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comparison fasterq_dump.xml @ 24:e08a7ad4378b draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit 52d835f027b052a0a887be14a55faf9fa9e456ae"
author iuc
date Mon, 01 Feb 2021 20:03:42 +0000
parents 653e89d73fc4
children 69ebb7f46e45
comparison
equal deleted inserted replaced
23:653e89d73fc4 24:e08a7ad4378b
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` ;
190 <element name="forward" file="SRR11953971_1.fastq.gz" decompress="True"/> 193 <element name="forward" file="SRR11953971_1.fastq.gz" decompress="True"/>
191 <element name="reverse" file="SRR11953971_2.fastq.gz" decompress="True"/> 194 <element name="reverse" file="SRR11953971_2.fastq.gz" decompress="True"/>
192 </element> 195 </element>
193 </output_collection> 196 </output_collection>
194 </test> 197 </test>
198 <test>
199 <!-- test accession downloaded from public bucket -->
200 <param name="input_select" value="accession_number"/>
201 <param name="accession" value="SRR11859153"/>
202 <output_collection name="output_collection" type="list">
203 <element name="SRR11859153" file="SRR11859153.fastq.gz" decompress="True"/>
204 </output_collection>
205 <output name="log">
206 <assert_contents>
207 <has_text text="download: s3://sra-pub-sars-cov2/"/>
208 </assert_contents>
209 </output>
210 </test>
195 </tests> 211 </tests>
196 <help><![CDATA[ 212 <help><![CDATA[
197 **What it does?** 213 **What it does?**
198 214
199 This tool extracts data (in fastq_ format) from the Short Read Archive (SRA) at the National Center for Biotechnology Information (NCBI). It is based on the fasterq-dump_ utility of the SRA Toolkit. 215 This tool extracts data (in fastq_ format) from the Short Read Archive (SRA) at the National Center for Biotechnology Information (NCBI). It is based on the fasterq-dump_ utility of the SRA Toolkit.