Mercurial > repos > richard-burhans > ncbi_egapx
changeset 16:d167f698d5e9 draft
planemo upload for repository https://github.com/richard-burhans/galaxytools/tree/main/tools/ncbi_egapx commit d5c4a9faa18df570d02ce208d301a160d8555f58
| author | richard-burhans |
|---|---|
| date | Sat, 16 Nov 2024 14:48:29 +0000 |
| parents | 815d401afcfe |
| children | e0de8669b340 |
| files | ncbi_egapx.xml |
| diffstat | 1 files changed, 22 insertions(+), 19 deletions(-) [+] |
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--- a/ncbi_egapx.xml Sat Nov 16 04:16:23 2024 +0000 +++ b/ncbi_egapx.xml Sat Nov 16 14:48:29 2024 +0000 @@ -24,16 +24,16 @@ <configfile name="egapx_config"><![CDATA[ #if str($cond_input_style.input_style) == "fillform" # yaml generated by ncbi_egapx.xml - #if str($reference_genome.genome_type_select) == "history" - #set genome_value = $reference_genome.genome - #elif str($reference_genome.genome_type_select) == "indexed" - #set genome_value = $reference_genome.genome.fields.path + #if str($cond_input_style.cond_genome_style.genome_style) == "history" + #set genome_value = $cond_input_style.cond_genome_style.genome + #elif str($cond_input_style.cond_genome_style.genome_style) == "indexed" + #set genome_value = $cond_input_style.cond_genome_style.genome.fields.path #else - #set genome_value = $reference_genome.uri + #set genome_value = $cond_input_style.cond_genome_style.uri #end if genome: $genome_value taxid: $taxid - #if str($condrnaseq.rna_type_select) == "list" + #if str($cond_rnaseq_style.rnaseq_style) == "list" #set $reads_values = $rnaseq.split() #else #set $reads_values = $rnaseq @@ -59,8 +59,8 @@ <option value="history">Use a pre-prepared yaml egapx configuration</option> </param> <when value="fillform"> - <conditional name="reference_genome"> - <param name="genome_type_select" type="select" label="Reference genome source for mapping supplied RNA-seq reads" + <conditional name="cond_genome_style"> + <param name="genome_style" type="select" label="Reference genome source for mapping supplied RNA-seq reads" help="Select a built in, history or remote URI for the reference genome FASTA"> <option value="history" selected="True">Use a genome FASTA file from the current history</option> <option value="indexed">Use a Galaxy server built-in genome</option> @@ -81,24 +81,27 @@ <param name="uri" type="text" label="URI pointing to the reference genome FASTA file"/> </when> </conditional> - <param name="taxid" type="integer" min="0" value="0" label="NCBI Taxon ID" help="Used to identify the HMM model files needed"/> + + <param name="taxid" type="text" label="NCBI Taxon ID" help="Used to identify the HMM model files needed"> + <validator type="regex" message="Numeric">^[0-9]+$</validator> + </param> - <conditional name="condrnaseq"> - <param name="rna_type_select" type="select" label="RNA sequence data source" + <conditional name="cond_rnaseq_style"> + <param name="rnaseq_style" 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> + <option value="history" selected="True">Select one or more RNA-seq fastq datasets from the current history</option> + <option value="list">Type in a list of SRA identifiers and/or remote RNA-seq FASTA URI</option> </param> + <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> <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,fasta.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" @@ -127,9 +130,9 @@ <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="genome_style" 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_style" 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="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>