# HG changeset patch
# User richard-burhans
# Date 1731768509 0
# Node ID d167f698d5e95e78b5e4adfeaedb699ddf694aea
# Parent  815d401afcfe212f6acb4c8d8bb8c92cef596fee
planemo upload for repository https://github.com/richard-burhans/galaxytools/tree/main/tools/ncbi_egapx commit d5c4a9faa18df570d02ce208d301a160d8555f58

diff -r 815d401afcfe -r d167f698d5e9 ncbi_egapx.xml
--- 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&#10;tasks:&#10;  star_wnode:&#10;    star_wnode: -cpus-per-worker 4"/>
             <output name="output"><assert_contents><has_size min="1"/></assert_contents></output>