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comparison fasterq_dump.xml @ 22:fe99dc15b7af draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit 21f935ba50d3e4b455246c681e54d5c57c67032f"
author iuc
date Fri, 03 Sep 2021 16:17:17 +0000
parents 9828888fc245
children 6669afa92957
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21:9828888fc245 22:fe99dc15b7af
1 <tool id="fasterq_dump" name="Faster Download and Extract Reads in FASTQ" version="@VERSION@+galaxy0" profile="18.01"> 1 <tool id="fasterq_dump" name="Faster Download and Extract Reads in FASTQ" version="@VERSION@+galaxy1" profile="18.01">
2 <description>format from NCBI SRA</description> 2 <description>format from NCBI SRA</description>
3 <expand macro="bio_tools"/>
3 <macros> 4 <macros>
4 <import>sra_macros.xml</import> 5 <import>sra_macros.xml</import>
5 </macros> 6 </macros>
6 <expand macro="requirements"/> 7 <expand macro="requirements"/>
7 <version_command>fasterq-dump --version</version_command> 8 <version_command>fasterq-dump --version</version_command>
12 #if $input.input_select == "file": 13 #if $input.input_select == "file":
13 acc='${input.file.name}' && 14 acc='${input.file.name}' &&
14 ln -s '${input.file}' "\$acc" && 15 ln -s '${input.file}' "\$acc" &&
15 #end if 16 #end if
16 @CONFIGURE_RETRY@ 17 @CONFIGURE_RETRY@
17 ## fetch from public s3 bucket if we can
18 export acc_or_path="\$acc" &&
19 aws s3 cp --no-sign-request "s3://sra-pub-sars-cov2/run/\$acc/\$acc" "\$acc.sra" 2>&1 | tee '$log' && export acc_or_path="\$acc.sra"|| true &&
20 while [ \$SRA_PREFETCH_ATTEMPT -le \$SRA_PREFETCH_RETRIES ] ; do 18 while [ \$SRA_PREFETCH_ATTEMPT -le \$SRA_PREFETCH_RETRIES ] ; do
21 fasterq-dump "\$acc_or_path" -e \${GALAXY_SLOTS:-1} 19 fasterq-dump "\$acc" -e \${GALAXY_SLOTS:-1}
22 $adv.split 20 $adv.split
23 #if str( $adv.minlen ) != "": 21 #if str( $adv.minlen ) != "":
24 --min-read-len "$adv.minlen" 22 --min-read-len "$adv.minlen"
25 #end if 23 #end if
26 $adv.skip_technical 2>&1 | tee -a '$log'; 24 $adv.skip_technical 2>&1 | tee -a '$log';
179 <element name="forward" file="SRR11953971_1.fastq.gz" decompress="True"/> 177 <element name="forward" file="SRR11953971_1.fastq.gz" decompress="True"/>
180 <element name="reverse" file="SRR11953971_2.fastq.gz" decompress="True"/> 178 <element name="reverse" file="SRR11953971_2.fastq.gz" decompress="True"/>
181 </element> 179 </element>
182 </output_collection> 180 </output_collection>
183 </test> 181 </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>
196 </test>
197 </tests> 182 </tests>
198 <help><![CDATA[ 183 <help><![CDATA[
199 **What it does?** 184 **What it does?**
200 185
201 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. 186 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.
257 242
258 ----- 243 -----
259 244
260 245
261 .. _fastq: https://en.wikipedia.org/wiki/FASTQ_format 246 .. _fastq: https://en.wikipedia.org/wiki/FASTQ_format
262 .. _fastq-dump: https://ncbi.github.io/sra-tools/fastq-dump.html 247 .. _fastq-dump: https://trace.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?view=toolkit_doc&f=fastq-dump
263 .. _fasterq-dump: https://github.com/ncbi/sra-tools/wiki/HowTo:-fasterq-dump 248 .. _fasterq-dump: https://github.com/ncbi/sra-tools/wiki/HowTo:-fasterq-dump
264 .. _collection: https://galaxyproject.org/tutorials/collections/ 249 .. _collection: https://galaxyproject.org/tutorials/collections/
265 .. _link: https://trace.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?view=studies 250 .. _link: https://trace.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?view=studies
266 251
267 @SRATOOLS_ATTRRIBUTION@ 252 @SRATOOLS_ATTRRIBUTION@