annotate snippy-core.xml @ 12:fa016f1eea1a draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snippy commit 7dec701af24e00b3328459f0a823eefd461237bb"
author iuc
date Wed, 07 Apr 2021 11:24:48 +0000
parents 5bbf9eada9c2
children
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"?>
12
fa016f1eea1a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snippy commit 7dec701af24e00b3328459f0a823eefd461237bb"
iuc
parents: 11
diff changeset
2 <tool id="snippy_core" name="snippy-core" version="@WRAPPER_VERSION@+galaxy@VERSION_SUFFIX@">
0
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[
5
0aa87d97847f "planemo upload commit 13d17dd18915767d3ca5bbd92ce3e5e80a287112"
iuc
parents: 4
diff changeset
11 @REFERENCE_SOURCE_FILE@
9
e4d0231d8595 "planemo upload commit 02413e02c9484cdb604bda2c09931599f9259792"
iuc
parents: 8
diff changeset
12 mkdir 'snippy_dirs' && cd 'snippy_dirs' &&
2
776ebd1239da planemo upload commit dcedcb76831fd639d1468a308a78ac359ecd2496
iuc
parents: 0
diff changeset
13 #for $indir in $indirs
9
e4d0231d8595 "planemo upload commit 02413e02c9484cdb604bda2c09931599f9259792"
iuc
parents: 8
diff changeset
14 tar -xf '$indir' -C . &&
2
776ebd1239da planemo upload commit dcedcb76831fd639d1468a308a78ac359ecd2496
iuc
parents: 0
diff changeset
15 #end for
9
e4d0231d8595 "planemo upload commit 02413e02c9484cdb604bda2c09931599f9259792"
iuc
parents: 8
diff changeset
16 cd - &&
2
776ebd1239da planemo upload commit dcedcb76831fd639d1468a308a78ac359ecd2496
iuc
parents: 0
diff changeset
17 snippy-core
5
0aa87d97847f "planemo upload commit 13d17dd18915767d3ca5bbd92ce3e5e80a287112"
iuc
parents: 4
diff changeset
18 @REFERENCE_COMMAND@
9
e4d0231d8595 "planemo upload commit 02413e02c9484cdb604bda2c09931599f9259792"
iuc
parents: 8
diff changeset
19 snippy_dirs/*
0
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
20 ]]></command>
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
21
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
22 <inputs>
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
23 <param name="indirs" type="data" multiple="true" format="zip" label="Snippy input zipped dirs" help="Select all the snippy inputs for alignment" />
5
0aa87d97847f "planemo upload commit 13d17dd18915767d3ca5bbd92ce3e5e80a287112"
iuc
parents: 4
diff changeset
24 <expand macro="reference_selector" />
0
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
25 <param name="outputs" type="select" multiple="true" display="checkboxes" label="Output selection">
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
26 <option value="outaln" selected="True">A core SNP alignment in the fasta format</option>
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
27 <option value="outfull" selected="False">A whole genome SNP alignment (includes invariant sites)</option>
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
28 <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
29 <option value="outtxt" selected="False">Tab-separated columnar list of alignment/core-size statistics</option>
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
30 </param>
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
31
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
32 </inputs>
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
33
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
34 <outputs>
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
35 <data format="fasta" name="alignment_fasta" label="${tool.name} on ${on_string} core alignment fasta" from_work_dir="core.aln">
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
36 <filter>outputs and 'outaln' in outputs</filter>
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
37 </data>
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
38 <data format="fasta" name="full_alignment_fasta" label="${tool.name} on ${on_string} full alignment fasta" from_work_dir="core.full.aln">
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
39 <filter>outputs and 'outfull' in outputs</filter>
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
40 </data>
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
41 <data format="tabular" name="alignment_table" label="${tool.name} on ${on_string} core alignment table" from_work_dir="core.tab">
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
42 <filter>outputs and 'outtab' in outputs</filter>
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
43 </data>
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
44 <data format="txt" name="alignment_summary" label="${tool.name} on ${on_string} core alignment summary" from_work_dir="core.txt">
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
45 <filter>outputs and 'outtxt' in outputs</filter>
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
46 </data>
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
47 </outputs>
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
48
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
49 <tests>
2
776ebd1239da planemo upload commit dcedcb76831fd639d1468a308a78ac359ecd2496
iuc
parents: 0
diff changeset
50 <test><!-- Test #1 - test with 3 zipped directories -->
776ebd1239da planemo upload commit dcedcb76831fd639d1468a308a78ac359ecd2496
iuc
parents: 0
diff changeset
51 <param name="indirs" value="a.tgz,b.tgz,c.tgz" />
5
0aa87d97847f "planemo upload commit 13d17dd18915767d3ca5bbd92ce3e5e80a287112"
iuc
parents: 4
diff changeset
52 <conditional name="reference_source">
0aa87d97847f "planemo upload commit 13d17dd18915767d3ca5bbd92ce3e5e80a287112"
iuc
parents: 4
diff changeset
53 <param name="reference_source_selector" value="history"/>
0aa87d97847f "planemo upload commit 13d17dd18915767d3ca5bbd92ce3e5e80a287112"
iuc
parents: 4
diff changeset
54 <param name="ref_file" value="reference.fasta" ftype="fasta"/>
0aa87d97847f "planemo upload commit 13d17dd18915767d3ca5bbd92ce3e5e80a287112"
iuc
parents: 4
diff changeset
55 </conditional>
0aa87d97847f "planemo upload commit 13d17dd18915767d3ca5bbd92ce3e5e80a287112"
iuc
parents: 4
diff changeset
56 <param name="outputs" value="outtxt" />
0aa87d97847f "planemo upload commit 13d17dd18915767d3ca5bbd92ce3e5e80a287112"
iuc
parents: 4
diff changeset
57 <output name="alignment_summary" ftype="txt" file="a_b_c.core.txt" />
0aa87d97847f "planemo upload commit 13d17dd18915767d3ca5bbd92ce3e5e80a287112"
iuc
parents: 4
diff changeset
58 </test>
0aa87d97847f "planemo upload commit 13d17dd18915767d3ca5bbd92ce3e5e80a287112"
iuc
parents: 4
diff changeset
59 <test><!-- Test #2 - test with 3 zipped directories -->
0aa87d97847f "planemo upload commit 13d17dd18915767d3ca5bbd92ce3e5e80a287112"
iuc
parents: 4
diff changeset
60 <param name="indirs" value="a.tgz,b.tgz,c.tgz" />
0aa87d97847f "planemo upload commit 13d17dd18915767d3ca5bbd92ce3e5e80a287112"
iuc
parents: 4
diff changeset
61 <conditional name="reference_source">
0aa87d97847f "planemo upload commit 13d17dd18915767d3ca5bbd92ce3e5e80a287112"
iuc
parents: 4
diff changeset
62 <param name="reference_source_selector" value="cached"/>
0aa87d97847f "planemo upload commit 13d17dd18915767d3ca5bbd92ce3e5e80a287112"
iuc
parents: 4
diff changeset
63 <param name="ref_file" value="test_id"/>
0aa87d97847f "planemo upload commit 13d17dd18915767d3ca5bbd92ce3e5e80a287112"
iuc
parents: 4
diff changeset
64 </conditional>
0
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
65 <param name="outputs" value="outtxt" />
2
776ebd1239da planemo upload commit dcedcb76831fd639d1468a308a78ac359ecd2496
iuc
parents: 0
diff changeset
66 <output name="alignment_summary" ftype="txt" file="a_b_c.core.txt" />
0
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
67 </test>
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
68 </tests>
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
69
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
70 <help><![CDATA[
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
71 **snippy-core @VERSION@**
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
72
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
73 Combine multiple Snippy outputs into a core SNP alignment
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
74
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
75 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
76
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
77
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
78 **Inputs:**
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
79
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
80 Multiple Snippy output directories. (At least 2 of)
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
81
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
82 **Options:**
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
83
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
84 - noreference Exclude reference (default '0').
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
85
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
86 **Note:**
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
87
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
88 snippy **must** have been run with --cleanup False
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
89
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
90 ]]></help>
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
91 <expand macro="citations" />
c9a8ef2aa380 planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
iuc
parents:
diff changeset
92 </tool>