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comparison fasterq_dump.xml @ 21:9828888fc245 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 08:54:57 +0000
parents b50c21c6e6bb
children fe99dc15b7af
comparison
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20:b50c21c6e6bb 21:9828888fc245
12 #if $input.input_select == "file": 12 #if $input.input_select == "file":
13 acc='${input.file.name}' && 13 acc='${input.file.name}' &&
14 ln -s '${input.file}' "\$acc" && 14 ln -s '${input.file}' "\$acc" &&
15 #end if 15 #end if
16 @CONFIGURE_RETRY@ 16 @CONFIGURE_RETRY@
17 ## fetch from public s3 bucket if we can
18 export acc_or_path="\$acc" &&
19 aws s3 cp --no-sign-request "s3://sra-pub-sars-cov2/run/\$acc/\$acc" "\$acc.sra" 2>&1 | tee '$log' && export acc_or_path="\$acc.sra"|| true &&
17 while [ \$SRA_PREFETCH_ATTEMPT -le \$SRA_PREFETCH_RETRIES ] ; do 20 while [ \$SRA_PREFETCH_ATTEMPT -le \$SRA_PREFETCH_RETRIES ] ; do
18 fasterq-dump "\$acc" -e \${GALAXY_SLOTS:-1} 21 fasterq-dump "\$acc_or_path" -e \${GALAXY_SLOTS:-1}
19 $adv.split 22 $adv.split
20 #if str( $adv.minlen ) != "": 23 #if str( $adv.minlen ) != "":
21 --min-read-len "$adv.minlen" 24 --min-read-len "$adv.minlen"
22 #end if 25 #end if
23 $adv.skip_technical 2>&1 | tee $log; 26 $adv.skip_technical 2>&1 | tee -a '$log';
24 if [ \$? == 0 ] && [ \$(ls *.fastq | wc -l) -ge 1 ]; then 27 if [ \$? == 0 ] && [ \$(ls *.fastq | wc -l) -ge 1 ]; then
25 break ; 28 break ;
26 else 29 else
27 echo "Prefetch attempt \$SRA_PREFETCH_ATTEMPT of \$SRA_PREFETCH_RETRIES exited with code \$?" ; 30 echo "Prefetch attempt \$SRA_PREFETCH_ATTEMPT of \$SRA_PREFETCH_RETRIES exited with code \$?" ;
28 SRA_PREFETCH_ATTEMPT=`expr \$SRA_PREFETCH_ATTEMPT + 1` ; 31 SRA_PREFETCH_ATTEMPT=`expr \$SRA_PREFETCH_ATTEMPT + 1` ;
101 <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)">
102 <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"/>
103 </collection> 106 </collection>
104 </outputs> 107 </outputs>
105 <tests> 108 <tests>
106 <test> 109 <test expect_num_outputs="4">
107 <param name="input_select" value="accession_number"/> 110 <param name="input_select" value="accession_number"/>
108 <param name="accession" value="ERR086330"/> 111 <param name="accession" value="ERR086330"/>
109 <output_collection name="list_paired" type="list:paired"> 112 <output_collection name="list_paired" type="list:paired" count="1">
110 <element name="ERR086330"> 113 <element name="ERR086330">
111 <element name="forward" file="ERR086330_1.fastq.gz" decompress="True"> 114 <element name="forward" file="ERR086330_1.fastq.gz" decompress="True">
112 </element> 115 </element>
113 <element name="reverse" file="ERR086330_2.fastq.gz" decompress="True"> 116 <element name="reverse" file="ERR086330_2.fastq.gz" decompress="True">
114 </element> 117 </element>
115 </element> 118 </element>
116 </output_collection> 119 </output_collection>
117 </test> 120 </test>
118 <test> 121 <test expect_num_outputs="4">
119 <param name="input_select" value="accession_number"/> 122 <param name="input_select" value="accession_number"/>
120 <param name="accession" value="SRR002702"/> 123 <param name="accession" value="SRR002702"/>
121 <param name="split" value="--split-files"/> 124 <param name="split" value="--split-files"/>
122 <param name="skip_technical" value="False"/> 125 <param name="skip_technical" value="False"/>
123 <output_collection name="output_collection_other" type="list"> 126 <output_collection name="output_collection_other" type="list" count="2">
124 <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"/>
125 <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"/>
126 </output_collection> 129 </output_collection>
127 </test> 130 </test>
128 <test> 131 <test expect_num_outputs="4">
129 <param name="input_select" value="file"/> 132 <param name="input_select" value="file"/>
130 <param name="file" value="SRR522874.sra"/> 133 <param name="file" value="SRR522874.sra"/>
131 <param name="split" value="--split-files"/> 134 <param name="split" value="--split-files"/>
132 <param name="skip_technical" value="True"/> 135 <param name="skip_technical" value="True"/>
133 <output_collection name="list_paired" type="list:paired"> 136 <output_collection name="list_paired" type="list:paired" count="1">
134 <element name="SRR522874.sra"> 137 <element name="SRR522874.sra">
135 <element name="forward" file="SRR522874.sra_2.fastq.gz" decompress="True"> 138 <element name="forward" file="SRR522874.sra_2.fastq.gz" decompress="True">
136 </element> 139 </element>
137 <element name="reverse" file="SRR522874.sra_4.fastq.gz" decompress="True"> 140 <element name="reverse" file="SRR522874.sra_4.fastq.gz" decompress="True">
138 </element> 141 </element>
139 </element> 142 </element>
140 </output_collection> 143 </output_collection>
141 </test> 144 </test>
142 <test> 145 <test expect_num_outputs="4">
143 <param name="input_select" value="file"/> 146 <param name="input_select" value="file"/>
144 <param name="file" value="SRR522874.sra"/> 147 <param name="file" value="SRR522874.sra"/>
145 <param name="split" value="--split-files"/> 148 <param name="split" value="--split-files"/>
146 <param name="skip_technical" value="False"/> 149 <param name="skip_technical" value="False"/>
147 <output_collection name="output_collection_other" type="list"> 150 <output_collection name="output_collection_other" type="list" count="4">
148 <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"/>
149 <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"/>
150 <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"/>
151 <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"/>
152 </output_collection> 155 </output_collection>
153 </test> 156 </test>
154 <test> 157 <test expect_num_outputs="4">
155 <param name="input_select" value="file_list"/> 158 <param name="input_select" value="file_list"/>
156 <param name="file_list" value="list_sra"/> 159 <param name="file_list" value="list_sra"/>
157 <param name="minlen" value="21"/> 160 <param name="minlen" value="21"/>
158 <output_collection name="output_collection_other" type="list"> 161 <output_collection name="output_collection_other" type="list">
159 <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"/>
160 </output_collection> 163 </output_collection>
161 <output_collection name="list_paired" type="list:paired"> 164 <output_collection name="list_paired" type="list:paired" count="1">
162 <element name="SRR522874"> 165 <element name="SRR522874">
163 <element name="forward" file="SRR522874_1.fastq.gz" decompress="True"> 166 <element name="forward" file="SRR522874_1.fastq.gz" decompress="True"/>
164 </element> 167 <element name="reverse" file="SRR522874_2.fastq.gz" decompress="True"/>
165 <element name="reverse" file="SRR522874_2.fastq.gz" decompress="True">
166 </element>
167 </element> 168 </element>
168 </output_collection> 169 </output_collection>
169 <output_collection name="output_collection" type="list"> 170 <output_collection name="output_collection" type="list">
170 <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"/>
171 </output_collection> 172 </output_collection>
172 </test> 173 </test>
173 <test> 174 <test expect_num_outputs="4">
174 <param name="input_select" value="file_list"/> 175 <param name="input_select" value="file_list"/>
175 <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"/>
176 <output_collection name="list_paired" type="list:paired"> 177 <output_collection name="list_paired" type="list:paired" count="1">
177 <element name="SRR11857975">
178 <element name="forward" file="SRR11857975_1.fastq.gz" decompress="True">
179 </element>
180 <element name="reverse" file="SRR11857975_2.fastq.gz" decompress="True">
181 </element>
182 </element>
183 </output_collection>
184 </test>
185 <test>
186 <param name="input_select" value="file_list"/>
187 <param name="file_list" value="sra_manifest.tabular" ftype="sra_manifest.tabular"/>
188 <output_collection name="list_paired" type="list:paired">
189 <element name="SRR11953971"> 178 <element name="SRR11953971">
190 <element name="forward" file="SRR11953971_1.fastq.gz" decompress="True"/> 179 <element name="forward" file="SRR11953971_1.fastq.gz" decompress="True"/>
191 <element name="reverse" file="SRR11953971_2.fastq.gz" decompress="True"/> 180 <element name="reverse" file="SRR11953971_2.fastq.gz" decompress="True"/>
192 </element> 181 </element>
193 </output_collection> 182 </output_collection>
183 </test>
184 <test expect_num_outputs="4">
185 <!-- test accession downloaded from public bucket -->
186 <param name="input_select" value="accession_number"/>
187 <param name="accession" value="SRR11859153"/>
188 <output_collection name="output_collection" type="list" count="1">
189 <element name="SRR11859153" file="SRR11859153.fastq.gz" decompress="True"/>
190 </output_collection>
191 <output name="log">
192 <assert_contents>
193 <has_text text="download: s3://sra-pub-sars-cov2/"/>
194 </assert_contents>
195 </output>
194 </test> 196 </test>
195 </tests> 197 </tests>
196 <help><![CDATA[ 198 <help><![CDATA[
197 **What it does?** 199 **What it does?**
198 200