Mercurial > repos > richard-burhans > ncbi_egapx
changeset 4:539ea4dee35a draft
planemo upload for repository https://github.com/richard-burhans/galaxytools/tree/main/tools/ncbi_egapx commit f47ba0b127d52901402fe9f830a0095c6f8fa36a
| author | richard-burhans |
|---|---|
| date | Tue, 10 Sep 2024 20:09:41 +0000 |
| parents | 4420dd857c41 |
| children | bf80a7ed8595 |
| files | macros.xml ncbi_egapx.xml |
| diffstat | 2 files changed, 34 insertions(+), 23 deletions(-) [+] |
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--- a/macros.xml Mon Sep 09 22:07:18 2024 +0000 +++ b/macros.xml Tue Sep 10 20:09:41 2024 +0000 @@ -5,7 +5,7 @@ </requirements> </xml> <token name="@TOOL_VERSION@">0.2-alpha</token> - <token name="@VERSION_SUFFIX@">1</token> + <token name="@VERSION_SUFFIX@">2</token> <token name="@PROFILE@">22.05</token> <xml name="edam_ontology"> <edam_operations>
--- a/ncbi_egapx.xml Mon Sep 09 22:07:18 2024 +0000 +++ b/ncbi_egapx.xml Tue Sep 10 20:09:41 2024 +0000 @@ -9,44 +9,44 @@ #if str($cond_input_style.input_style) == "history": #set yamlconfig = $yamlin #else: - #set yamlconfig = 'egapx.yaml' - rm -rf 'egapx.yaml' && - touch 'egapx.yaml' && - echo '# yaml generated by ncbi_egapx.xml' >> egapx.yaml && - echo 'taxid: $taxid' >> egapx.yaml && + #set yamlconfig = "egapx.yaml" + rm -rf '$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' >> 'egapx.yaml' && + echo 'genome: $reference_genome.genome.fields.path' >> '$yamlconfig' && #elif str($reference_genome.genome_type_select) == "history" - echo 'genome: $reference_genome.genome' >> 'egapx.yaml' && + echo 'genome: $reference_genome.genome' >> '$yamlconfig' && #else: - echo 'genome: $reference_genome.uri' >> 'egapx.yaml' && + echo 'genome: $reference_genome.uri' >> '$yamlconfig' && #end if - echo 'reads:' >> 'egapx.yaml' && + echo 'reads:' >> '$yamlconfig' && #if str($condrnaseq.rna_type_select) == "history": #for $r in $rnaseq: - echo ' - $r' >> 'egapx.yaml' && + echo ' - $r' >> '$yamlconfig' && #end for #else: #set rs = $rnaseq.split() #set rsplit = [x.strip() for x in $rs] #for $r in $rsplit: - echo ' - $r' >> 'egapx.yaml' && + echo ' - $r' >> '$yamlconfig' && #end for #end if #if len($xtra.strip()) > 0: - #set lxtra = $xtra.split('\n') + #set lxtra = $xtra.split("\n") #for row in $lxtra: - echo '$row' >> 'egapx.yaml' && + echo '$row' >> '$yamlconfig' && #end for #end if - echo '' >> 'egapx.yaml' && + echo '' >> '$yamlconfig' && echo "Calculated contents of egapx yaml" && - cat 'egapx.yaml' && + cat '$yamlconfig' && #end if source /galaxy/env.bash && echo \${PATH} && ln -s /galaxy/egapx/egapx_config && - python3 /galaxy/egapx/ui/egapx.py '$yamlconfig' -e galaxy -o 'egapx_out' + python3 /galaxy/egapx/ui/egapx.py '$yamlconfig' -e galaxy -o 'egapx_out' ]]></command> <inputs> <conditional name="cond_input_style"> @@ -61,14 +61,14 @@ <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" + <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="false" label="Select a built in reference genome or custom genome" + <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"/> @@ -76,10 +76,10 @@ </param> </when> <when value="history"> - <param name="genome" type="data" format="fasta" optional="false" label="Select the reference genome fasta from the current 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" label="URI pointing to the reference genome fasta file" help=""/> + <param name="uri" type="text" optional="false" label="URI pointing to the reference genome fasta file" help=""/> </when> </conditional> <conditional name="condrnaseq"> @@ -88,7 +88,7 @@ <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" + <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"/> </when> <when value="list"> @@ -98,7 +98,7 @@ </param> </when> </conditional> - <param name="xtra" type="text" area="true" optional="true" label="Additional yaml to append to the egapx.yaml configuration" + <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"> @@ -115,9 +115,20 @@ </outputs> <tests> <test expect_test_failure="true"> + <param name="input_style" value="history"/> <param name="yamlin" value="input.yaml"/> <output_collection name="egapx_out" type="list" count="8"/> </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_collection name="egapx_out" type="list" count="8"/> + </test> </tests> <help><![CDATA[ Galaxy tool wrapping the Eukaryotic Genome Annotation Pipeline (EGAPx)