comparison egapx_runner.xml @ 8:1680e72e27be draft default tip

planemo upload for repository https://github.com/ncbi/egapx commit bdbe05027c2c40e217a2ff0c9e0556450c443e54

7:9c778770514f

<tool name="egapx_runner" id="egapx_runner" version="6.0.1" profile="22.05">
  <description>Runs egapx</description>
  <requirements>
    <requirement version="3.12.3" type="package">python</requirement>
    <requirement version="24.04.4-0" type="package">nextflow</requirement>
    <requirement version="6.0.1" type="package">pyyaml</requirement>
  </requirements>
  <version_command><![CDATA[echo "6.0.1"]]></version_command>
  <command><![CDATA[mkdir -p ./egapx_config &&
#set econfigfile = $econfig + '.config'
cp  '$__tool_directory__/ui/assets/config/executor/$econfigfile' ./egapx_config/ &&
python '$__tool_directory__/ui/egapx.py' '$yamlconfig' -e '$econfig' -o 'egapx_out']]></command>
  <inputs>

YAML sample configurations can be uploaded into your Galaxy history from the `EGAPx github repository <https://github.com/ncbi/egapx/tree/main/examples/>`_. 
The simplest possible example is shown below - can be cut/paste into a history dataset in the upload tool.


*./examples/input_D_farinae_small.yaml* is included in the examples linked above. RNA-seq data is provided as URI to the reads FASTA files.
These FASTA files are a sampling of the reads from the complete SRA read files to expedite testing. 

::

  genome: https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/020/809/275/GCF_020809275.1_ASM2080927v1/GCF_020809275.1_ASM2080927v1_genomic.fna.gz
  taxid: 6954

    - https://ftp.ncbi.nlm.nih.gov/genomes/TOOLS/EGAP/data/Dermatophagoides_farinae_small/SRR8506572.2
    - https://ftp.ncbi.nlm.nih.gov/genomes/TOOLS/EGAP/data/Dermatophagoides_farinae_small/SRR9005248.1
    - https://ftp.ncbi.nlm.nih.gov/genomes/TOOLS/EGAP/data/Dermatophagoides_farinae_small/SRR9005248.2



Purpose
========

**This is not intended for production** 

**Warning:**
The current version is an alpha release with limited features and organism scope to collect initial feedback on execution. Outputs are not yet complete and not intended for production use. Please open a GitHub [Issue](https://github.com/ncbi/egapx/issues)  if you encounter any problems with EGAPx. You can also write to [e-mail] to give us your feedback or if you have any questions.  

EGAPx is the publicly accessible version of the updated NCBI [Eukaryotic Genome Annotation Pipeline](https://www.ncbi.nlm.nih.gov/genome/annotation_euk/process/). 

EGAPx takes an assembly fasta file, a taxid of the organism, and RNA-seq data. Based on the taxid, EGAPx will pick protein sets and HMM models. The pipeline runs `miniprot` to align protein sequences, and `STAR` to align RNA-seq to the assembly. Protein alignments and RNA-seq read alignments are then passed to `Gnomon` for gene prediction. In the first step of `Gnomon`, the short alignments are chained together into putative gene models. In the second step, these predictions are further supplemented by _ab-initio_ predictions based on HMM models. The final annotation for the input assembly is produced as a `gff` file. 

**Security Notice:**

EGAPx has dependencies in and outside of its execution path that include several thousand files from the [NCBI C++ toolkit](https://www.ncbi.nlm.nih.gov/toolkit), and more than a million total lines of code. Static Application Security Testing has shown a small number of verified buffer overrun security vulnerabilities. Users should consult with their organizational security team on risk and if there is concern, consider mitigating options like running via VM or cloud instance. 

8:1680e72e27be

<tool name="egapx_runner" id="egapx_runner" version="@TOOL_VERSION@" profile="22.05">
  <description>Runs egapx</description>
  <macros>
    <token name="@TOOL_VERSION@">0.02-alpha</token>
  </macros>
  <requirements>
    <requirement version="3.12.3" type="package">python</requirement>
    <requirement version="24.04.4-0" type="package">nextflow</requirement>
    <requirement version="6.0.1" type="package">pyyaml</requirement>
  </requirements>
  <version_command><![CDATA[echo "@TOOL_VERSION@"]]></version_command>
  <command><![CDATA[mkdir -p ./egapx_config &&
#set econfigfile = $econfig + '.config'
cp  '$__tool_directory__/ui/assets/config/executor/$econfigfile' ./egapx_config/ &&
python '$__tool_directory__/ui/egapx.py' '$yamlconfig' -e '$econfig' -o 'egapx_out']]></command>
  <inputs>

YAML sample configurations can be uploaded into your Galaxy history from the `EGAPx github repository <https://github.com/ncbi/egapx/tree/main/examples/>`_. 
The simplest possible example is shown below - can be cut/paste into a history dataset in the upload tool.


*./examples/input_D_farinae_small.yaml* is shown below and can be cut and pasted into the upload form to create a yaml file. 
RNA-seq data is provided as URI to the reads FASTA files.

input_D_farinae_small.yaml

::

  genome: https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/020/809/275/GCF_020809275.1_ASM2080927v1/GCF_020809275.1_ASM2080927v1_genomic.fna.gz
  taxid: 6954

    - https://ftp.ncbi.nlm.nih.gov/genomes/TOOLS/EGAP/data/Dermatophagoides_farinae_small/SRR8506572.2
    - https://ftp.ncbi.nlm.nih.gov/genomes/TOOLS/EGAP/data/Dermatophagoides_farinae_small/SRR9005248.1
    - https://ftp.ncbi.nlm.nih.gov/genomes/TOOLS/EGAP/data/Dermatophagoides_farinae_small/SRR9005248.2


input_Gavia_stellata.yaml

::

  genome: https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/030/936/135/GCF_030936135.1_bGavSte3.hap2/GCF_030936135.1_bGavSte3.hap2_genomic.fna.gz
  reads: txid37040[Organism] AND biomol_transcript[properties] NOT SRS024887[Accession]
  taxid: 37040

input_C_longicornis.yaml

::

  genome: https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/029//603/195/GCF_029603195.1_ASM2960319v2/GCF_029603195.1_ASM2960319v2_genomic.fna.gz
  reads: txid2530218[Organism] AND biomol_transcript[properties] NOT SRS024887[Accession]
  taxid: 2530218
  
Purpose
========

**This is not intended for production** 

**Warning:**
The current version is an alpha release with limited features and organism scope to collect initial feedback on execution. Outputs are not yet complete and not intended for production use. Please open a GitHub [Issue](https://github.com/ncbi/egapx/issues)  if you encounter any problems with EGAPx. You can also write to [e-mail] to give us your feedback or if you have any questions.  

EGAPx is the publicly accessible version of the updated NCBI [Eukaryotic Genome Annotation Pipeline](https://www.ncbi.nlm.nih.gov/genome/annotation_euk/process/). 

EGAPx takes an assembly fasta file, a taxid of the organism, and RNA-seq data. Based on the taxid, EGAPx will pick protein sets and HMM models. The pipeline runs `miniprot` to align protein sequences, and `STAR` to align RNA-seq to the assembly. Protein alignments and RNA-seq read alignments are then passed to `Gnomon` for gene prediction. In the first step of `Gnomon`, the short alignments are chained together into putative gene models. 
In the second step, these predictions are further supplemented by *ab-initio* predictions based on HMM models. The final annotation for the input assembly is produced as a `gff` file. 

**Security Notice:**

EGAPx has dependencies in and outside of its execution path that include several thousand files from the [NCBI C++ toolkit](https://www.ncbi.nlm.nih.gov/toolkit), and more than a million total lines of code. Static Application Security Testing has shown a small number of verified buffer overrun security vulnerabilities. Users should consult with their organizational security team on risk and if there is concern, consider mitigating options like running via VM or cloud instance.