Mercurial > repos > stephenshank > assemblyqc
changeset 0:48a6ea2de0da draft default tip
planemo upload commit 3a0a853d0f21f2eac12b959d1eba7ee9fa289cc3-dirty
author | stephenshank |
---|---|
date | Wed, 28 Jun 2023 16:22:28 +0000 |
parents | |
children | |
files | bamtocov.xml regal.xml |
diffstat | 2 files changed, 90 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/bamtocov.xml Wed Jun 28 16:22:28 2023 +0000 @@ -0,0 +1,49 @@ +<tool id="bamtocov" name="BAM to Coverage" version="1.0" profile="21.05"> + <description>Get a BED file of coverage from a BAM</description> + <requirements> + <requirement type="package" version="2.7.0">bamtocov</requirement> + </requirements> + <command detect_errors="exit_code"><![CDATA[ + bamtocov '$bam' > '$bed' + ]]> + </command> + <inputs> + <param argument="bam" type="data" format="bam" label="BAM file" help="BAM file to get coverage from."/> + </inputs> + <outputs> + <data name="bed" format="bed" label="${tool.name} on ${on_string}: Coverage"></data> + </outputs> + <tests> + </tests> + <help><![CDATA[ + + .. class:: infomark + +**Purpose** + +Calculate coverage from a BAM file. + +------ + + .. class:: infomark + +**Outputs** + +This tool generates a BED file containing coverage information from the associated BAM file. + ]]> + </help> + <citations> + <citation type="bibtex"> + @article{birolo2022bamtocov, + title={BamToCov: an efficient toolkit for sequence coverage calculations}, + author={Birolo, Giovanni and Telatin, Andrea}, + journal={Bioinformatics}, + volume={38}, + number={9}, + pages={2617--2618}, + year={2022}, + publisher={Oxford University Press} + } + </citation> + </citations> +</tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/regal.xml Wed Jun 28 16:22:28 2023 +0000 @@ -0,0 +1,41 @@ +<tool id="regal" name="Read-based evaluation of Genome Assemblies" version="1.0" profile="21.05"> + <description>Assembly statistics from a BED coverage file</description> + <requirements> + <requirement type="package" version="0.0.1">assemblyqc</requirement> + </requirements> + <command detect_errors="exit_code"><![CDATA[ + regal -c $bed -a $ref -o $json -p $percentiles + ]]> + </command> + <inputs> + <param argument="bed" type="data" format="bed" label="BED file" help="BED file containing coverage."/> + <param argument="ref" type="data" format="fasta" label="FASTA file" help="FASTA file of existing assembly."/> + <param argument="percentiles" type="text" label="Percentiles" help="Percentiles for assembly statistics (comma delimited)."/> + </inputs> + <outputs> + <data name="json" format="json" label="${tool.name} on ${on_string}: Assembly JSON"></data> + </outputs> + <tests> + </tests> + <help><![CDATA[ + + .. class:: infomark + +**Purpose** + +Calculate some statistics associated to assembly quality. + +------ + + .. class:: infomark + +**Outputs** + +This tool generates a JSON file containing contiguous regions and assembly statistics based on the +reads that were used to produce a given assembly. + ]]> + </help> + <citations> + </citations> +</tool> +