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comparison plasmidfinder.xml @ 3:7075b7a5441b draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/plasmidfinder commit 464661a59ed12a642d365f485a222764b55048a5
author iuc
date Thu, 02 Mar 2023 14:58:17 +0000
parents eccc7495c3d9
children
comparison
equal deleted inserted replaced
2:e23b96d79dc0 3:7075b7a5441b
31 </command> 31 </command>
32 <inputs> 32 <inputs>
33 <section name="input" title="Input parameters" expanded="true"> 33 <section name="input" title="Input parameters" expanded="true">
34 <param name="input_file" type="data" format="fasta,fasta.gz,fastqsanger,fastqsanger.gz" label="Choose a fasta or fastq file" help="File to be analyzed"/> 34 <param name="input_file" type="data" format="fasta,fasta.gz,fastqsanger,fastqsanger.gz" label="Choose a fasta or fastq file" help="File to be analyzed"/>
35 <param name="database_name" type="select" label="PlasmidFinder database"> 35 <param name="database_name" type="select" label="PlasmidFinder database">
36 <options from_data_table="plasmidfinder_db"> 36 <options from_data_table="plasmidfinder_database">
37 <validator message="No PlasmidFinder database is available" type="no_options"/> 37 <validator message="No PlasmidFinder database is available" type="no_options"/>
38 </options> 38 </options>
39 </param> 39 </param>
40 </section> 40 </section>
41 <section name="options" title="Options"> 41 <section name="options" title="Options">
77 <!--test_1 with default value and all output files for contigs --> 77 <!--test_1 with default value and all output files for contigs -->
78 <test expect_num_outputs="6"> 78 <test expect_num_outputs="6">
79 <section name="input"> 79 <section name="input">
80 <param name="input_file" value="contigs.fasta"/> 80 <param name="input_file" value="contigs.fasta"/>
81 <param name="input_type" value="genome"/> 81 <param name="input_type" value="genome"/>
82 <param name="database_name" value="test-plasmindfinder-db"/> 82 <param name="database_name" value="plasmidfinder_9002e7282dd0_2022-12-20"/>
83 </section> 83 </section>
84 <section name="output_files"> 84 <section name="output_files">
85 <param name="output_selection" value="data_json,hit_fasta,plasmid_fasta,result_tsv,result_txt,logfile"/> 85 <param name="output_selection" value="data_json,hit_fasta,plasmid_fasta,result_tsv,result_txt,logfile"/>
86 </section> 86 </section>
87 <output name="json_file" value="test_1/data_test1.json" ftype="json" compare="sim_size"/> 87 <output name="json_file" value="test_1/data_test1.json" ftype="json" compare="sim_size"/>
94 <!--test_2 with default value and for fastq file --> 94 <!--test_2 with default value and for fastq file -->
95 <test expect_num_outputs="4"> 95 <test expect_num_outputs="4">
96 <section name="input"> 96 <section name="input">
97 <param name="input_file" value="data.fastq.gz"/> 97 <param name="input_file" value="data.fastq.gz"/>
98 <param name="input_type" value="raw"/> 98 <param name="input_type" value="raw"/>
99 <param name="database_name" value="test-plasmindfinder-db"/> 99 <param name="database_name" value="plasmidfinder_9002e7282dd0_2022-12-20"/>
100 </section> 100 </section>
101 <section name="output_files"> 101 <section name="output_files">
102 <param name="output_selection" value="data_json,result_tsv,result_txt,logfile"/> 102 <param name="output_selection" value="data_json,result_tsv,result_txt,logfile"/>
103 </section> 103 </section>
104 <output name="json_file" value="test_2/data_test2.json" ftype="json" compare="sim_size"/> 104 <output name="json_file" value="test_2/data_test2.json" ftype="json" compare="sim_size"/>
109 <!--test_3 with default value and for fastq file --> 109 <!--test_3 with default value and for fastq file -->
110 <test expect_num_outputs="3"> 110 <test expect_num_outputs="3">
111 <section name="input"> 111 <section name="input">
112 <param name="input_file" value="contigs.fasta"/> 112 <param name="input_file" value="contigs.fasta"/>
113 <param name="input_type" value="genome"/> 113 <param name="input_type" value="genome"/>
114 <param name="database_name" value="test-plasmindfinder-db"/> 114 <param name="database_name" value="plasmidfinder_9002e7282dd0_2022-12-20"/>
115 </section> 115 </section>
116 <section name="options"> 116 <section name="options">
117 <param name="min_cov" value="0.2" /> 117 <param name="min_cov" value="0.2" />
118 <param name="threshold" value="0.6"/> 118 <param name="threshold" value="0.6"/>
119 </section> 119 </section>