Mercurial > repos > fubar > bbgbigwig_dev

annotate bam_bed_gff_to_bigwig.xml @ 4:78e7461e8946 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://www.encodeproject.org/software/bedgraphtobigwig/
author fubar
date Fri, 14 Jun 2024 23:46:42 +0000
parents 3899b3091d4a
children f132065ac170
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
3
3899b3091d4a planemo upload for repository https://www.encodeproject.org/software/bedgraphtobigwig/
fubar
parents: 2
diff changeset
1 <tool id="bbgtobigwig_dev" name="BAM BED GFF coverage bigWigs" version="0.1" profile="22.05">
3899b3091d4a planemo upload for repository https://www.encodeproject.org/software/bedgraphtobigwig/
fubar
parents: 2
diff changeset
2 <xrefs>
3899b3091d4a planemo upload for repository https://www.encodeproject.org/software/bedgraphtobigwig/
fubar
parents: 2
diff changeset
3 <xref type="bio.tools">UCSC_Genome_Browser_Utilities</xref>
3899b3091d4a planemo upload for repository https://www.encodeproject.org/software/bedgraphtobigwig/
fubar
parents: 2
diff changeset
4 </xrefs>
1
49c6f715bc82 planemo upload for repository https://www.encodeproject.org/software/bedgraphtobigwig/
fubar
parents:
diff changeset
5 <requirements>
49c6f715bc82 planemo upload for repository https://www.encodeproject.org/software/bedgraphtobigwig/
fubar
parents:
diff changeset
6 <requirement type="package" version="455">ucsc-bedgraphtobigwig</requirement>
49c6f715bc82 planemo upload for repository https://www.encodeproject.org/software/bedgraphtobigwig/
fubar
parents:
diff changeset
7 <requirement type="package" version="2.31.1">bedtools</requirement>
49c6f715bc82 planemo upload for repository https://www.encodeproject.org/software/bedgraphtobigwig/
fubar
parents:
diff changeset
8 <requirement type="package" version="9.5">coreutils</requirement>
49c6f715bc82 planemo upload for repository https://www.encodeproject.org/software/bedgraphtobigwig/
fubar
parents:
diff changeset
9 <requirement type="package" version="3.12.3">python</requirement>
49c6f715bc82 planemo upload for repository https://www.encodeproject.org/software/bedgraphtobigwig/
fubar
parents:
diff changeset
10 </requirements>
49c6f715bc82 planemo upload for repository https://www.encodeproject.org/software/bedgraphtobigwig/
fubar
parents:
diff changeset
11 <required_files>
49c6f715bc82 planemo upload for repository https://www.encodeproject.org/software/bedgraphtobigwig/
fubar
parents:
diff changeset
12 <include path="gff_to_bed_converter.py"/>
49c6f715bc82 planemo upload for repository https://www.encodeproject.org/software/bedgraphtobigwig/
fubar
parents:
diff changeset
13 </required_files>
49c6f715bc82 planemo upload for repository https://www.encodeproject.org/software/bedgraphtobigwig/
fubar
parents:
diff changeset
14 <command detect_errors="aggressive"><![CDATA[
49c6f715bc82 planemo upload for repository https://www.encodeproject.org/software/bedgraphtobigwig/
fubar
parents:
diff changeset
15 #if $hist_or_builtin.genosrc == "indexed":
49c6f715bc82 planemo upload for repository https://www.encodeproject.org/software/bedgraphtobigwig/
fubar
parents:
diff changeset
16 ln -s '$hist_or_builtin.chromfile.fields.len_path' ./CHROMFILE &&
49c6f715bc82 planemo upload for repository https://www.encodeproject.org/software/bedgraphtobigwig/
fubar
parents:
diff changeset
17 #else:
49c6f715bc82 planemo upload for repository https://www.encodeproject.org/software/bedgraphtobigwig/
fubar
parents:
diff changeset
18 ln -s '$chromfile' ./CHROMFILE &&
49c6f715bc82 planemo upload for repository https://www.encodeproject.org/software/bedgraphtobigwig/
fubar
parents:
diff changeset
19 #end if
49c6f715bc82 planemo upload for repository https://www.encodeproject.org/software/bedgraphtobigwig/
fubar
parents:
diff changeset
20 #if $input1.ext in ['gff', 'gff3']:
49c6f715bc82 planemo upload for repository https://www.encodeproject.org/software/bedgraphtobigwig/
fubar
parents:
diff changeset
21 python '$__tool_directory__/gff_to_bed_converter.py' < '$input1' > input2 &&
49c6f715bc82 planemo upload for repository https://www.encodeproject.org/software/bedgraphtobigwig/
fubar
parents:
diff changeset
22 #else:
49c6f715bc82 planemo upload for repository https://www.encodeproject.org/software/bedgraphtobigwig/
fubar
parents:
diff changeset
23 ln -s '$input1' input2 &&
49c6f715bc82 planemo upload for repository https://www.encodeproject.org/software/bedgraphtobigwig/
fubar
parents:
diff changeset
24 #end if
49c6f715bc82 planemo upload for repository https://www.encodeproject.org/software/bedgraphtobigwig/
fubar
parents:
diff changeset
25 #if $input1.ext == "bam":
49c6f715bc82 planemo upload for repository https://www.encodeproject.org/software/bedgraphtobigwig/
fubar
parents:
diff changeset
26 bedtools genomecov -bg -split -ibam input2 |
49c6f715bc82 planemo upload for repository https://www.encodeproject.org/software/bedgraphtobigwig/
fubar
parents:
diff changeset
27 #else
49c6f715bc82 planemo upload for repository https://www.encodeproject.org/software/bedgraphtobigwig/
fubar
parents:
diff changeset
28 bedtools genomecov -bg -i input2 -g ./CHROMFILE |
49c6f715bc82 planemo upload for repository https://www.encodeproject.org/software/bedgraphtobigwig/
fubar
parents:
diff changeset
29 #end if
49c6f715bc82 planemo upload for repository https://www.encodeproject.org/software/bedgraphtobigwig/
fubar
parents:
diff changeset
30 LC_COLLATE=C sort -k1,1 -k2,2n > temp.bg &&
49c6f715bc82 planemo upload for repository https://www.encodeproject.org/software/bedgraphtobigwig/
fubar
parents:
diff changeset
31 bedGraphToBigWig temp.bg ./CHROMFILE '$output'
49c6f715bc82 planemo upload for repository https://www.encodeproject.org/software/bedgraphtobigwig/
fubar
parents:
diff changeset
32 ]]></command>
49c6f715bc82 planemo upload for repository https://www.encodeproject.org/software/bedgraphtobigwig/
fubar
parents:
diff changeset
33 <inputs>
49c6f715bc82 planemo upload for repository https://www.encodeproject.org/software/bedgraphtobigwig/
fubar
parents:
diff changeset
34 <conditional name="hist_or_builtin">
49c6f715bc82 planemo upload for repository https://www.encodeproject.org/software/bedgraphtobigwig/
fubar
parents:
diff changeset
35 <param name="genosrc" type="select" label="Is the input assigned to a built-in or custom reference genome?"
49c6f715bc82 planemo upload for repository https://www.encodeproject.org/software/bedgraphtobigwig/
fubar
parents:
diff changeset
36 help="If the input has no dbkey, supply a chromosome lengths file">
49c6f715bc82 planemo upload for repository https://www.encodeproject.org/software/bedgraphtobigwig/
fubar
parents:
diff changeset
37 <option selected="True" value="indexed">Input data was made with a built-in genome or already has a custom genome dbkey</option>
49c6f715bc82 planemo upload for repository https://www.encodeproject.org/software/bedgraphtobigwig/
fubar
parents:
diff changeset
38 <option value="history">Input data mapped on a genome from the current history. The chromosome lengths file is also in the history</option>
49c6f715bc82 planemo upload for repository https://www.encodeproject.org/software/bedgraphtobigwig/
fubar
parents:
diff changeset
39 </param>
49c6f715bc82 planemo upload for repository https://www.encodeproject.org/software/bedgraphtobigwig/
fubar
parents:
diff changeset
40 <when value="indexed">
49c6f715bc82 planemo upload for repository https://www.encodeproject.org/software/bedgraphtobigwig/
fubar
parents:
diff changeset
41 <param name="input1" type="data" format="bam,unsorted.bam,bed,gff,gff3" label="bam/bed/gff to convert">
49c6f715bc82 planemo upload for repository https://www.encodeproject.org/software/bedgraphtobigwig/
fubar
parents:
diff changeset
42 <validator type="unspecified_build" />
49c6f715bc82 planemo upload for repository https://www.encodeproject.org/software/bedgraphtobigwig/
fubar
parents:
diff changeset
43 </param>
49c6f715bc82 planemo upload for repository https://www.encodeproject.org/software/bedgraphtobigwig/
fubar
parents:
diff changeset
44 <param name="chromfile" type="select" label="Source Genome Build">
49c6f715bc82 planemo upload for repository https://www.encodeproject.org/software/bedgraphtobigwig/
fubar
parents:
diff changeset
45 <options from_data_table="__dbkeys__">
49c6f715bc82 planemo upload for repository https://www.encodeproject.org/software/bedgraphtobigwig/
fubar
parents:
diff changeset
46 <filter type="data_meta" column="0" key="dbkey" ref="input1"/>
49c6f715bc82 planemo upload for repository https://www.encodeproject.org/software/bedgraphtobigwig/
fubar
parents:
diff changeset
47 </options>
49c6f715bc82 planemo upload for repository https://www.encodeproject.org/software/bedgraphtobigwig/
fubar
parents:
diff changeset
48 <validator type="no_options" message="The chosen genome build is not available."/>
49c6f715bc82 planemo upload for repository https://www.encodeproject.org/software/bedgraphtobigwig/
fubar
parents:
diff changeset
49 </param>
49c6f715bc82 planemo upload for repository https://www.encodeproject.org/software/bedgraphtobigwig/
fubar
parents:
diff changeset
50 </when>
49c6f715bc82 planemo upload for repository https://www.encodeproject.org/software/bedgraphtobigwig/
fubar
parents:
diff changeset
51 <when value="history">
49c6f715bc82 planemo upload for repository https://www.encodeproject.org/software/bedgraphtobigwig/
fubar
parents:
diff changeset
52 <param name="input1" type="data" format="bam,unsorted.bam,bed,gff,gff3" label="bam/bed/gff to convert"/>
49c6f715bc82 planemo upload for repository https://www.encodeproject.org/software/bedgraphtobigwig/
fubar
parents:
diff changeset
53 <param name="chromfile" type="data" format="len,txt,tabular" label="Chromosome length file"
49c6f715bc82 planemo upload for repository https://www.encodeproject.org/software/bedgraphtobigwig/
fubar
parents:
diff changeset
54 help="Sequence lengths for the history reference are required to make a bigwig. Compute sequence length tool makes these from fasta files"/>
49c6f715bc82 planemo upload for repository https://www.encodeproject.org/software/bedgraphtobigwig/
fubar
parents:
diff changeset
55 </when>
49c6f715bc82 planemo upload for repository https://www.encodeproject.org/software/bedgraphtobigwig/
fubar
parents:
diff changeset
56 </conditional>
49c6f715bc82 planemo upload for repository https://www.encodeproject.org/software/bedgraphtobigwig/
fubar
parents:
diff changeset
57 </inputs>
49c6f715bc82 planemo upload for repository https://www.encodeproject.org/software/bedgraphtobigwig/
fubar
parents:
diff changeset
58 <outputs>
49c6f715bc82 planemo upload for repository https://www.encodeproject.org/software/bedgraphtobigwig/
fubar
parents:
diff changeset
59 <data name="output" format="bigwig"/>
49c6f715bc82 planemo upload for repository https://www.encodeproject.org/software/bedgraphtobigwig/
fubar
parents:
diff changeset
60 </outputs>
49c6f715bc82 planemo upload for repository https://www.encodeproject.org/software/bedgraphtobigwig/
fubar
parents:
diff changeset
61 <tests>
49c6f715bc82 planemo upload for repository https://www.encodeproject.org/software/bedgraphtobigwig/
fubar
parents:
diff changeset
62 <test expect_num_outputs="1">
49c6f715bc82 planemo upload for repository https://www.encodeproject.org/software/bedgraphtobigwig/
fubar
parents:
diff changeset
63 <conditional name="hist_or_builtin">
49c6f715bc82 planemo upload for repository https://www.encodeproject.org/software/bedgraphtobigwig/
fubar
parents:
diff changeset
64 <param name="genosrc" value="indexed"/>
49c6f715bc82 planemo upload for repository https://www.encodeproject.org/software/bedgraphtobigwig/
fubar
parents:
diff changeset
65 <param name="input1" value="featureCounts_input1.bam" dbkey="hg38"/>
49c6f715bc82 planemo upload for repository https://www.encodeproject.org/software/bedgraphtobigwig/
fubar
parents:
diff changeset
66 <param name="chromfile" value="hg38"/>
49c6f715bc82 planemo upload for repository https://www.encodeproject.org/software/bedgraphtobigwig/
fubar
parents:
diff changeset
67 </conditional>
49c6f715bc82 planemo upload for repository https://www.encodeproject.org/software/bedgraphtobigwig/
fubar
parents:
diff changeset
68 <output name="output" value="featureCounts_input1.bigwig" compare="sim_size"/>
49c6f715bc82 planemo upload for repository https://www.encodeproject.org/software/bedgraphtobigwig/
fubar
parents:
diff changeset
69 </test>
49c6f715bc82 planemo upload for repository https://www.encodeproject.org/software/bedgraphtobigwig/
fubar
parents:
diff changeset
70 <test expect_num_outputs="1">
49c6f715bc82 planemo upload for repository https://www.encodeproject.org/software/bedgraphtobigwig/
fubar
parents:
diff changeset
71 <conditional name="hist_or_builtin">
49c6f715bc82 planemo upload for repository https://www.encodeproject.org/software/bedgraphtobigwig/
fubar
parents:
diff changeset
72 <param name="genosrc" value="history"/>
49c6f715bc82 planemo upload for repository https://www.encodeproject.org/software/bedgraphtobigwig/
fubar
parents:
diff changeset
73 <param name="input1" value="srma_out2.bam"/>
49c6f715bc82 planemo upload for repository https://www.encodeproject.org/software/bedgraphtobigwig/
fubar
parents:
diff changeset
74 <param name="chromfile" value="testing.len"/>
49c6f715bc82 planemo upload for repository https://www.encodeproject.org/software/bedgraphtobigwig/
fubar
parents:
diff changeset
75 </conditional>
49c6f715bc82 planemo upload for repository https://www.encodeproject.org/software/bedgraphtobigwig/
fubar
parents:
diff changeset
76 <output name="output" value="srma_out2.bigwig" compare="sim_size"/>
49c6f715bc82 planemo upload for repository https://www.encodeproject.org/software/bedgraphtobigwig/
fubar
parents:
diff changeset
77 </test>
49c6f715bc82 planemo upload for repository https://www.encodeproject.org/software/bedgraphtobigwig/
fubar
parents:
diff changeset
78 <test expect_num_outputs="1">
49c6f715bc82 planemo upload for repository https://www.encodeproject.org/software/bedgraphtobigwig/
fubar
parents:
diff changeset
79 <conditional name="hist_or_builtin">
49c6f715bc82 planemo upload for repository https://www.encodeproject.org/software/bedgraphtobigwig/
fubar
parents:
diff changeset
80 <param name="genosrc" value="history"/>
49c6f715bc82 planemo upload for repository https://www.encodeproject.org/software/bedgraphtobigwig/
fubar
parents:
diff changeset
81 <param name="input1" value="test5.gff3"/>
49c6f715bc82 planemo upload for repository https://www.encodeproject.org/software/bedgraphtobigwig/
fubar
parents:
diff changeset
82 <param name="chromfile" value="testing.len"/>
49c6f715bc82 planemo upload for repository https://www.encodeproject.org/software/bedgraphtobigwig/
fubar
parents:
diff changeset
83 </conditional>
49c6f715bc82 planemo upload for repository https://www.encodeproject.org/software/bedgraphtobigwig/
fubar
parents:
diff changeset
84 <output name="output" value="test5.gff.bigwig" compare="sim_size"/>
49c6f715bc82 planemo upload for repository https://www.encodeproject.org/software/bedgraphtobigwig/
fubar
parents:
diff changeset
85 </test>
49c6f715bc82 planemo upload for repository https://www.encodeproject.org/software/bedgraphtobigwig/
fubar
parents:
diff changeset
86 <test expect_num_outputs="1">
49c6f715bc82 planemo upload for repository https://www.encodeproject.org/software/bedgraphtobigwig/
fubar
parents:
diff changeset
87 <conditional name="hist_or_builtin">
49c6f715bc82 planemo upload for repository https://www.encodeproject.org/software/bedgraphtobigwig/
fubar
parents:
diff changeset
88 <param name="genosrc" value="history"/>
49c6f715bc82 planemo upload for repository https://www.encodeproject.org/software/bedgraphtobigwig/
fubar
parents:
diff changeset
89 <param name="input1" value="test5.bed"/>
49c6f715bc82 planemo upload for repository https://www.encodeproject.org/software/bedgraphtobigwig/
fubar
parents:
diff changeset
90 <param name="chromfile" value="testing.len"/>
49c6f715bc82 planemo upload for repository https://www.encodeproject.org/software/bedgraphtobigwig/
fubar
parents:
diff changeset
91 </conditional>
49c6f715bc82 planemo upload for repository https://www.encodeproject.org/software/bedgraphtobigwig/
fubar
parents:
diff changeset
92 <output name="output" value="test5.bed.bigwig" compare="sim_size"/>
49c6f715bc82 planemo upload for repository https://www.encodeproject.org/software/bedgraphtobigwig/
fubar
parents:
diff changeset
93 </test>
49c6f715bc82 planemo upload for repository https://www.encodeproject.org/software/bedgraphtobigwig/
fubar
parents:
diff changeset
94 </tests>
49c6f715bc82 planemo upload for repository https://www.encodeproject.org/software/bedgraphtobigwig/
fubar
parents:
diff changeset
95 <help>
49c6f715bc82 planemo upload for repository https://www.encodeproject.org/software/bedgraphtobigwig/
fubar
parents:
diff changeset
96
49c6f715bc82 planemo upload for repository https://www.encodeproject.org/software/bedgraphtobigwig/
fubar
parents:
diff changeset
97 Estimates coverage of a reference genome for bam, bed or gff as a bigwig, suitable for viewing in JBrowse2 or other browser.
49c6f715bc82 planemo upload for repository https://www.encodeproject.org/software/bedgraphtobigwig/
fubar
parents:
diff changeset
98
2
460f523c8ff4 planemo upload for repository https://www.encodeproject.org/software/bedgraphtobigwig/
fubar
parents: 1
diff changeset
99 A chromosome lengths file must be provided if the input has a missing dbkey='?' on the pencil (edit attributes) tab.
460f523c8ff4 planemo upload for repository https://www.encodeproject.org/software/bedgraphtobigwig/
fubar
parents: 1
diff changeset
100
460f523c8ff4 planemo upload for repository https://www.encodeproject.org/software/bedgraphtobigwig/
fubar
parents: 1
diff changeset
101 The actual reference is not needed. The Compute sequence length tool can generate the lengths file.
1
49c6f715bc82 planemo upload for repository https://www.encodeproject.org/software/bedgraphtobigwig/
fubar
parents:
diff changeset
102
49c6f715bc82 planemo upload for repository https://www.encodeproject.org/software/bedgraphtobigwig/
fubar
parents:
diff changeset
103 This can be useful in workflows with assemblies in progress before a stable reference is available for a custom or built in reference dbkey.
49c6f715bc82 planemo upload for repository https://www.encodeproject.org/software/bedgraphtobigwig/
fubar
parents:
diff changeset
104
49c6f715bc82 planemo upload for repository https://www.encodeproject.org/software/bedgraphtobigwig/
fubar
parents:
diff changeset
105 </help>
49c6f715bc82 planemo upload for repository https://www.encodeproject.org/software/bedgraphtobigwig/
fubar
parents:
diff changeset
106 <citations>
49c6f715bc82 planemo upload for repository https://www.encodeproject.org/software/bedgraphtobigwig/
fubar
parents:
diff changeset
107 <citation type="doi">10.1093/bioinformatics/btq351</citation>
49c6f715bc82 planemo upload for repository https://www.encodeproject.org/software/bedgraphtobigwig/
fubar
parents:
diff changeset
108 </citations>
49c6f715bc82 planemo upload for repository https://www.encodeproject.org/software/bedgraphtobigwig/
fubar
parents:
diff changeset
109 </tool>