Mercurial > repos > iuc > snippy

annotate snippy-core.xml @ 4:9bccc8404a3c draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload commit b5890b40c257a093ebf358294544aa69087da51e
author iuc
date Thu, 11 Jul 2019 09:41:13 -0400
parents 776ebd1239da
children 0aa87d97847f
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
2
776ebd1239da planemo upload commit dcedcb76831fd639d1468a308a78ac359ecd2496
iuc
parents: 0
diff changeset
1 <?xml version="1.0" encoding="utf-8"?>
0
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
2 <tool id="snippy_core" name="snippy-core" version="@VERSION@">
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
3 <description>
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
4 Combine multiple Snippy outputs into a core SNP alignment
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
5 </description>
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
6 <macros>
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
7 <import>macros.xml</import>
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
8 </macros>
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
9 <expand macro="requirements" />
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
10 <command detect_errors="exit_code"><![CDATA[
2
776ebd1239da planemo upload commit dcedcb76831fd639d1468a308a78ac359ecd2496
iuc
parents: 0
diff changeset
11 #for $indir in $indirs
776ebd1239da planemo upload commit dcedcb76831fd639d1468a308a78ac359ecd2496
iuc
parents: 0
diff changeset
12 #set $sample_name = os.path.splitext(os.path.basename(str($indir.name)))[0]
776ebd1239da planemo upload commit dcedcb76831fd639d1468a308a78ac359ecd2496
iuc
parents: 0
diff changeset
13 mkdir '$sample_name' && tar -xf '$indir' -C '$sample_name' --strip-components=1 &&
776ebd1239da planemo upload commit dcedcb76831fd639d1468a308a78ac359ecd2496
iuc
parents: 0
diff changeset
14 #end for
4
9bccc8404a3c planemo upload commit b5890b40c257a093ebf358294544aa69087da51e
iuc
parents: 2
diff changeset
15 #set snippy_dirs = " ".join(["'{0}'".format(os.path.splitext(os.path.basename(str($indir.name)))[0]) for $indir in $indirs])
2
776ebd1239da planemo upload commit dcedcb76831fd639d1468a308a78ac359ecd2496
iuc
parents: 0
diff changeset
16 snippy-core
776ebd1239da planemo upload commit dcedcb76831fd639d1468a308a78ac359ecd2496
iuc
parents: 0
diff changeset
17 --ref '$ref'
776ebd1239da planemo upload commit dcedcb76831fd639d1468a308a78ac359ecd2496
iuc
parents: 0
diff changeset
18 ${snippy_dirs}
0
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
19 ]]></command>
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
20
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
21 <inputs>
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
22 <param name="indirs" type="data" multiple="true" format="zip" label="Snippy input zipped dirs" help="Select all the snippy inputs for alignment" />
2
776ebd1239da planemo upload commit dcedcb76831fd639d1468a308a78ac359ecd2496
iuc
parents: 0
diff changeset
23 <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
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
24 <param name="outputs" type="select" multiple="true" display="checkboxes" label="Output selection">
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
25 <option value="outaln" selected="True">A core SNP alignment in the fasta format</option>
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
26 <option value="outfull" selected="False">A whole genome SNP alignment (includes invariant sites)</option>
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
27 <option value="outtab" selected="False">Tab-separated columnar list of core SNP sites with alleles and annotations</option>
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
28 <option value="outtxt" selected="False">Tab-separated columnar list of alignment/core-size statistics</option>
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
29 </param>
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
30
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
31 </inputs>
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
32
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
33 <outputs>
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
34 <data format="fasta" name="alignment_fasta" label="${tool.name} on ${on_string} core alignment fasta" from_work_dir="core.aln">
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
35 <filter>outputs and 'outaln' in outputs</filter>
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
36 </data>
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
37 <data format="fasta" name="full_alignment_fasta" label="${tool.name} on ${on_string} full alignment fasta" from_work_dir="core.full.aln">
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
38 <filter>outputs and 'outfull' in outputs</filter>
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
39 </data>
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
40 <data format="tabular" name="alignment_table" label="${tool.name} on ${on_string} core alignment table" from_work_dir="core.tab">
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
41 <filter>outputs and 'outtab' in outputs</filter>
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
42 </data>
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
43 <data format="txt" name="alignment_summary" label="${tool.name} on ${on_string} core alignment summary" from_work_dir="core.txt">
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
44 <filter>outputs and 'outtxt' in outputs</filter>
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
45 </data>
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
46 </outputs>
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
47
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
48 <tests>
2
776ebd1239da planemo upload commit dcedcb76831fd639d1468a308a78ac359ecd2496
iuc
parents: 0
diff changeset
49 <test><!-- Test #1 - test with 3 zipped directories -->
776ebd1239da planemo upload commit dcedcb76831fd639d1468a308a78ac359ecd2496
iuc
parents: 0
diff changeset
50 <param name="indirs" value="a.tgz,b.tgz,c.tgz" />
776ebd1239da planemo upload commit dcedcb76831fd639d1468a308a78ac359ecd2496
iuc
parents: 0
diff changeset
51 <param name="ref" value="reference.fasta" />
0
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
52 <param name="outputs" value="outtxt" />
2
776ebd1239da planemo upload commit dcedcb76831fd639d1468a308a78ac359ecd2496
iuc
parents: 0
diff changeset
53 <output name="alignment_summary" ftype="txt" file="a_b_c.core.txt" />
0
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
54 </test>
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
55 </tests>
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
56
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
57 <help><![CDATA[
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
58 **snippy-core @VERSION@**
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
59
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
60 Combine multiple Snippy outputs into a core SNP alignment
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
61
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
62 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".
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
63
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
64
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
65 **Inputs:**
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
66
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
67 Multiple Snippy output directories. (At least 2 of)
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
68
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
69 **Options:**
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
70
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
71 - noreference Exclude reference (default '0').
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
72
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
73 **Note:**
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
74
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
75 snippy **must** have been run with --cleanup False
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
76
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
77 ]]></help>
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
78 <expand macro="citations" />
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
79 </tool>