Mercurial > repos > richard-burhans > ncbi_egapx
diff ncbi_egapx.xml @ 9:28ab345ebab3 draft
planemo upload for repository https://github.com/richard-burhans/galaxytools/tree/main/tools/ncbi_egapx commit 92ff2adad69b7a8a49d067e525a97f3ec25a275a
| author | richard-burhans |
|---|---|
| date | Mon, 14 Oct 2024 18:07:07 +0000 |
| parents | 42734f3397cd |
| children | 5bec47dfe99a |
line wrap: on
line diff
--- a/ncbi_egapx.xml Fri Oct 11 20:03:16 2024 +0000 +++ b/ncbi_egapx.xml Mon Oct 14 18:07:07 2024 +0000 @@ -6,42 +6,43 @@ <expand macro="edam_ontology"/> <expand macro="requirements"/> <command detect_errors="aggressive"><![CDATA[ - #if str($cond_input_style.input_style) == "history": - #set yamlconfig = $yamlin + #if str($cond_input_style.input_style) == "fillform": + #set yamlconfig = "egapx.yaml" + echo '# yaml generated by ncbi_egapx.xml' > '$yamlconfig' && + #if str($reference_genome.genome_type_select) == "history" + echo 'genome: $reference_genome.genome' >> '$yamlconfig' && + #elif str($reference_genome.genome_type_select) == "indexed": + echo 'genome: $reference_genome.genome.fields.path' >> '$yamlconfig' && + #else: + echo 'genome: $reference_genome.uri' >> '$yamlconfig' && + #end if + echo 'taxid: $taxid' >> '$yamlconfig' && + echo 'reads:' >> '$yamlconfig' && + #if str($condrnaseq.rna_type_select) == "list": + #set rs = $rnaseq.split() + #set rsplit = [x.strip() for x in $rs] + #for $r in $rsplit: + echo ' - $r' >> '$yamlconfig' && + #end for + #else: + #for $r in $rnaseq: + echo ' - $r' >> '$yamlconfig' && + #end for + #end if + #if $proteins: + echo 'proteins: $proteins' >> '$yamlconfig' && + #end if + #if len($xtra.strip()) > 0: + #set lxtra = $xtra.split("\n") + #for row in $lxtra: + echo '$row' >> '$yamlconfig' && + #end for + #end if + echo '' >> '$yamlconfig' && + echo "Calculated contents of egapx yaml" && + cat '$yamlconfig' && #else: - #set yamlconfig = "egapx.yaml" - rm -rf '$yamlconfig' && - touch '$yamlconfig' && - echo '# yaml generated by ncbi_egapx.xml' >> '$yamlconfig' && - echo 'taxid: $taxid' >> '$yamlconfig' && - #if str($reference_genome.genome_type_select) == "indexed": - echo 'genome: $reference_genome.genome.fields.path' >> '$yamlconfig' && - #elif str($reference_genome.genome_type_select) == "history" - echo 'genome: $reference_genome.genome' >> '$yamlconfig' && - #else: - echo 'genome: $reference_genome.uri' >> '$yamlconfig' && - #end if - echo 'reads:' >> '$yamlconfig' && - #if str($condrnaseq.rna_type_select) == "history": - #for $r in $rnaseq: - echo ' - $r' >> '$yamlconfig' && - #end for - #else: - #set rs = $rnaseq.split() - #set rsplit = [x.strip() for x in $rs] - #for $r in $rsplit: - echo ' - $r' >> '$yamlconfig' && - #end for - #end if - #if len($xtra.strip()) > 0: - #set lxtra = $xtra.split("\n") - #for row in $lxtra: - echo '$row' >> '$yamlconfig' && - #end for - #end if - echo '' >> '$yamlconfig' && - echo "Calculated contents of egapx yaml" && - cat '$yamlconfig' && + #set yamlconfig = $yamlin #end if source /galaxy/env.bash && echo \${PATH} && @@ -49,107 +50,108 @@ python3 /galaxy/egapx/ui/egapx.py '$yamlconfig' -e galaxy -o 'egapx_out' ]]></command> <inputs> - <conditional name="cond_input_style"> - <param name="input_style" type="select" label="Fill in a tool form or use an existing yaml configuration from the current history?" - help="Use a pre-prepared yaml if available. Use the tool form if history files are needed as rna-seq or reference genome inputs for this job"> - <option selected="True" value="history">Use a pre-prepared yaml egapx configuration</option> - <option value="fillform">Provide configuration details for conversion into a configuration yaml</option> - </param> - <when value="history"> - <param name="yamlin" type="data" optional="false" label="egapx configuration yaml file to pass to Nextflow" help="" format="yaml,txt"/> - </when> - <when value="fillform"> - <param name="taxid" type="text" optional="false" label="NCBI Taxon ID" help="Used to identify the HMM model files needed"/> - <conditional name="reference_genome"> - <param name="genome_type_select" type="select" label="Reference genome source for mapping supplied RNA-seq reads" - help="Select a built in, history or remote URI for the reference genome fasta"> - <option value="indexed">Use a Galaxy server built-in genome</option> - <option value="history" selected="True">Use a genome fasta file from the current history</option> - <option value="uri">Provide a remote web link URI ("https://...") pointing at the required genome reference fasta file</option> - </param> - <when value="indexed"> - <param name="genome" type="select" optional="true" label="Select a built in reference genome or custom genome" - help="If not listed, add a custom genome or use a reference genome from the history"> - <options from_data_table="all_fasta"> - <validator message="No genomes are available " type="no_options"/> - </options> + <conditional name="cond_input_style"> + <param name="input_style" type="select" label="Fill in a tool form or use an existing yaml configuration from the current history?" + help="Use the tool form to select inputs from the history, or use a pre-prepared yaml file."> + <option value="fillform" selected="True">Provide configuration details for conversion into a configuration yaml</option> + <option value="history">Use a pre-prepared yaml egapx configuration</option> + </param> + <when value="fillform"> + <conditional name="reference_genome"> + <param name="genome_type_select" type="select" label="Reference genome source for mapping supplied RNA-seq reads" + help="Select a built in, history or remote URI for the reference genome fasta"> + <option value="history" selected="True">Use a genome fasta file from the current history</option> + <option value="indexed">Use a Galaxy server built-in genome</option> + <option value="uri">Provide a remote web link URI ("https://...") pointing at the required genome reference fasta file</option> + </param> + <when value="history"> + <param name="genome" type="data" format="fasta" label="Select the reference genome fasta from the current history"/> + </when> + <when value="indexed"> + <param name="genome" type="select" label="Select a built in reference genome or custom genome" + help="If not listed, add a custom genome or use a reference genome from the history"> + <options from_data_table="all_fasta"> + <validator message="No genomes are available " type="no_options"/> + </options> + </param> + </when> + <when value="uri"> + <param name="uri" type="text" label="URI pointing to the reference genome fasta file"/> + </when> + </conditional> + <param name="taxid" type="text" label="NCBI Taxon ID" help="Used to identify the HMM model files needed"/> + <conditional name="condrnaseq"> + <param name="rna_type_select" type="select" label="RNA sequence data source" + help="Select RNAseq input data from history or input a list of SRA identifiers or remote URI"> + <option value="list" selected="True">Type in a list of SRA identifiers and/or remote RNA-seq fasta URI</option> + <option value="history">Select one or more RNA-seq fastq datasets from the current history</option> + </param> + <when value="list"> + <param name="rnaseq" type="text" area="true" label="List all required individual RNA-seq URI or SRA identifiers, separated by spaces or newlines" + help="Either a working URI for a RNA-seq fasta, or a bare SRA identifier will work - can be mixed"> + <validator type="empty_field"/> + </param> + </when> + <when value="history"> + <param name="rnaseq" type="data" format="fastqsanger,fastqsanger.gz" multiple="true" label="Select multiple RNA-seq fastqsanger inputs from the current history" + help="All selected rna-seq fastqsanger will be added to the yaml for egapx configuration"/> + </when> + </conditional> + <param name="proteins" type="data" format="fasta,tasta.gz" optional="true" label="Select a protein set"/> + <param name="xtra" type="text" area="true" label="Additional yaml to append to the egapx.yaml configuration" + help="Not normally needed but useful for testing additional configuration elements"> + <sanitizer invalid_char=""> + <valid initial="string.printable"/> + </sanitizer> </param> </when> <when value="history"> - <param name="genome" type="data" optional="true" format="fasta" label="Select the reference genome fasta from the current history"/> - </when> - <when value="uri"> - <param name="uri" type="text" optional="false" label="URI pointing to the reference genome fasta file" help=""/> - </when> - </conditional> - <conditional name="condrnaseq"> - <param name="rna_type_select" type="select" label="RNA sequence data source" help="Select RNAseq input data from history or input a list of SRA identifiers or remote URI"> - <option selected="True" value="list">Type in a list of SRA identifiers and/or remote RNA-seq fasta URI</option> - <option value="history">Select one or more RNA-seq fastq datasets from the current history</option> - </param> - <when value="history"> - <param name="rnaseq" type="data" format="fastqsanger, fastqsanger.gz" optional="false" multiple="true" - label="Select multiple RNA-seq fastqsanger inputs from the current history" help="All selected rna-seq fastqsanger will be added to the yaml for egapx configuration"/> + <param name="yamlin" type="data" format="yaml,txt" label="egapx configuration yaml file to pass to Nextflow"/> </when> - <when value="list"> - <param name="rnaseq" type="text" area="true" optional="false" label="List all required individual RNA-seq URI or SRA identifiers, separated by spaces or newlines" - help="Either a working URI for a RNA-seq fasta, or a bare SRA identifier will work - can be mixed"> - <validator type="empty_field"/> - </param> - </when> - </conditional> - <param name="xtra" type="text" area="true" label="Additional yaml to append to the egapx.yaml configuration" - help="Not normally needed but useful for testing additional configuration elements"> - <sanitizer invalid_char=""> - <valid initial="string.printable"> - </valid> - </sanitizer> - </param> - </when> - </conditional> + </conditional> </inputs> <outputs> - <data name="output" format="gff" label="EGAPx annotation for ${on_string}" from_work_dir="egapx_out/accept.gff"/> - <collection name="nextflow_stats" label="EGAPx nextflow stats for ${on_string}" type="list"> - <data name="nf_log" format="txt" label="Nextflow execution log" from_work_dir="egapx_out/nextflow.log"/> - <data name="nf_report" format="html" label="Nextflow execution report" from_work_dir="egapx_out/run.report.html"/> - <data name="nf_trace" format="tabular" label="Nextflow trace file" from_work_dir="egapx_out/run.trace.txt"/> - <data name="nf_timeline" format="html" label="Nextflow execution timeline" from_work_dir="egapx_out/run.timeline.html"/> - <data name="nf_params" format="yaml" label="Nextflow run parameters" from_work_dir="egapx_out/run_params.yaml"/> - </collection> + <data name="output" format="gff" label="EGAPx annotation for ${on_string}" from_work_dir="egapx_out/accept.gff"/> + <collection name="nextflow_stats" type="list" label="EGAPx nextflow stats for ${on_string}"> + <data name="nf_log" format="txt" label="Nextflow execution log" from_work_dir="egapx_out/nextflow.log"/> + <data name="nf_report" format="html" label="Nextflow execution report" from_work_dir="egapx_out/run.report.html"/> + <data name="nf_trace" format="tabular" label="Nextflow trace file" from_work_dir="egapx_out/run.trace.txt"/> + <data name="nf_timeline" format="html" label="Nextflow execution timeline" from_work_dir="egapx_out/run.timeline.html"/> + <data name="nf_params" format="yaml" label="Nextflow run parameters" from_work_dir="egapx_out/run_params.yaml"/> + </collection> </outputs> <tests> - <test expect_test_failure="true"> - <param name="input_style" value="history"/> - <param name="yamlin" value="input.yaml"/> - <output name="output"><assert_contents><has_size min="1"/></assert_contents></output> - <output_collection name="nextflow_stats" type="list"> - <element name="nf_log"><assert_contents><has_size min="1"/></assert_contents></element> - <element name="nf_report"><assert_contents><has_size min="1"/></assert_contents></element> - <element name="nf_trace"><assert_contents><has_size min="1"/></assert_contents></element> - <element name="nf_timeline"><assert_contents><has_size min="1"/></assert_contents></element> - <element name="nf_params"><assert_contents><has_size min="1"/></assert_contents></element> - </output_collection> - </test> - <test expect_test_failure="true"> - <param name="input_style" value="fillform"/> - <param name="taxid" value="6954"/> - <param name="genome_type_select" value="uri"/> - <param name="uri" value="https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/020/809/275/GCF_020809275.1_ASM2080927v1/GCF_020809275.1_ASM2080927v1_genomic.fna.gz"/> - <param name="rna_type_select" value="list"/> - <param name="rnaseq" value="https://ftp.ncbi.nlm.nih.gov/genomes/TOOLS/EGAP/sample_data/Dermatophagoides_farinae_small/SRR8506572.1 https://ftp.ncbi.nlm.nih.gov/genomes/TOOLS/EGAP/sample_data/Dermatophagoides_farinae_small/SRR8506572.2 https://ftp.ncbi.nlm.nih.gov/genomes/TOOLS/EGAP/sample_data/Dermatophagoides_farinae_small/SRR9005248.1 https://ftp.ncbi.nlm.nih.gov/genomes/TOOLS/EGAP/sample_data/Dermatophagoides_farinae_small/SRR9005248.2"/> - <param name="xtra" value="proteins: [] hmm: https://ftp.ncbi.nlm.nih.gov/genomes/TOOLS/EGAP/gnomon/hmm_parameters/6956.params tasks: star_wnode: star_wnode: -cpus-per-worker 4"/> - <output name="output"><assert_contents><has_size min="1"/></assert_contents></output> - <output_collection name="nextflow_stats" type="list"> - <element name="nf_log"><assert_contents><has_size min="1"/></assert_contents></element> - <element name="nf_report"><assert_contents><has_size min="1"/></assert_contents></element> - <element name="nf_trace"><assert_contents><has_size min="1"/></assert_contents></element> - <element name="nf_timeline"><assert_contents><has_size min="1"/></assert_contents></element> - <element name="nf_params"><assert_contents><has_size min="1"/></assert_contents></element> - </output_collection> - </test> + <test expect_test_failure="true"> + <param name="input_style" value="history"/> + <param name="yamlin" value="input.yaml"/> + <output name="output"><assert_contents><has_size min="1"/></assert_contents></output> + <output_collection name="nextflow_stats" type="list"> + <element name="nf_log"><assert_contents><has_size min="1"/></assert_contents></element> + <element name="nf_report"><assert_contents><has_size min="1"/></assert_contents></element> + <element name="nf_trace"><assert_contents><has_size min="1"/></assert_contents></element> + <element name="nf_timeline"><assert_contents><has_size min="1"/></assert_contents></element> + <element name="nf_params"><assert_contents><has_size min="1"/></assert_contents></element> + </output_collection> + </test> + <test expect_test_failure="true"> + <param name="input_style" value="fillform"/> + <param name="taxid" value="6954"/> + <param name="genome_type_select" value="uri"/> + <param name="uri" value="https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/020/809/275/GCF_020809275.1_ASM2080927v1/GCF_020809275.1_ASM2080927v1_genomic.fna.gz"/> + <param name="rna_type_select" value="list"/> + <param name="rnaseq" value="https://ftp.ncbi.nlm.nih.gov/genomes/TOOLS/EGAP/sample_data/Dermatophagoides_farinae_small/SRR8506572.1 https://ftp.ncbi.nlm.nih.gov/genomes/TOOLS/EGAP/sample_data/Dermatophagoides_farinae_small/SRR8506572.2 https://ftp.ncbi.nlm.nih.gov/genomes/TOOLS/EGAP/sample_data/Dermatophagoides_farinae_small/SRR9005248.1 https://ftp.ncbi.nlm.nih.gov/genomes/TOOLS/EGAP/sample_data/Dermatophagoides_farinae_small/SRR9005248.2"/> + <param name="xtra" value="proteins: [] hmm: https://ftp.ncbi.nlm.nih.gov/genomes/TOOLS/EGAP/gnomon/hmm_parameters/6956.params tasks: star_wnode: star_wnode: -cpus-per-worker 4"/> + <output name="output"><assert_contents><has_size min="1"/></assert_contents></output> + <output_collection name="nextflow_stats" type="list"> + <element name="nf_log"><assert_contents><has_size min="1"/></assert_contents></element> + <element name="nf_report"><assert_contents><has_size min="1"/></assert_contents></element> + <element name="nf_trace"><assert_contents><has_size min="1"/></assert_contents></element> + <element name="nf_timeline"><assert_contents><has_size min="1"/></assert_contents></element> + <element name="nf_params"><assert_contents><has_size min="1"/></assert_contents></element> + </output_collection> + </test> </tests> - <help><![CDATA[ + <help><![CDATA[ Galaxy tool wrapping the Eukaryotic Genome Annotation Pipeline (EGAPx) ================================================================================================= @@ -306,8 +308,6 @@ 2024-03-27 11:20:25 1 .exitcode $ aws s3 ls s3://temp_datapath/D_farinae/96/621c4ba4e6e87a4d869c696fe50034/output/ 2024-03-27 11:20:24 17127134 aligns.paf - - - ]]></help> - <expand macro="citations"/> + ]]></help> + <expand macro="citations"/> </tool>