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comparison fasterq_dump.xml @ 25:69ebb7f46e45 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit a464017f4a599697101dbd26cf5eb902588359b5"
author iuc
date Tue, 27 Apr 2021 08:55:34 +0000
parents e08a7ad4378b
children 83c7d564b128
comparison
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24:e08a7ad4378b 25:69ebb7f46e45
104 <collection name="output_collection_other" type='list' label="Other data (fasterq-dump)"> 104 <collection name="output_collection_other" type='list' label="Other data (fasterq-dump)">
105 <discover_datasets pattern="(?P&lt;designation&gt;.+)\.fastqsanger\.gz" directory="outputOther" format="fastqsanger.gz"/> 105 <discover_datasets pattern="(?P&lt;designation&gt;.+)\.fastqsanger\.gz" directory="outputOther" format="fastqsanger.gz"/>
106 </collection> 106 </collection>
107 </outputs> 107 </outputs>
108 <tests> 108 <tests>
109 <test> 109 <test expect_num_outputs="4">
110 <param name="input_select" value="accession_number"/> 110 <param name="input_select" value="accession_number"/>
111 <param name="accession" value="ERR086330"/> 111 <param name="accession" value="ERR086330"/>
112 <output_collection name="list_paired" type="list:paired"> 112 <output_collection name="list_paired" type="list:paired" count="1">
113 <element name="ERR086330"> 113 <element name="ERR086330">
114 <element name="forward" file="ERR086330_1.fastq.gz" decompress="True"> 114 <element name="forward" file="ERR086330_1.fastq.gz" decompress="True">
115 </element> 115 </element>
116 <element name="reverse" file="ERR086330_2.fastq.gz" decompress="True"> 116 <element name="reverse" file="ERR086330_2.fastq.gz" decompress="True">
117 </element> 117 </element>
118 </element> 118 </element>
119 </output_collection> 119 </output_collection>
120 </test> 120 </test>
121 <test> 121 <test expect_num_outputs="4">
122 <param name="input_select" value="accession_number"/> 122 <param name="input_select" value="accession_number"/>
123 <param name="accession" value="SRR002702"/> 123 <param name="accession" value="SRR002702"/>
124 <param name="split" value="--split-files"/> 124 <param name="split" value="--split-files"/>
125 <param name="skip_technical" value="False"/> 125 <param name="skip_technical" value="False"/>
126 <output_collection name="output_collection_other" type="list"> 126 <output_collection name="output_collection_other" type="list" count="2">
127 <element name="SRR002702_1" file="SRR002702_1.fastq.gz" ftype="fastqsanger.gz" decompress="True"/> 127 <element name="SRR002702_1" file="SRR002702_1.fastq.gz" ftype="fastqsanger.gz" decompress="True"/>
128 <element name="SRR002702_2" file="SRR002702_2.fastq.gz" ftype="fastqsanger.gz" decompress="True"/> 128 <element name="SRR002702_2" file="SRR002702_2.fastq.gz" ftype="fastqsanger.gz" decompress="True"/>
129 </output_collection> 129 </output_collection>
130 </test> 130 </test>
131 <test> 131 <test expect_num_outputs="4">
132 <param name="input_select" value="file"/> 132 <param name="input_select" value="file"/>
133 <param name="file" value="SRR522874.sra"/> 133 <param name="file" value="SRR522874.sra"/>
134 <param name="split" value="--split-files"/> 134 <param name="split" value="--split-files"/>
135 <param name="skip_technical" value="True"/> 135 <param name="skip_technical" value="True"/>
136 <output_collection name="list_paired" type="list:paired"> 136 <output_collection name="list_paired" type="list:paired" count="1">
137 <element name="SRR522874.sra"> 137 <element name="SRR522874.sra">
138 <element name="forward" file="SRR522874.sra_2.fastq.gz" decompress="True"> 138 <element name="forward" file="SRR522874.sra_2.fastq.gz" decompress="True">
139 </element> 139 </element>
140 <element name="reverse" file="SRR522874.sra_4.fastq.gz" decompress="True"> 140 <element name="reverse" file="SRR522874.sra_4.fastq.gz" decompress="True">
141 </element> 141 </element>
142 </element> 142 </element>
143 </output_collection> 143 </output_collection>
144 </test> 144 </test>
145 <test> 145 <test expect_num_outputs="4">
146 <param name="input_select" value="file"/> 146 <param name="input_select" value="file"/>
147 <param name="file" value="SRR522874.sra"/> 147 <param name="file" value="SRR522874.sra"/>
148 <param name="split" value="--split-files"/> 148 <param name="split" value="--split-files"/>
149 <param name="skip_technical" value="False"/> 149 <param name="skip_technical" value="False"/>
150 <output_collection name="output_collection_other" type="list"> 150 <output_collection name="output_collection_other" type="list" count="4">
151 <element name="SRR522874.sra_1" file="SRR522874.sra_1.fastq.gz" ftype="fastqsanger.gz" decompress="True"/> 151 <element name="SRR522874_1" file="SRR522874.sra_1.fastq.gz" ftype="fastqsanger.gz" decompress="True"/>
152 <element name="SRR522874.sra_2" file="SRR522874.sra_2.fastq.gz" ftype="fastqsanger.gz" decompress="True"/> 152 <element name="SRR522874_2" file="SRR522874.sra_2.fastq.gz" ftype="fastqsanger.gz" decompress="True"/>
153 <element name="SRR522874.sra_3" file="SRR522874.sra_3.fastq.gz" ftype="fastqsanger.gz" decompress="True"/> 153 <element name="SRR522874_3" file="SRR522874.sra_3.fastq.gz" ftype="fastqsanger.gz" decompress="True"/>
154 <element name="SRR522874.sra_4" file="SRR522874.sra_4.fastq.gz" ftype="fastqsanger.gz" decompress="True"/> 154 <element name="SRR522874_4" file="SRR522874.sra_4.fastq.gz" ftype="fastqsanger.gz" decompress="True"/>
155 </output_collection> 155 </output_collection>
156 </test> 156 </test>
157 <test> 157 <test expect_num_outputs="4">
158 <param name="input_select" value="file_list"/> 158 <param name="input_select" value="file_list"/>
159 <param name="file_list" value="list_sra"/> 159 <param name="file_list" value="list_sra"/>
160 <param name="minlen" value="21"/> 160 <param name="minlen" value="21"/>
161 <output_collection name="output_collection_other" type="list"> 161 <output_collection name="output_collection_other" type="list">
162 <element name="SRR522874__single" file="SRR522874.fastq.gz" ftype="fastqsanger.gz" decompress="True"/> 162 <element name="SRR522874__single" file="SRR522874.fastq.gz" ftype="fastqsanger.gz" decompress="True"/>
163 </output_collection> 163 </output_collection>
164 <output_collection name="list_paired" type="list:paired"> 164 <output_collection name="list_paired" type="list:paired" count="1">
165 <element name="SRR522874"> 165 <element name="SRR522874">
166 <element name="forward" file="SRR522874_1.fastq.gz" decompress="True"> 166 <element name="forward" file="SRR522874_1.fastq.gz" decompress="True"/>
167 </element> 167 <element name="reverse" file="SRR522874_2.fastq.gz" decompress="True"/>
168 <element name="reverse" file="SRR522874_2.fastq.gz" decompress="True">
169 </element>
170 </element> 168 </element>
171 </output_collection> 169 </output_collection>
172 <output_collection name="output_collection" type="list"> 170 <output_collection name="output_collection" type="list">
173 <element name="SRR002702" file="SRR002702_2.fastq.gz" ftype="fastqsanger.gz" decompress="True"/> 171 <element name="SRR002702" file="SRR002702_2.fastq.gz" ftype="fastqsanger.gz" decompress="True"/>
174 </output_collection> 172 </output_collection>
175 </test> 173 </test>
176 <test> 174 <test expect_num_outputs="4">
177 <param name="input_select" value="file_list"/> 175 <param name="input_select" value="file_list"/>
178 <param name="file_list" value="sra_manifest.tabular" ftype="sra_manifest.tabular"/> 176 <param name="file_list" value="sra_manifest.tabular" ftype="sra_manifest.tabular"/>
179 <output_collection name="list_paired" type="list:paired"> 177 <output_collection name="list_paired" type="list:paired" count="1">
180 <element name="SRR11857975">
181 <element name="forward" file="SRR11857975_1.fastq.gz" decompress="True">
182 </element>
183 <element name="reverse" file="SRR11857975_2.fastq.gz" decompress="True">
184 </element>
185 </element>
186 </output_collection>
187 </test>
188 <test>
189 <param name="input_select" value="file_list"/>
190 <param name="file_list" value="sra_manifest.tabular" ftype="sra_manifest.tabular"/>
191 <output_collection name="list_paired" type="list:paired">
192 <element name="SRR11953971"> 178 <element name="SRR11953971">
193 <element name="forward" file="SRR11953971_1.fastq.gz" decompress="True"/> 179 <element name="forward" file="SRR11953971_1.fastq.gz" decompress="True"/>
194 <element name="reverse" file="SRR11953971_2.fastq.gz" decompress="True"/> 180 <element name="reverse" file="SRR11953971_2.fastq.gz" decompress="True"/>
195 </element> 181 </element>
196 </output_collection> 182 </output_collection>
197 </test> 183 </test>
198 <test> 184 <test expect_num_outputs="4">
199 <!-- test accession downloaded from public bucket --> 185 <!-- test accession downloaded from public bucket -->
200 <param name="input_select" value="accession_number"/> 186 <param name="input_select" value="accession_number"/>
201 <param name="accession" value="SRR11859153"/> 187 <param name="accession" value="SRR11859153"/>
202 <output_collection name="output_collection" type="list"> 188 <output_collection name="output_collection" type="list" count="1">
203 <element name="SRR11859153" file="SRR11859153.fastq.gz" decompress="True"/> 189 <element name="SRR11859153" file="SRR11859153.fastq.gz" decompress="True"/>
204 </output_collection> 190 </output_collection>
205 <output name="log"> 191 <output name="log">
206 <assert_contents> 192 <assert_contents>
207 <has_text text="download: s3://sra-pub-sars-cov2/"/> 193 <has_text text="download: s3://sra-pub-sars-cov2/"/>