Mercurial > repos > iuc > bbgbigwig

annotate bam_bed_gff_to_bigwig.xml @ 0:498748c87252 draft

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planemo upload for repository https://www.encodeproject.org/software/bedgraphtobigwig/ commit fa9d44f1ca94a7522f21db6c7771764e1b8d92a5
author iuc
date Fri, 14 Jun 2024 21:23:54 +0000
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498748c87252 planemo upload for repository https://www.encodeproject.org/software/bedgraphtobigwig/ commit fa9d44f1ca94a7522f21db6c7771764e1b8d92a5
iuc
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1 <tool id="bbgtobigwig" name="BAM BED GFF coverage bigWigs" version="0.1" profile="22.05">
498748c87252 planemo upload for repository https://www.encodeproject.org/software/bedgraphtobigwig/ commit fa9d44f1ca94a7522f21db6c7771764e1b8d92a5
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2 <xrefs>
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3 <xref type="bio.tools">UCSC_Genome_Browser_Utilities</xref>
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4 </xrefs>
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5 <requirements>
498748c87252 planemo upload for repository https://www.encodeproject.org/software/bedgraphtobigwig/ commit fa9d44f1ca94a7522f21db6c7771764e1b8d92a5
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6 <requirement type="package" version="455">ucsc-bedgraphtobigwig</requirement>
498748c87252 planemo upload for repository https://www.encodeproject.org/software/bedgraphtobigwig/ commit fa9d44f1ca94a7522f21db6c7771764e1b8d92a5
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7 <requirement type="package" version="2.31.1">bedtools</requirement>
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8 <requirement type="package" version="9.5">coreutils</requirement>
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9 <requirement type="package" version="3.12.3">python</requirement>
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10 </requirements>
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11 <required_files>
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12 <include path="gff_to_bed_converter.py"/>
498748c87252 planemo upload for repository https://www.encodeproject.org/software/bedgraphtobigwig/ commit fa9d44f1ca94a7522f21db6c7771764e1b8d92a5
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13 </required_files>
498748c87252 planemo upload for repository https://www.encodeproject.org/software/bedgraphtobigwig/ commit fa9d44f1ca94a7522f21db6c7771764e1b8d92a5
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14 <command detect_errors="aggressive"><![CDATA[
498748c87252 planemo upload for repository https://www.encodeproject.org/software/bedgraphtobigwig/ commit fa9d44f1ca94a7522f21db6c7771764e1b8d92a5
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15 #if $hist_or_builtin.genosrc == "indexed":
498748c87252 planemo upload for repository https://www.encodeproject.org/software/bedgraphtobigwig/ commit fa9d44f1ca94a7522f21db6c7771764e1b8d92a5
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16 ln -s '$hist_or_builtin.chromfile.fields.len_path' ./CHROMFILE &&
498748c87252 planemo upload for repository https://www.encodeproject.org/software/bedgraphtobigwig/ commit fa9d44f1ca94a7522f21db6c7771764e1b8d92a5
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17 #else:
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18 ln -s '$chromfile' ./CHROMFILE &&
498748c87252 planemo upload for repository https://www.encodeproject.org/software/bedgraphtobigwig/ commit fa9d44f1ca94a7522f21db6c7771764e1b8d92a5
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19 #end if
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20 #if $input1.ext in ['gff', 'gff3']:
498748c87252 planemo upload for repository https://www.encodeproject.org/software/bedgraphtobigwig/ commit fa9d44f1ca94a7522f21db6c7771764e1b8d92a5
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21 python '$__tool_directory__/gff_to_bed_converter.py' < '$input1' > input2 &&
498748c87252 planemo upload for repository https://www.encodeproject.org/software/bedgraphtobigwig/ commit fa9d44f1ca94a7522f21db6c7771764e1b8d92a5
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22 #else:
498748c87252 planemo upload for repository https://www.encodeproject.org/software/bedgraphtobigwig/ commit fa9d44f1ca94a7522f21db6c7771764e1b8d92a5
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23 ln -s '$input1' input2 &&
498748c87252 planemo upload for repository https://www.encodeproject.org/software/bedgraphtobigwig/ commit fa9d44f1ca94a7522f21db6c7771764e1b8d92a5
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24 #end if
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25 #if $input1.ext == "bam":
498748c87252 planemo upload for repository https://www.encodeproject.org/software/bedgraphtobigwig/ commit fa9d44f1ca94a7522f21db6c7771764e1b8d92a5
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26 bedtools genomecov -bg -split -ibam input2 |
498748c87252 planemo upload for repository https://www.encodeproject.org/software/bedgraphtobigwig/ commit fa9d44f1ca94a7522f21db6c7771764e1b8d92a5
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27 #else
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28 bedtools genomecov -bg -i input2 -g ./CHROMFILE |
498748c87252 planemo upload for repository https://www.encodeproject.org/software/bedgraphtobigwig/ commit fa9d44f1ca94a7522f21db6c7771764e1b8d92a5
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29 #end if
498748c87252 planemo upload for repository https://www.encodeproject.org/software/bedgraphtobigwig/ commit fa9d44f1ca94a7522f21db6c7771764e1b8d92a5
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30 LC_COLLATE=C sort -k1,1 -k2,2n > temp.bg &&
498748c87252 planemo upload for repository https://www.encodeproject.org/software/bedgraphtobigwig/ commit fa9d44f1ca94a7522f21db6c7771764e1b8d92a5
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31 bedGraphToBigWig temp.bg ./CHROMFILE '$output'
498748c87252 planemo upload for repository https://www.encodeproject.org/software/bedgraphtobigwig/ commit fa9d44f1ca94a7522f21db6c7771764e1b8d92a5
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32 ]]></command>
498748c87252 planemo upload for repository https://www.encodeproject.org/software/bedgraphtobigwig/ commit fa9d44f1ca94a7522f21db6c7771764e1b8d92a5
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33 <inputs>
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34 <conditional name="hist_or_builtin">
498748c87252 planemo upload for repository https://www.encodeproject.org/software/bedgraphtobigwig/ commit fa9d44f1ca94a7522f21db6c7771764e1b8d92a5
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35 <param name="genosrc" type="select" label="Is the input assigned to a built-in or custom reference genome?"
498748c87252 planemo upload for repository https://www.encodeproject.org/software/bedgraphtobigwig/ commit fa9d44f1ca94a7522f21db6c7771764e1b8d92a5
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36 help="If the input has no dbkey, supply a chromosome lengths file">
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37 <option selected="True" value="indexed">Input data was made with a built-in genome or already has a custom genome dbkey</option>
498748c87252 planemo upload for repository https://www.encodeproject.org/software/bedgraphtobigwig/ commit fa9d44f1ca94a7522f21db6c7771764e1b8d92a5
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38 <option value="history">Input data mapped on a genome from the current history. The chromosome lengths file is also in the history</option>
498748c87252 planemo upload for repository https://www.encodeproject.org/software/bedgraphtobigwig/ commit fa9d44f1ca94a7522f21db6c7771764e1b8d92a5
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39 </param>
498748c87252 planemo upload for repository https://www.encodeproject.org/software/bedgraphtobigwig/ commit fa9d44f1ca94a7522f21db6c7771764e1b8d92a5
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40 <when value="indexed">
498748c87252 planemo upload for repository https://www.encodeproject.org/software/bedgraphtobigwig/ commit fa9d44f1ca94a7522f21db6c7771764e1b8d92a5
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41 <param name="input1" type="data" format="bam,unsorted.bam,bed,gff,gff3" label="bam/bed/gff to convert">
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42 <validator type="unspecified_build" />
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43 </param>
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44 <param name="chromfile" type="select" label="Source Genome Build">
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45 <options from_data_table="__dbkeys__">
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46 <filter type="data_meta" column="0" key="dbkey" ref="input1"/>
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47 </options>
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48 <validator type="no_options" message="The chosen genome build is not available."/>
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49 </param>
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50 </when>
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51 <when value="history">
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52 <param name="input1" type="data" format="bam,unsorted.bam,bed,gff,gff3" label="bam/bed/gff to convert"/>
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53 <param name="chromfile" type="data" format="len,txt,tabular" label="Chromosome length file"
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54 help="Sequence lengths for the history reference are required to make a bigwig. Compute sequence length tool makes these from fasta files"/>
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55 </when>
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56 </conditional>
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57 </inputs>
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58 <outputs>
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59 <data name="output" format="bigwig"/>
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60 </outputs>
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61 <tests>
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62 <test expect_num_outputs="1">
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63 <conditional name="hist_or_builtin">
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64 <param name="genosrc" value="indexed"/>
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65 <param name="input1" value="featureCounts_input1.bam" dbkey="hg38"/>
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66 <param name="chromfile" value="hg38"/>
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67 </conditional>
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68 <output name="output" value="featureCounts_input1.bigwig" compare="sim_size"/>
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69 </test>
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70 <test expect_num_outputs="1">
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71 <conditional name="hist_or_builtin">
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72 <param name="genosrc" value="history"/>
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73 <param name="input1" value="srma_out2.bam"/>
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74 <param name="chromfile" value="testing.len"/>
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75 </conditional>
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76 <output name="output" value="srma_out2.bigwig" compare="sim_size"/>
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77 </test>
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78 <test expect_num_outputs="1">
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79 <conditional name="hist_or_builtin">
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80 <param name="genosrc" value="history"/>
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81 <param name="input1" value="test5.gff3"/>
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82 <param name="chromfile" value="testing.len"/>
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83 </conditional>
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84 <output name="output" value="test5.gff.bigwig" compare="sim_size"/>
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85 </test>
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86 <test expect_num_outputs="1">
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87 <conditional name="hist_or_builtin">
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88 <param name="genosrc" value="history"/>
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89 <param name="input1" value="test5.bed"/>
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90 <param name="chromfile" value="testing.len"/>
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91 </conditional>
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92 <output name="output" value="test5.bed.bigwig" compare="sim_size"/>
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93 </test>
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94 </tests>
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95 <help>
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96
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97 Estimates coverage of a reference genome for bam, bed or gff as a bigwig, suitable for viewing in JBrowse2 or other browser.
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98
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99 A chromosome lengths file must be provided if the input has a missing dbkey='?' on the pencil (edit attributes) tab.
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100
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101 The actual reference is not needed. The Compute sequence length tool can generate the lengths file.
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102
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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.
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104
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105 </help>
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106 <citations>
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107 <citation type="doi">10.1093/bioinformatics/btq351</citation>
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108 </citations>
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109 </tool>