Mercurial > repos > iuc > squirrel_qc

annotate squirrel-qc.xml @ 0:f63d24309f49 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
author iuc
date Thu, 16 Jan 2025 07:07:52 +0000
parents
children cd668d67431e
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
f63d24309f49 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
iuc
parents:
diff changeset
1 <tool id="squirrel_qc" name="Squirrel QC" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
f63d24309f49 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
iuc
parents:
diff changeset
2 <description>QC of MPXV (Mpox virus) sequences</description>
f63d24309f49 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
iuc
parents:
diff changeset
3 <macros>
f63d24309f49 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
iuc
parents:
diff changeset
4 <import>macros.xml</import>
f63d24309f49 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
iuc
parents:
diff changeset
5 </macros>
f63d24309f49 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
iuc
parents:
diff changeset
6 <expand macro="requirements"/>
f63d24309f49 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
iuc
parents:
diff changeset
7 <expand macro="version_command"/>
f63d24309f49 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
iuc
parents:
diff changeset
8
f63d24309f49 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
iuc
parents:
diff changeset
9 <command detect_errors="exit_code"><![CDATA[
f63d24309f49 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
iuc
parents:
diff changeset
10 #set $mask_output = 'input.suggested_mask.csv'
f63d24309f49 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
iuc
parents:
diff changeset
11 #set $exclude_output = 'suggested_to_exclude.csv'
f63d24309f49 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
iuc
parents:
diff changeset
12
f63d24309f49 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
iuc
parents:
diff changeset
13 ln -s '${sequences}' input.fasta &&
f63d24309f49 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
iuc
parents:
diff changeset
14
f63d24309f49 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
iuc
parents:
diff changeset
15 squirrel
f63d24309f49 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
iuc
parents:
diff changeset
16 --seq-qc
f63d24309f49 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
iuc
parents:
diff changeset
17 --clade $clade
f63d24309f49 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
iuc
parents:
diff changeset
18
f63d24309f49 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
iuc
parents:
diff changeset
19 --threads \${GALAXY_SLOTS:-1}
f63d24309f49 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
iuc
parents:
diff changeset
20
f63d24309f49 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
iuc
parents:
diff changeset
21 input.fasta &&
f63d24309f49 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
iuc
parents:
diff changeset
22
f63d24309f49 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
iuc
parents:
diff changeset
23 mv '${mask_output}' '$mask' &&
f63d24309f49 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
iuc
parents:
diff changeset
24 mv '${exclude_output}' '$exclude'
f63d24309f49 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
iuc
parents:
diff changeset
25 ]]></command>
f63d24309f49 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
iuc
parents:
diff changeset
26
f63d24309f49 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
iuc
parents:
diff changeset
27 <inputs>
f63d24309f49 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
iuc
parents:
diff changeset
28 <param name="sequences"
f63d24309f49 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
iuc
parents:
diff changeset
29 type="data"
f63d24309f49 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
iuc
parents:
diff changeset
30 format="fasta"
f63d24309f49 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
iuc
parents:
diff changeset
31 label="Sequences in FASTA format" />
f63d24309f49 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
iuc
parents:
diff changeset
32 <param name="clade"
f63d24309f49 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
iuc
parents:
diff changeset
33 type="select"
f63d24309f49 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
iuc
parents:
diff changeset
34 label="Select MPXV Clade">
f63d24309f49 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
iuc
parents:
diff changeset
35 <option value="cladei">Clade I</option>
f63d24309f49 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
iuc
parents:
diff changeset
36 <option value="cladeia">Clade Ia</option>
f63d24309f49 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
iuc
parents:
diff changeset
37 <option value="cladeib">Clade Ib</option>
f63d24309f49 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
iuc
parents:
diff changeset
38 <option value="cladeii">Clade II</option>
f63d24309f49 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
iuc
parents:
diff changeset
39 <option value="cladeiia">Clade IIa</option>
f63d24309f49 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
iuc
parents:
diff changeset
40 <option value="cladeiib">Clade IIb</option>
f63d24309f49 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
iuc
parents:
diff changeset
41 </param>
f63d24309f49 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
iuc
parents:
diff changeset
42
f63d24309f49 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
iuc
parents:
diff changeset
43 </inputs>
f63d24309f49 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
iuc
parents:
diff changeset
44
f63d24309f49 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
iuc
parents:
diff changeset
45 <outputs>
f63d24309f49 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
iuc
parents:
diff changeset
46 <!-- standard outputs-->
f63d24309f49 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
iuc
parents:
diff changeset
47 <data name="mask" format="csv" label="${tool.name} - flagged mutations to mask" />
f63d24309f49 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
iuc
parents:
diff changeset
48 <data name="exclude" format="csv" label="${tool.name} - flagged sequences to exclude" />
f63d24309f49 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
iuc
parents:
diff changeset
49 </outputs>
f63d24309f49 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
iuc
parents:
diff changeset
50
f63d24309f49 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
iuc
parents:
diff changeset
51 <tests>
f63d24309f49 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
iuc
parents:
diff changeset
52 <test expect_num_outputs="2">
f63d24309f49 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
iuc
parents:
diff changeset
53 <param name="sequences" value="test-sequences.fasta" />
f63d24309f49 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
iuc
parents:
diff changeset
54 <param name="clade" value="cladeii" />
f63d24309f49 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
iuc
parents:
diff changeset
55 <output name="mask" file="sequences.suggested_mask.csv" />
f63d24309f49 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
iuc
parents:
diff changeset
56 <output name="exclude" file="suggested_to_exclude.csv" />
f63d24309f49 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
iuc
parents:
diff changeset
57 </test>
f63d24309f49 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
iuc
parents:
diff changeset
58 </tests>
f63d24309f49 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
iuc
parents:
diff changeset
59 <help><![CDATA[
f63d24309f49 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
iuc
parents:
diff changeset
60 Squirrel in QC mode can run quality control (QC) on the alignment and flag certain sites to the user that may need to be masked. Squirrel can flag potential issues in the MPXV sequences that have been provided for alignment (e.g. SNPS near tracts of N, clusters of unique SNPs, reversions to reference alleles and convergent mutations) and outputs these in a mask file for investigation.
f63d24309f49 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
iuc
parents:
diff changeset
61
f63d24309f49 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
iuc
parents:
diff changeset
62 It is recommended that the user looks at these sites in an alignment viewer to judge whether the sites should be masked or not.
f63d24309f49 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
iuc
parents:
diff changeset
63
f63d24309f49 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
iuc
parents:
diff changeset
64 Squirrel with check within the alignment for:
f63d24309f49 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
iuc
parents:
diff changeset
65
f63d24309f49 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
iuc
parents:
diff changeset
66 - Mutations that are adjacent to N bases
f63d24309f49 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
iuc
parents:
diff changeset
67
f63d24309f49 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
iuc
parents:
diff changeset
68 The rationale for this is that N sites are usually a product of low coverage regions. Mutations that occur directly adjacent to low coverage regions may be a result of mis-alignment prior to the low coverage masking and may not be real SNPs. In squirrel, non-majority alleles that are present next to an N are flagged as potential sites for masking
f63d24309f49 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
iuc
parents:
diff changeset
69
f63d24309f49 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
iuc
parents:
diff changeset
70 - Unique mutations that clump together
f63d24309f49 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
iuc
parents:
diff changeset
71
f63d24309f49 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
iuc
parents:
diff changeset
72 If mutations are observed in only a single sequence in the genome, they are classed as unique mutations. Usually mutations do not clump closely together and may suggest an alignment or assembly issue. If these mutations are not shared with any other sequences, they are flagged for masking.
f63d24309f49 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
iuc
parents:
diff changeset
73
f63d24309f49 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
iuc
parents:
diff changeset
74 - Sequences with a high N content
f63d24309f49 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
iuc
parents:
diff changeset
75
f63d24309f49 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
iuc
parents:
diff changeset
76 Sequences that have many ambiguous bases in them are flagged that they may want to be excluded in further analysis. This may not always be appropriate, often genomes that have a lot of ambiguity can still be informative, however if there is something unusual about a sequence, having lots of ambiguities can be a flag for wider problems (like low read count during assembly).
f63d24309f49 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
iuc
parents:
diff changeset
77 ]]></help>
f63d24309f49 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
iuc
parents:
diff changeset
78 <expand macro="citations"/>
f63d24309f49 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
iuc
parents:
diff changeset
79 </tool>