# HG changeset patch
# User richard-burhans
# Date 1728929227 0
# Node ID 28ab345ebab3f97df1c8f68ad6bb75dab6155d7b
# Parent  908c494fa84e75e5ee175550d2ac7b5e79648de1
planemo upload for repository https://github.com/richard-burhans/galaxytools/tree/main/tools/ncbi_egapx commit 92ff2adad69b7a8a49d067e525a97f3ec25a275a

diff -r 908c494fa84e -r 28ab345ebab3 ncbi_egapx.xml
--- 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: []&#10;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>
-        <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: []&#10;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>
+            <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>