snippy commit d9e4e18619d5b9378f4fcbe518856fc1fa202d73-dirty
dfornika
parents:
diff changeset
39 <data format="txt" name="alignment_summary" label="${tool.name} on ${on_string} core alignment summary" from_work_dir="core.txt">
0276bb8bd561 planemo upload for repository https://github.com/tseemann/snippy commit d9e4e18619d5b9378f4fcbe518856fc1fa202d73-dirty
dfornika
parents:
diff changeset
40 <filter>outputs and 'outtxt' in outputs</filter>
0276bb8bd561 planemo upload for repository https://github.com/tseemann/snippy commit d9e4e18619d5b9378f4fcbe518856fc1fa202d73-dirty
dfornika
parents:
diff changeset
41 </data>
0276bb8bd561 planemo upload for repository https://github.com/tseemann/snippy commit d9e4e18619d5b9378f4fcbe518856fc1fa202d73-dirty
dfornika
parents:
diff changeset
42 </outputs>
0276bb8bd561 planemo upload for repository https://github.com/tseemann/snippy commit d9e4e18619d5b9378f4fcbe518856fc1fa202d73-dirty
dfornika
parents:
diff changeset
43
0276bb8bd561 planemo upload for repository https://github.com/tseemann/snippy commit d9e4e18619d5b9378f4fcbe518856fc1fa202d73-dirty
dfornika
parents:
diff changeset
44 <tests>
0276bb8bd561 planemo upload for repository https://github.com/tseemann/snippy commit d9e4e18619d5b9378f4fcbe518856fc1fa202d73-dirty
dfornika
parents:
diff changeset
45 <test><!-- Test #1 - test with 2 zipped directories -->
2
1a3c85497d96 planemo upload for repository https://github.com/tseemann/snippy commit 73ec6ea773b1b88f7c32a2e8bc57b644b82f7ff9-dirty
dfornika
parents: 0
diff changeset
46 <param name="indirs" value="S1.tgz,S2.tgz,S3.tgz" />
1a3c85497d96 planemo upload for repository https://github.com/tseemann/snippy commit 73ec6ea773b1b88f7c32a2e8bc57b644b82f7ff9-dirty
dfornika
parents: 0
diff changeset
47 <param name="ref" value="GCF_000293905.1_ASM29390v1_genomic.fna" />
0
0276bb8bd561 planemo upload for repository https://github.com/tseemann/snippy commit d9e4e18619d5b9378f4fcbe518856fc1fa202d73-dirty
dfornika
parents:
diff changeset
48 <param name="outputs" value="outtxt" />
0276bb8bd561 planemo upload for repository https://github.com/tseemann/snippy commit d9e4e18619d5b9378f4fcbe518856fc1fa202d73-dirty
dfornika
parents:
diff changeset
49 <output name="alignment_summary" ftype="txt" file="core/core.txt" />
0276bb8bd561 planemo upload for repository https://github.com/tseemann/snippy commit d9e4e18619d5b9378f4fcbe518856fc1fa202d73-dirty
dfornika
parents:
diff changeset
50 </test>
0276bb8bd561 planemo upload for repository https://github.com/tseemann/snippy commit d9e4e18619d5b9378f4fcbe518856fc1fa202d73-dirty
dfornika
parents:
diff changeset
51 </tests>
0276bb8bd561 planemo upload for repository https://github.com/tseemann/snippy commit d9e4e18619d5b9378f4fcbe518856fc1fa202d73-dirty
dfornika
parents:
diff changeset
52
0276bb8bd561 planemo upload for repository https://github.com/tseemann/snippy commit d9e4e18619d5b9378f4fcbe518856fc1fa202d73-dirty
dfornika
parents:
diff changeset
53 <help><![CDATA[
0276bb8bd561 planemo upload for repository https://github.com/tseemann/snippy commit d9e4e18619d5b9378f4fcbe518856fc1fa202d73-dirty
dfornika
parents:
diff changeset
54 **snippy-core @VERSION@**
0276bb8bd561 planemo upload for repository https://github.com/tseemann/snippy commit d9e4e18619d5b9378f4fcbe518856fc1fa202d73-dirty
dfornika
parents:
diff changeset
55
0276bb8bd561 planemo upload for repository https://github.com/tseemann/snippy commit d9e4e18619d5b9378f4fcbe518856fc1fa202d73-dirty
dfornika
parents:
diff changeset
56 Combine multiple Snippy outputs into a core SNP alignment
0276bb8bd561 planemo upload for repository https://github.com/tseemann/snippy commit d9e4e18619d5b9378f4fcbe518856fc1fa202d73-dirty
dfornika
parents:
diff changeset
57
0276bb8bd561 planemo upload for repository https://github.com/tseemann/snippy commit d9e4e18619d5b9378f4fcbe518856fc1fa202d73-dirty
dfornika
parents:
diff changeset
58 If you call SNPs for multiple isolates from the same reference, you can produce an alignment of "core SNPs" which can be used to build a high-resolution phylogeny (ignoring possible recombination). A "core site" is a genomic position that is present in all the samples. A core site can have the same nucleotide in every sample ("monomorphic") or some samples can be different ("polymorphic" or "variant"). If we ignore the complications of "ins", "del" variant types, and just use variant sites, these are the "core SNP genome".
0276bb8bd561 planemo upload for repository https://github.com/tseemann/snippy commit d9e4e18619d5b9378f4fcbe518856fc1fa202d73-dirty
dfornika
parents:
diff changeset
59
0276bb8bd561 planemo upload for repository https://github.com/tseemann/snippy commit d9e4e18619d5b9378f4fcbe518856fc1fa202d73-dirty
dfornika
parents:
diff changeset
60
0276bb8bd561 planemo upload for repository https://github.com/tseemann/snippy commit d9e4e18619d5b9378f4fcbe518856fc1fa202d73-dirty
dfornika
parents:
diff changeset
61 **Inputs:**
0276bb8bd561 planemo upload for repository https://github.com/tseemann/snippy commit d9e4e18619d5b9378f4fcbe518856fc1fa202d73-dirty
dfornika
parents:
diff changeset
62
0276bb8bd561 planemo upload for repository https://github.com/tseemann/snippy commit d9e4e18619d5b9378f4fcbe518856fc1fa202d73-dirty
dfornika
parents:
diff changeset
63 Multiple Snippy output directories. (At least 2 of)
0276bb8bd561 planemo upload for repository https://github.com/tseemann/snippy commit d9e4e18619d5b9378f4fcbe518856fc1fa202d73-dirty
dfornika
parents:
diff changeset
64
0276bb8bd561 planemo upload for repository https://github.com/tseemann/snippy commit d9e4e18619d5b9378f4fcbe518856fc1fa202d73-dirty
dfornika
parents:
diff changeset
65 **Options:**
0276bb8bd561 planemo upload for repository https://github.com/tseemann/snippy commit d9e4e18619d5b9378f4fcbe518856fc1fa202d73-dirty
dfornika
parents:
diff changeset
66
0276bb8bd561 planemo upload for repository https://github.com/tseemann/snippy commit d9e4e18619d5b9378f4fcbe518856fc1fa202d73-dirty
dfornika
parents:
diff changeset
67 - noreference Exclude reference (default '0').
0276bb8bd561 planemo upload for repository https://github.com/tseemann/snippy commit d9e4e18619d5b9378f4fcbe518856fc1fa202d73-dirty
dfornika
parents:
diff changeset
68
0276bb8bd561 planemo upload for repository https://github.com/tseemann/snippy commit d9e4e18619d5b9378f4fcbe518856fc1fa202d73-dirty
dfornika
parents:
diff changeset
69 **Note:**
0276bb8bd561 planemo upload for repository https://github.com/tseemann/snippy commit d9e4e18619d5b9378f4fcbe518856fc1fa202d73-dirty
dfornika
parents:
diff changeset
70
0276bb8bd561 planemo upload for repository https://github.com/tseemann/snippy commit d9e4e18619d5b9378f4fcbe518856fc1fa202d73-dirty
dfornika
parents:
diff changeset
71 snippy **must** have been run with --cleanup False
0276bb8bd561 planemo upload for repository https://github.com/tseemann/snippy commit d9e4e18619d5b9378f4fcbe518856fc1fa202d73-dirty
dfornika
parents:
diff changeset
72
0276bb8bd561 planemo upload for repository https://github.com/tseemann/snippy commit d9e4e18619d5b9378f4fcbe518856fc1fa202d73-dirty
dfornika
parents:
diff changeset
73 ]]></help>
0276bb8bd561 planemo upload for repository https://github.com/tseemann/snippy commit d9e4e18619d5b9378f4fcbe518856fc1fa202d73-dirty
dfornika
parents:
diff changeset
74
0276bb8bd561 planemo upload for repository https://github.com/tseemann/snippy commit d9e4e18619d5b9378f4fcbe518856fc1fa202d73-dirty
dfornika
parents:
diff changeset
75 <expand macro="citations" />
0276bb8bd561 planemo upload for repository https://github.com/tseemann/snippy commit d9e4e18619d5b9378f4fcbe518856fc1fa202d73-dirty
dfornika
parents:
diff changeset
76 </tool>