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Update egapx (#43)
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@richard-burhans
richard-burhans authored Nov 16, 2024
1 parent 420f9c9 commit d5c4a9f
Showing 1 changed file with 22 additions and 19 deletions.
41 changes: 22 additions & 19 deletions tools/ncbi_egapx/ncbi_egapx.xml
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Original file line number Diff line number Diff line change
Expand Up @@ -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
Expand All @@ -59,8 +59,8 @@ $row
<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>
Expand All @@ -81,24 +81,27 @@ $row
<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"/>

<conditional name="condrnaseq">
<param name="rna_type_select" type="select" label="RNA sequence data source"
<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="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"
Expand Down Expand Up @@ -127,9 +130,9 @@ $row
<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&#10;tasks:&#10; star_wnode:&#10; star_wnode: -cpus-per-worker 4"/>
<output name="output"><assert_contents><has_size min="1"/></assert_contents></output>
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