comparison bam_bed_gff_to_bigwig.xml @ 2:460f523c8ff4 draft

planemo upload for repository https://www.encodeproject.org/software/bedgraphtobigwig/

1:49c6f715bc82

<tool id="bbgtobigwig" name="Convert BAM/BED/GFF to BigWig" version="0.1" profile="22.05"> 
    <requirements>
        <requirement type="package" version="455">ucsc-bedgraphtobigwig</requirement>
        <requirement type="package" version="2.31.1">bedtools</requirement>
        <requirement type="package" version="9.5">coreutils</requirement> 
        <requirement type="package" version="3.12.3">python</requirement>

    </tests>
    <help>

   Estimates coverage of a reference genome for bam, bed or gff as a bigwig, suitable for viewing in JBrowse2 or other browser.
 
   If the input does not have a dbkey, a chromosome lengths file must be provided. The actual reference is not needed.
 
   This can be useful in workflows with assemblies in progress before a stable reference is available for a custom or built in reference dbkey.

    </help>    
    <citations>

2:460f523c8ff4

<tool id="bbgtobigwig" name="Convert BAM BED GFF to BigWig" version="0.1" profile="22.05"> 
    <requirements>
        <requirement type="package" version="455">ucsc-bedgraphtobigwig</requirement>
        <requirement type="package" version="2.31.1">bedtools</requirement>
        <requirement type="package" version="9.5">coreutils</requirement> 
        <requirement type="package" version="3.12.3">python</requirement>

    </tests>
    <help>

   Estimates coverage of a reference genome for bam, bed or gff as a bigwig, suitable for viewing in JBrowse2 or other browser.
 
   A chromosome lengths file must be provided if the input has a missing dbkey='?' on the pencil (edit attributes) tab. 
   
   The actual reference is not needed. The Compute sequence length tool can generate the lengths file.
 
   This can be useful in workflows with assemblies in progress before a stable reference is available for a custom or built in reference dbkey.

    </help>    
    <citations>