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adding a new test, small updates #30

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Sep 10, 2024
Merged

adding a new test, small updates #30

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2 changes: 1 addition & 1 deletion tools/ncbi_egapx/macros.xml
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Original file line number Diff line number Diff line change
Expand Up @@ -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>
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55 changes: 33 additions & 22 deletions tools/ncbi_egapx/ncbi_egapx.xml
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Original file line number Diff line number Diff line change
Expand Up @@ -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">
Expand All @@ -61,25 +61,25 @@
<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"/>
</options>
</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">
Expand All @@ -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">
Expand All @@ -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">
Expand All @@ -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: []&#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_collection name="egapx_out" type="list" count="8"/>
</test>
</tests>
<help><![CDATA[
Galaxy tool wrapping the Eukaryotic Genome Annotation Pipeline (EGAPx)
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