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comparison fastq_dl.xml @ 2:0095a278a085 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastq_dl commit 3253434cee1e88dcab77c1cc99264900c78eadb9
author iuc
date Thu, 13 Nov 2025 13:33:35 +0000
parents f1a958f3e3f6
children
comparison
equal deleted inserted replaced
1:f1a958f3e3f6 2:0095a278a085
55 </collection> 55 </collection>
56 </outputs> 56 </outputs>
57 <tests> 57 <tests>
58 <!-- #1 Testing single end and paired end using accessions file --> 58 <!-- #1 Testing single end and paired end using accessions file -->
59 <test expect_num_outputs="3"> 59 <test expect_num_outputs="3">
60 <param name="select_input_type" value="accessions_list" /> 60 <conditional name="input_type">
61 <param name="accessions_file" value="accessions.txt" /> 61 <param name="select_input_type" value="accessions_list" />
62 <param name="accessions_file" value="accessions.txt" />
63 </conditional>
62 <output_collection name="metadata" type="list" count="4"> 64 <output_collection name="metadata" type="list" count="4">
63 <element name="DRR011117" file="Metadata_files/DRR011117.tsv" /> 65 <element name="DRR011117" file="Metadata_files/DRR011117.tsv" />
64 <element name="ERR2651925" file="Metadata_files/ERR2651925.tsv" /> 66 <element name="ERR2651925" file="Metadata_files/ERR2651925.tsv" />
65 <element name="ERR4319712" file="Metadata_files/ERR4319712.tsv" /> 67 <element name="ERR4319712" file="Metadata_files/ERR4319712.tsv" />
66 <element name="SRR9678965" file="Metadata_files/SRR9678965.tsv" /> 68 <element name="SRR9678965" file="Metadata_files/SRR9678965.tsv" />
110 </element> 112 </element>
111 </output_collection> 113 </output_collection>
112 </test> 114 </test>
113 <!-- #2 Testing single end and paired end using accessions as text input --> 115 <!-- #2 Testing single end and paired end using accessions as text input -->
114 <test expect_num_outputs="3"> 116 <test expect_num_outputs="3">
115 <param name="select_input_type" value="accession_ids" /> 117 <conditional name="input_type">
116 <param name="accessions" value="ERR4319712 DRR011117 ERR2651925 SRR9678965" /> 118 <param name="select_input_type" value="accession_ids" />
119 <param name="accessions" value="ERR4319712 DRR011117 ERR2651925 SRR9678965" />
120 </conditional>
117 <output_collection name="metadata" type="list" count="4"> 121 <output_collection name="metadata" type="list" count="4">
118 <element name="DRR011117" file="Metadata_files/DRR011117.tsv" /> 122 <element name="DRR011117" file="Metadata_files/DRR011117.tsv" />
119 <element name="ERR2651925" file="Metadata_files/ERR2651925.tsv" /> 123 <element name="ERR2651925" file="Metadata_files/ERR2651925.tsv" />
120 <element name="ERR4319712" file="Metadata_files/ERR4319712.tsv" /> 124 <element name="ERR4319712" file="Metadata_files/ERR4319712.tsv" />
121 <element name="SRR9678965" file="Metadata_files/SRR9678965.tsv" /> 125 <element name="SRR9678965" file="Metadata_files/SRR9678965.tsv" />
159 </element> 163 </element>
160 </output_collection> 164 </output_collection>
161 </test> 165 </test>
162 <!-- #3 Testing only download metadata --> 166 <!-- #3 Testing only download metadata -->
163 <test expect_num_outputs="1"> 167 <test expect_num_outputs="1">
164 <param name="select_input_type" value="accessions_list" /> 168 <conditional name="input_type">
165 <param name="accessions_file" value="accessions.txt" /> 169 <param name="select_input_type" value="accessions_list" />
166 <param name="only_download_metadata" value="--only-download-metadata" /> 170 <param name="accessions_file" value="accessions.txt" />
171 </conditional>
172 <param name="only_download_metadata" value="true" />
167 <output_collection name="metadata" type="list" count="4"> 173 <output_collection name="metadata" type="list" count="4">
168 <element name="DRR011117" file="Metadata_files/DRR011117.tsv" /> 174 <element name="DRR011117" file="Metadata_files/DRR011117.tsv" />
169 <element name="ERR2651925" file="Metadata_files/ERR2651925.tsv" /> 175 <element name="ERR2651925" file="Metadata_files/ERR2651925.tsv" />
170 <element name="ERR4319712" file="Metadata_files/ERR4319712.tsv" /> 176 <element name="ERR4319712" file="Metadata_files/ERR4319712.tsv" />
171 <element name="SRR9678965" file="Metadata_files/SRR9678965.tsv" /> 177 <element name="SRR9678965" file="Metadata_files/SRR9678965.tsv" />
172 </output_collection> 178 </output_collection>
173 </test> 179 </test>
174 <!-- #4 Testing group by experiment --> 180 <!-- #4 Testing group by experiment -->
175 <test expect_num_outputs="3"> 181 <test expect_num_outputs="3">
176 <param name="select_input_type" value="accessions_list" /> 182 <conditional name="input_type">
177 <param name="accessions_file" value="accessions.txt" /> 183 <param name="select_input_type" value="accessions_list" />
178 <param name="group_by_experiment" value="--group-by-experiment" /> 184 <param name="accessions_file" value="accessions.txt" />
185 </conditional>
186 <param name="group_by_experiment" value="true" />
179 <output_collection name="metadata" type="list" count="4"> 187 <output_collection name="metadata" type="list" count="4">
180 <element name="DRR011117" file="Metadata_files/DRR011117.tsv" /> 188 <element name="DRR011117" file="Metadata_files/DRR011117.tsv" />
181 <element name="ERR2651925" file="Metadata_files/ERR2651925.tsv" /> 189 <element name="ERR2651925" file="Metadata_files/ERR2651925.tsv" />
182 <element name="ERR4319712" file="Metadata_files/ERR4319712.tsv" /> 190 <element name="ERR4319712" file="Metadata_files/ERR4319712.tsv" />
183 <element name="SRR9678965" file="Metadata_files/SRR9678965.tsv" /> 191 <element name="SRR9678965" file="Metadata_files/SRR9678965.tsv" />
221 </element> 229 </element>
222 </output_collection> 230 </output_collection>
223 </test> 231 </test>
224 <!-- #5 Testing group by sample --> 232 <!-- #5 Testing group by sample -->
225 <test expect_num_outputs="3"> 233 <test expect_num_outputs="3">
226 <param name="select_input_type" value="accessions_list" /> 234 <conditional name="input_type">
227 <param name="accessions_file" value="accessions.txt" /> 235 <param name="select_input_type" value="accessions_list" />
228 <param name="group_by_sample" value="--group-by-sample" /> 236 <param name="accessions_file" value="accessions.txt" />
237 </conditional>
238 <param name="group_by_sample" value="true" />
229 <output_collection name="metadata" type="list" count="4"> 239 <output_collection name="metadata" type="list" count="4">
230 <element name="DRR011117" file="Metadata_files/DRR011117.tsv" /> 240 <element name="DRR011117" file="Metadata_files/DRR011117.tsv" />
231 <element name="ERR2651925" file="Metadata_files/ERR2651925.tsv" /> 241 <element name="ERR2651925" file="Metadata_files/ERR2651925.tsv" />
232 <element name="ERR4319712" file="Metadata_files/ERR4319712.tsv" /> 242 <element name="ERR4319712" file="Metadata_files/ERR4319712.tsv" />
233 <element name="SRR9678965" file="Metadata_files/SRR9678965.tsv" /> 243 <element name="SRR9678965" file="Metadata_files/SRR9678965.tsv" />
268 <has_size size="2578613" /> 278 <has_size size="2578613" />
269 </assert_contents> 279 </assert_contents>
270 </element> 280 </element>
271 </element> 281 </element>
272 </output_collection> 282 </output_collection>
283 </test>
284 <!-- #6 Testing exit code capture in the for loop -->
285 <test expect_exit_code="1" expect_failure="true">
286 <conditional name="input_type">
287 <param name="select_input_type" value="accession_ids" />
288 <param name="accessions" value="DRR0117 ERR2651925" />
289 </conditional>
290 <assert_stderr>
291 <has_text text="fastq-dl failed for accession: DRR0117" />
292 </assert_stderr>
273 </test> 293 </test>
274 </tests> 294 </tests>
275 <help><![CDATA[ 295 <help><![CDATA[
276 296
277 This tool downloads FASTQ files from the European Nucleotide Archive (ENA) based on a list of ENA accession IDs. 297 This tool downloads FASTQ files from the European Nucleotide Archive (ENA) based on a list of ENA accession IDs.