Mercurial > repos > iuc > cnvkit_breaks

annotate breaks.xml @ 3:9ff8e2b2cca1 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 11:48:14 +0000
parents 382f61e50156
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
27b8228a4d84 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">
27b8228a4d84 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>
27b8228a4d84 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit e927b17a345b18c1b51dc1b112db5129278dcd22
iuc
parents:
diff changeset
3 <macros>
27b8228a4d84 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>
27b8228a4d84 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit e927b17a345b18c1b51dc1b112db5129278dcd22
iuc
parents:
diff changeset
5 </macros>
27b8228a4d84 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit e927b17a345b18c1b51dc1b112db5129278dcd22
iuc
parents:
diff changeset
6 <expand macro="xrefs"/>
27b8228a4d84 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"/>
27b8228a4d84 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit e927b17a345b18c1b51dc1b112db5129278dcd22
iuc
parents:
diff changeset
8 <expand macro="requirements"/>
27b8228a4d84 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[
27b8228a4d84 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit e927b17a345b18c1b51dc1b112db5129278dcd22
iuc
parents:
diff changeset
10 ln -s '$input_filename_file' ./sample.cnr &&
27b8228a4d84 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit e927b17a345b18c1b51dc1b112db5129278dcd22
iuc
parents:
diff changeset
11 ln -s '$input_segment_file' ./sample.cns &&
27b8228a4d84 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit e927b17a345b18c1b51dc1b112db5129278dcd22
iuc
parents:
diff changeset
12 cnvkit.py breaks
27b8228a4d84 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit e927b17a345b18c1b51dc1b112db5129278dcd22
iuc
parents:
diff changeset
13 ./sample.cnr
27b8228a4d84 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit e927b17a345b18c1b51dc1b112db5129278dcd22
iuc
parents:
diff changeset
14 ./sample.cns
27b8228a4d84 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
27b8228a4d84 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit e927b17a345b18c1b51dc1b112db5129278dcd22
iuc
parents:
diff changeset
16 #if $min_probes
27b8228a4d84 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
27b8228a4d84 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit e927b17a345b18c1b51dc1b112db5129278dcd22
iuc
parents:
diff changeset
18 #end if
27b8228a4d84 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit e927b17a345b18c1b51dc1b112db5129278dcd22
iuc
parents:
diff changeset
19 ]]></command>
27b8228a4d84 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit e927b17a345b18c1b51dc1b112db5129278dcd22
iuc
parents:
diff changeset
20 <inputs>
3
9ff8e2b2cca1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit fc1282ec68b346988203ead860e9b9d6a47e9efb
iuc
parents: 1
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" />
9ff8e2b2cca1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit fc1282ec68b346988203ead860e9b9d6a47e9efb
iuc
parents: 1
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
27b8228a4d84 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" />
27b8228a4d84 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit e927b17a345b18c1b51dc1b112db5129278dcd22
iuc
parents:
diff changeset
24 </inputs>
27b8228a4d84 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit e927b17a345b18c1b51dc1b112db5129278dcd22
iuc
parents:
diff changeset
25 <outputs>
1
382f61e50156 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
27b8228a4d84 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit e927b17a345b18c1b51dc1b112db5129278dcd22
iuc
parents:
diff changeset
27 </outputs>
27b8228a4d84 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit e927b17a345b18c1b51dc1b112db5129278dcd22
iuc
parents:
diff changeset
28 <tests>
27b8228a4d84 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">
3
9ff8e2b2cca1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit fc1282ec68b346988203ead860e9b9d6a47e9efb
iuc
parents: 1
diff changeset
30 <param name="input_filename_file" ftype="cnr" value="sample.cnr" />
9ff8e2b2cca1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit fc1282ec68b346988203ead860e9b9d6a47e9efb
iuc
parents: 1
diff changeset
31 <param name="input_segment_file" ftype="cns" value="sample.cns" />
0
27b8228a4d84 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" />
27b8228a4d84 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">
27b8228a4d84 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>
27b8228a4d84 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit e927b17a345b18c1b51dc1b112db5129278dcd22
iuc
parents:
diff changeset
35 </output>
27b8228a4d84 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit e927b17a345b18c1b51dc1b112db5129278dcd22
iuc
parents:
diff changeset
36 </test>
27b8228a4d84 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit e927b17a345b18c1b51dc1b112db5129278dcd22
iuc
parents:
diff changeset
37 </tests>
27b8228a4d84 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit e927b17a345b18c1b51dc1b112db5129278dcd22
iuc
parents:
diff changeset
38 <help><![CDATA[
27b8228a4d84 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit e927b17a345b18c1b51dc1b112db5129278dcd22
iuc
parents:
diff changeset
39
27b8228a4d84 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:
27b8228a4d84 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
27b8228a4d84 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
27b8228a4d84 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit e927b17a345b18c1b51dc1b112db5129278dcd22
iuc
parents:
diff changeset
43
27b8228a4d84 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
27b8228a4d84 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.
3
9ff8e2b2cca1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit fc1282ec68b346988203ead860e9b9d6a47e9efb
iuc
parents: 1
diff changeset
46
9ff8e2b2cca1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit fc1282ec68b346988203ead860e9b9d6a47e9efb
iuc
parents: 1
diff changeset
47 -----
9ff8e2b2cca1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit fc1282ec68b346988203ead860e9b9d6a47e9efb
iuc
parents: 1
diff changeset
48
9ff8e2b2cca1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit fc1282ec68b346988203ead860e9b9d6a47e9efb
iuc
parents: 1
diff changeset
49 **Bin-level log2 ratios (.cnr)**
9ff8e2b2cca1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit fc1282ec68b346988203ead860e9b9d6a47e9efb
iuc
parents: 1
diff changeset
50
9ff8e2b2cca1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit fc1282ec68b346988203ead860e9b9d6a47e9efb
iuc
parents: 1
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.
9ff8e2b2cca1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit fc1282ec68b346988203ead860e9b9d6a47e9efb
iuc
parents: 1
diff changeset
52
9ff8e2b2cca1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit fc1282ec68b346988203ead860e9b9d6a47e9efb
iuc
parents: 1
diff changeset
53 .. csv-table::
9ff8e2b2cca1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit fc1282ec68b346988203ead860e9b9d6a47e9efb
iuc
parents: 1
diff changeset
54 :header-rows: 0
9ff8e2b2cca1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit fc1282ec68b346988203ead860e9b9d6a47e9efb
iuc
parents: 1
diff changeset
55
9ff8e2b2cca1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit fc1282ec68b346988203ead860e9b9d6a47e9efb
iuc
parents: 1
diff changeset
56 "chromosome","Genomic chromosome (e.g., chr1, chrX)"
9ff8e2b2cca1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit fc1282ec68b346988203ead860e9b9d6a47e9efb
iuc
parents: 1
diff changeset
57 "start","Start position of the bin."
9ff8e2b2cca1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit fc1282ec68b346988203ead860e9b9d6a47e9efb
iuc
parents: 1
diff changeset
58 "end","End position of the bin."
9ff8e2b2cca1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit fc1282ec68b346988203ead860e9b9d6a47e9efb
iuc
parents: 1
diff changeset
59 "gene","Gene name(s) overlapping the bin (if applicable)."
9ff8e2b2cca1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit fc1282ec68b346988203ead860e9b9d6a47e9efb
iuc
parents: 1
diff changeset
60 "log2","Normalized log2 ratio (sample coverage / reference coverage)."
9ff8e2b2cca1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit fc1282ec68b346988203ead860e9b9d6a47e9efb
iuc
parents: 1
diff changeset
61 "depth","Average read depth in the bin."
9ff8e2b2cca1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit fc1282ec68b346988203ead860e9b9d6a47e9efb
iuc
parents: 1
diff changeset
62 "weight","Reliability weight of the bin (higher = more reliable)."
9ff8e2b2cca1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit fc1282ec68b346988203ead860e9b9d6a47e9efb
iuc
parents: 1
diff changeset
63
9ff8e2b2cca1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit fc1282ec68b346988203ead860e9b9d6a47e9efb
iuc
parents: 1
diff changeset
64 -----
9ff8e2b2cca1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit fc1282ec68b346988203ead860e9b9d6a47e9efb
iuc
parents: 1
diff changeset
65
9ff8e2b2cca1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit fc1282ec68b346988203ead860e9b9d6a47e9efb
iuc
parents: 1
diff changeset
66 **Segmented log2 ratios (.cns)**
9ff8e2b2cca1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit fc1282ec68b346988203ead860e9b9d6a47e9efb
iuc
parents: 1
diff changeset
67
9ff8e2b2cca1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit fc1282ec68b346988203ead860e9b9d6a47e9efb
iuc
parents: 1
diff changeset
68 Tabular file with smoothed, merged segments of stable copy number, derived from the .cnr file. Represents final CNV calls.
9ff8e2b2cca1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit fc1282ec68b346988203ead860e9b9d6a47e9efb
iuc
parents: 1
diff changeset
69
9ff8e2b2cca1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit fc1282ec68b346988203ead860e9b9d6a47e9efb
iuc
parents: 1
diff changeset
70 .. csv-table::
9ff8e2b2cca1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit fc1282ec68b346988203ead860e9b9d6a47e9efb
iuc
parents: 1
diff changeset
71 :header-rows: 0
9ff8e2b2cca1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit fc1282ec68b346988203ead860e9b9d6a47e9efb
iuc
parents: 1
diff changeset
72
9ff8e2b2cca1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit fc1282ec68b346988203ead860e9b9d6a47e9efb
iuc
parents: 1
diff changeset
73 "chromosome","start, end: Genomic coordinates of the segment"
9ff8e2b2cca1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit fc1282ec68b346988203ead860e9b9d6a47e9efb
iuc
parents: 1
diff changeset
74 "gene","Gene(s) overlapping the segment."
9ff8e2b2cca1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit fc1282ec68b346988203ead860e9b9d6a47e9efb
iuc
parents: 1
diff changeset
75 "log2","Mean log2 ratio of the segment."
9ff8e2b2cca1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit fc1282ec68b346988203ead860e9b9d6a47e9efb
iuc
parents: 1
diff changeset
76 "probes","Mean log2 ratio of the segment."
9ff8e2b2cca1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit fc1282ec68b346988203ead860e9b9d6a47e9efb
iuc
parents: 1
diff changeset
77 "depth","Average read depth."
9ff8e2b2cca1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit fc1282ec68b346988203ead860e9b9d6a47e9efb
iuc
parents: 1
diff changeset
78 "weight","Reliability weight."
9ff8e2b2cca1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit fc1282ec68b346988203ead860e9b9d6a47e9efb
iuc
parents: 1
diff changeset
79 "p_value","Statistical confidence (lower = more significant)."
9ff8e2b2cca1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit fc1282ec68b346988203ead860e9b9d6a47e9efb
iuc
parents: 1
diff changeset
80
0
27b8228a4d84 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit e927b17a345b18c1b51dc1b112db5129278dcd22
iuc
parents:
diff changeset
81 ]]></help>
27b8228a4d84 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit e927b17a345b18c1b51dc1b112db5129278dcd22
iuc
parents:
diff changeset
82 <expand macro="citations" />
27b8228a4d84 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit e927b17a345b18c1b51dc1b112db5129278dcd22
iuc
parents:
diff changeset
83 </tool>
27b8228a4d84 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit e927b17a345b18c1b51dc1b112db5129278dcd22
iuc
parents:
diff changeset
84
27b8228a4d84 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit e927b17a345b18c1b51dc1b112db5129278dcd22
iuc
parents:
diff changeset
85
27b8228a4d84 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit e927b17a345b18c1b51dc1b112db5129278dcd22
iuc
parents:
diff changeset
86
27b8228a4d84 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit e927b17a345b18c1b51dc1b112db5129278dcd22
iuc
parents:
diff changeset
87