Mercurial > repos > iuc > cnvkit_breaks

annotate breaks.xml @ 4:d889cf77ec0d 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/cnvkit commit fc1282ec68b346988203ead860e9b9d6a47e9efb
author iuc
date Sat, 01 Mar 2025 11:57:53 +0000
parents 384fa596e5d9
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
ef9a50eb20ce planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit e927b17a345b18c1b51dc1b112db5129278dcd22
iuc
parents:
diff changeset
1 <tool id="cnvkit_breaks" name="CNVkit Breaks" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
ef9a50eb20ce planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit e927b17a345b18c1b51dc1b112db5129278dcd22
iuc
parents:
diff changeset
2 <description>List the targeted genes with segmentaion breakpoint</description>
ef9a50eb20ce planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit e927b17a345b18c1b51dc1b112db5129278dcd22
iuc
parents:
diff changeset
3 <macros>
ef9a50eb20ce planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit e927b17a345b18c1b51dc1b112db5129278dcd22
iuc
parents:
diff changeset
4 <import>macros.xml</import>
ef9a50eb20ce planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit e927b17a345b18c1b51dc1b112db5129278dcd22
iuc
parents:
diff changeset
5 </macros>
ef9a50eb20ce planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit e927b17a345b18c1b51dc1b112db5129278dcd22
iuc
parents:
diff changeset
6 <expand macro="xrefs"/>
ef9a50eb20ce planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit e927b17a345b18c1b51dc1b112db5129278dcd22
iuc
parents:
diff changeset
7 <expand macro="creators_and_zahra"/>
ef9a50eb20ce planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit e927b17a345b18c1b51dc1b112db5129278dcd22
iuc
parents:
diff changeset
8 <expand macro="requirements"/>
ef9a50eb20ce planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit e927b17a345b18c1b51dc1b112db5129278dcd22
iuc
parents:
diff changeset
9 <command detect_errors="exit_code"><![CDATA[
ef9a50eb20ce planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit e927b17a345b18c1b51dc1b112db5129278dcd22
iuc
parents:
diff changeset
10 ln -s '$input_filename_file' ./sample.cnr &&
ef9a50eb20ce planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit e927b17a345b18c1b51dc1b112db5129278dcd22
iuc
parents:
diff changeset
11 ln -s '$input_segment_file' ./sample.cns &&
ef9a50eb20ce planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit e927b17a345b18c1b51dc1b112db5129278dcd22
iuc
parents:
diff changeset
12 cnvkit.py breaks
ef9a50eb20ce planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit e927b17a345b18c1b51dc1b112db5129278dcd22
iuc
parents:
diff changeset
13 ./sample.cnr
ef9a50eb20ce planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit e927b17a345b18c1b51dc1b112db5129278dcd22
iuc
parents:
diff changeset
14 ./sample.cns
ef9a50eb20ce planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit e927b17a345b18c1b51dc1b112db5129278dcd22
iuc
parents:
diff changeset
15 --output gene-breaks.txt
ef9a50eb20ce planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit e927b17a345b18c1b51dc1b112db5129278dcd22
iuc
parents:
diff changeset
16 #if $min_probes
ef9a50eb20ce planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit e927b17a345b18c1b51dc1b112db5129278dcd22
iuc
parents:
diff changeset
17 --min-probes $min_probes
ef9a50eb20ce planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit e927b17a345b18c1b51dc1b112db5129278dcd22
iuc
parents:
diff changeset
18 #end if
ef9a50eb20ce planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit e927b17a345b18c1b51dc1b112db5129278dcd22
iuc
parents:
diff changeset
19 ]]></command>
ef9a50eb20ce planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit e927b17a345b18c1b51dc1b112db5129278dcd22
iuc
parents:
diff changeset
20 <inputs>
4
d889cf77ec0d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit fc1282ec68b346988203ead860e9b9d6a47e9efb
iuc
parents: 2
diff changeset
21 <param name="input_filename_file" type="data" format="cnr" label="Bin-Level log2 Ratios/Coverages cnr file" help="The output of the CNVkit fix" />
d889cf77ec0d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit fc1282ec68b346988203ead860e9b9d6a47e9efb
iuc
parents: 2
diff changeset
22 <param name="input_segment_file" type="data" format="cns" label="CN segmentation calls cns file" help="The output of the CNVkit segment" />
0
ef9a50eb20ce planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit e927b17a345b18c1b51dc1b112db5129278dcd22
iuc
parents:
diff changeset
23 <param argument="--min-probes" optional="true" type="integer" label="Minimum propes" value="1" help="Minimum number of covered probes to label a gene" />
ef9a50eb20ce planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit e927b17a345b18c1b51dc1b112db5129278dcd22
iuc
parents:
diff changeset
24 </inputs>
ef9a50eb20ce planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit e927b17a345b18c1b51dc1b112db5129278dcd22
iuc
parents:
diff changeset
25 <outputs>
2
384fa596e5d9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit 9d922676808c5f57e9c01b148eec6cc0a63c53e5
iuc
parents: 0
diff changeset
26 <data name="gene_breaks" format="txt" label="${tool.name} on ${on_string}:genes with copy number breakpoints" from_work_dir="gene-breaks.txt" />
0
ef9a50eb20ce planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit e927b17a345b18c1b51dc1b112db5129278dcd22
iuc
parents:
diff changeset
27 </outputs>
ef9a50eb20ce planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit e927b17a345b18c1b51dc1b112db5129278dcd22
iuc
parents:
diff changeset
28 <tests>
ef9a50eb20ce planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit e927b17a345b18c1b51dc1b112db5129278dcd22
iuc
parents:
diff changeset
29 <test expect_num_outputs="1">
4
d889cf77ec0d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit fc1282ec68b346988203ead860e9b9d6a47e9efb
iuc
parents: 2
diff changeset
30 <param name="input_filename_file" ftype="cnr" value="sample.cnr" />
d889cf77ec0d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit fc1282ec68b346988203ead860e9b9d6a47e9efb
iuc
parents: 2
diff changeset
31 <param name="input_segment_file" ftype="cns" value="sample.cns" />
0
ef9a50eb20ce planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit e927b17a345b18c1b51dc1b112db5129278dcd22
iuc
parents:
diff changeset
32 <param name="min_probes" value="1" />
ef9a50eb20ce planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit e927b17a345b18c1b51dc1b112db5129278dcd22
iuc
parents:
diff changeset
33 <output name="gene_breaks">
ef9a50eb20ce planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit e927b17a345b18c1b51dc1b112db5129278dcd22
iuc
parents:
diff changeset
34 <assert_contents><has_text text="chromosome"/></assert_contents>
ef9a50eb20ce planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit e927b17a345b18c1b51dc1b112db5129278dcd22
iuc
parents:
diff changeset
35 </output>
ef9a50eb20ce planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit e927b17a345b18c1b51dc1b112db5129278dcd22
iuc
parents:
diff changeset
36 </test>
ef9a50eb20ce planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit e927b17a345b18c1b51dc1b112db5129278dcd22
iuc
parents:
diff changeset
37 </tests>
ef9a50eb20ce planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit e927b17a345b18c1b51dc1b112db5129278dcd22
iuc
parents:
diff changeset
38 <help><![CDATA[
ef9a50eb20ce planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit e927b17a345b18c1b51dc1b112db5129278dcd22
iuc
parents:
diff changeset
39
ef9a50eb20ce planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit e927b17a345b18c1b51dc1b112db5129278dcd22
iuc
parents:
diff changeset
40 Identify genes in which:
ef9a50eb20ce planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit e927b17a345b18c1b51dc1b112db5129278dcd22
iuc
parents:
diff changeset
41 (I) an unbalanced fusion or other structural rearrangement breakpoint occured
ef9a50eb20ce planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit e927b17a345b18c1b51dc1b112db5129278dcd22
iuc
parents:
diff changeset
42 (II) CNV calling is simply difficult due to an inconsistent copy number signal
ef9a50eb20ce planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit e927b17a345b18c1b51dc1b112db5129278dcd22
iuc
parents:
diff changeset
43
ef9a50eb20ce planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit e927b17a345b18c1b51dc1b112db5129278dcd22
iuc
parents:
diff changeset
44 The breaks output is a text table of tab-separated values, which is amenable to further processing by
ef9a50eb20ce planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit e927b17a345b18c1b51dc1b112db5129278dcd22
iuc
parents:
diff changeset
45 scripts and standard Unix tools such as grep, sort, cut and awk.
4
d889cf77ec0d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit fc1282ec68b346988203ead860e9b9d6a47e9efb
iuc
parents: 2
diff changeset
46
d889cf77ec0d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit fc1282ec68b346988203ead860e9b9d6a47e9efb
iuc
parents: 2
diff changeset
47 -----
d889cf77ec0d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit fc1282ec68b346988203ead860e9b9d6a47e9efb
iuc
parents: 2
diff changeset
48
d889cf77ec0d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit fc1282ec68b346988203ead860e9b9d6a47e9efb
iuc
parents: 2
diff changeset
49 **Bin-level log2 ratios (.cnr)**
d889cf77ec0d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit fc1282ec68b346988203ead860e9b9d6a47e9efb
iuc
parents: 2
diff changeset
50
d889cf77ec0d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit fc1282ec68b346988203ead860e9b9d6a47e9efb
iuc
parents: 2
diff changeset
51 Tabular file containing normalized log2 ratios for small genomic bins (divided regions of the genome). Used to detect raw copy number variations (CNVs) before segmentation.
d889cf77ec0d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit fc1282ec68b346988203ead860e9b9d6a47e9efb
iuc
parents: 2
diff changeset
52
d889cf77ec0d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit fc1282ec68b346988203ead860e9b9d6a47e9efb
iuc
parents: 2
diff changeset
53 .. csv-table::
d889cf77ec0d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit fc1282ec68b346988203ead860e9b9d6a47e9efb
iuc
parents: 2
diff changeset
54 :header-rows: 0
d889cf77ec0d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit fc1282ec68b346988203ead860e9b9d6a47e9efb
iuc
parents: 2
diff changeset
55
d889cf77ec0d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit fc1282ec68b346988203ead860e9b9d6a47e9efb
iuc
parents: 2
diff changeset
56 "chromosome","Genomic chromosome (e.g., chr1, chrX)"
d889cf77ec0d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit fc1282ec68b346988203ead860e9b9d6a47e9efb
iuc
parents: 2
diff changeset
57 "start","Start position of the bin."
d889cf77ec0d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit fc1282ec68b346988203ead860e9b9d6a47e9efb
iuc
parents: 2
diff changeset
58 "end","End position of the bin."
d889cf77ec0d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit fc1282ec68b346988203ead860e9b9d6a47e9efb
iuc
parents: 2
diff changeset
59 "gene","Gene name(s) overlapping the bin (if applicable)."
d889cf77ec0d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit fc1282ec68b346988203ead860e9b9d6a47e9efb
iuc
parents: 2
diff changeset
60 "log2","Normalized log2 ratio (sample coverage / reference coverage)."
d889cf77ec0d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit fc1282ec68b346988203ead860e9b9d6a47e9efb
iuc
parents: 2
diff changeset
61 "depth","Average read depth in the bin."
d889cf77ec0d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit fc1282ec68b346988203ead860e9b9d6a47e9efb
iuc
parents: 2
diff changeset
62 "weight","Reliability weight of the bin (higher = more reliable)."
d889cf77ec0d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit fc1282ec68b346988203ead860e9b9d6a47e9efb
iuc
parents: 2
diff changeset
63
d889cf77ec0d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit fc1282ec68b346988203ead860e9b9d6a47e9efb
iuc
parents: 2
diff changeset
64 -----
d889cf77ec0d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit fc1282ec68b346988203ead860e9b9d6a47e9efb
iuc
parents: 2
diff changeset
65
d889cf77ec0d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit fc1282ec68b346988203ead860e9b9d6a47e9efb
iuc
parents: 2
diff changeset
66 **Segmented log2 ratios (.cns)**
d889cf77ec0d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit fc1282ec68b346988203ead860e9b9d6a47e9efb
iuc
parents: 2
diff changeset
67
d889cf77ec0d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit fc1282ec68b346988203ead860e9b9d6a47e9efb
iuc
parents: 2
diff changeset
68 Tabular file with smoothed, merged segments of stable copy number, derived from the .cnr file. Represents final CNV calls.
d889cf77ec0d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit fc1282ec68b346988203ead860e9b9d6a47e9efb
iuc
parents: 2
diff changeset
69
d889cf77ec0d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit fc1282ec68b346988203ead860e9b9d6a47e9efb
iuc
parents: 2
diff changeset
70 .. csv-table::
d889cf77ec0d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit fc1282ec68b346988203ead860e9b9d6a47e9efb
iuc
parents: 2
diff changeset
71 :header-rows: 0
d889cf77ec0d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit fc1282ec68b346988203ead860e9b9d6a47e9efb
iuc
parents: 2
diff changeset
72
d889cf77ec0d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit fc1282ec68b346988203ead860e9b9d6a47e9efb
iuc
parents: 2
diff changeset
73 "chromosome","start, end: Genomic coordinates of the segment"
d889cf77ec0d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit fc1282ec68b346988203ead860e9b9d6a47e9efb
iuc
parents: 2
diff changeset
74 "gene","Gene(s) overlapping the segment."
d889cf77ec0d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit fc1282ec68b346988203ead860e9b9d6a47e9efb
iuc
parents: 2
diff changeset
75 "log2","Mean log2 ratio of the segment."
d889cf77ec0d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit fc1282ec68b346988203ead860e9b9d6a47e9efb
iuc
parents: 2
diff changeset
76 "probes","Mean log2 ratio of the segment."
d889cf77ec0d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit fc1282ec68b346988203ead860e9b9d6a47e9efb
iuc
parents: 2
diff changeset
77 "depth","Average read depth."
d889cf77ec0d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit fc1282ec68b346988203ead860e9b9d6a47e9efb
iuc
parents: 2
diff changeset
78 "weight","Reliability weight."
d889cf77ec0d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit fc1282ec68b346988203ead860e9b9d6a47e9efb
iuc
parents: 2
diff changeset
79 "p_value","Statistical confidence (lower = more significant)."
d889cf77ec0d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit fc1282ec68b346988203ead860e9b9d6a47e9efb
iuc
parents: 2
diff changeset
80
0
ef9a50eb20ce planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit e927b17a345b18c1b51dc1b112db5129278dcd22
iuc
parents:
diff changeset
81 ]]></help>
ef9a50eb20ce planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit e927b17a345b18c1b51dc1b112db5129278dcd22
iuc
parents:
diff changeset
82 <expand macro="citations" />
ef9a50eb20ce planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit e927b17a345b18c1b51dc1b112db5129278dcd22
iuc
parents:
diff changeset
83 </tool>
ef9a50eb20ce planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit e927b17a345b18c1b51dc1b112db5129278dcd22
iuc
parents:
diff changeset
84
ef9a50eb20ce planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit e927b17a345b18c1b51dc1b112db5129278dcd22
iuc
parents:
diff changeset
85
ef9a50eb20ce planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit e927b17a345b18c1b51dc1b112db5129278dcd22
iuc
parents:
diff changeset
86
ef9a50eb20ce planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit e927b17a345b18c1b51dc1b112db5129278dcd22
iuc
parents:
diff changeset
87