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comparison ncbi_egapx.xml @ 7:42734f3397cd draft

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planemo upload for repository https://github.com/richard-burhans/galaxytools/tree/main/tools/ncbi_egapx commit 6ae533b0ae510a4a856c14c79219e31a2837daab
author richard-burhans
date Fri, 11 Oct 2024 19:54:09 +0000
parents 539ea4dee35a
children 28ab345ebab3
comparison
equal deleted inserted replaced
6:3a8a37414e56 7:42734f3397cd
107 </param> 107 </param>
108 </when> 108 </when>
109 </conditional> 109 </conditional>
110 </inputs> 110 </inputs>
111 <outputs> 111 <outputs>
112 <collection name="egapx_out" type="list" label="Outputs from egapx"> 112 <data name="output" format="gff" label="EGAPx annotation for ${on_string}" from_work_dir="egapx_out/accept.gff"/>
113 <discover_datasets pattern="__name_and_ext__" directory="egapx_out" visible="false"/> 113 <collection name="nextflow_stats" label="EGAPx nextflow stats for ${on_string}" type="list">
114 <data name="nf_log" format="txt" label="Nextflow execution log" from_work_dir="egapx_out/nextflow.log"/>
115 <data name="nf_report" format="html" label="Nextflow execution report" from_work_dir="egapx_out/run.report.html"/>
116 <data name="nf_trace" format="tabular" label="Nextflow trace file" from_work_dir="egapx_out/run.trace.txt"/>
117 <data name="nf_timeline" format="html" label="Nextflow execution timeline" from_work_dir="egapx_out/run.timeline.html"/>
118 <data name="nf_params" format="yaml" label="Nextflow run parameters" from_work_dir="egapx_out/run_params.yaml"/>
114 </collection> 119 </collection>
115 </outputs> 120 </outputs>
116 <tests> 121 <tests>
117 <test expect_test_failure="true"> 122 <test expect_test_failure="true">
118 <param name="input_style" value="history"/> 123 <param name="input_style" value="history"/>
119 <param name="yamlin" value="input.yaml"/> 124 <param name="yamlin" value="input.yaml"/>
120 <output_collection name="egapx_out" type="list" count="8"/> 125 <output name="output"><assert_contents><has_size min="1"/></assert_contents></output>
126 <output_collection name="nextflow_stats" type="list">
127 <element name="nf_log"><assert_contents><has_size min="1"/></assert_contents></element>
128 <element name="nf_report"><assert_contents><has_size min="1"/></assert_contents></element>
129 <element name="nf_trace"><assert_contents><has_size min="1"/></assert_contents></element>
130 <element name="nf_timeline"><assert_contents><has_size min="1"/></assert_contents></element>
131 <element name="nf_params"><assert_contents><has_size min="1"/></assert_contents></element>
132 </output_collection>
121 </test> 133 </test>
122 <test expect_test_failure="true"> 134 <test expect_test_failure="true">
123 <param name="input_style" value="fillform"/> 135 <param name="input_style" value="fillform"/>
124 <param name="taxid" value="6954"/> 136 <param name="taxid" value="6954"/>
125 <param name="genome_type_select" value="uri"/> 137 <param name="genome_type_select" value="uri"/>
126 <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"/> 138 <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"/>
127 <param name="rna_type_select" value="list"/> 139 <param name="rna_type_select" value="list"/>
128 <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"/> 140 <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"/>
129 <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"/> 141 <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"/>
130 <output_collection name="egapx_out" type="list" count="8"/> 142 <output name="output"><assert_contents><has_size min="1"/></assert_contents></output>
143 <output_collection name="nextflow_stats" type="list">
144 <element name="nf_log"><assert_contents><has_size min="1"/></assert_contents></element>
145 <element name="nf_report"><assert_contents><has_size min="1"/></assert_contents></element>
146 <element name="nf_trace"><assert_contents><has_size min="1"/></assert_contents></element>
147 <element name="nf_timeline"><assert_contents><has_size min="1"/></assert_contents></element>
148 <element name="nf_params"><assert_contents><has_size min="1"/></assert_contents></element>
149 </output_collection>
131 </test> 150 </test>
132 </tests> 151 </tests>
133 <help><![CDATA[ 152 <help><![CDATA[
134 Galaxy tool wrapping the Eukaryotic Genome Annotation Pipeline (EGAPx) 153 Galaxy tool wrapping the Eukaryotic Genome Annotation Pipeline (EGAPx)
135 ================================================================================================= 154 =================================================================================================