Mercurial > repos > iuc > sra_tools

comparison fastq_dump.xml @ 32:fb723c531be5 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit ac10fe34f1b2d5e8109dcaaf42b7870bee57827b
author iuc
date Wed, 25 Oct 2023 07:10:06 +0000
parents 734abc7ac21d
children 8848455c0270
comparison
equal deleted inserted replaced
31:734abc7ac21d 32:fb723c531be5
10 <command detect_errors="exit_code"><![CDATA[ 10 <command detect_errors="exit_code"><![CDATA[
11 @COPY_CONFIGFILE@ 11 @COPY_CONFIGFILE@
12 @SET_ACCESSIONS@ 12 @SET_ACCESSIONS@
13 13
14 #if $input.input_select == "sra_file": 14 #if $input.input_select == "sra_file":
15 fastq-dump --log-level fatal --accession '${input.file.name}' 15 fastq-dump --log-level fatal --accession "\$acc"
16 #else: 16 #else:
17 ## Do not use prefetch if region is specified, to avoid downloading 17 ## Do not use prefetch if region is specified, to avoid downloading
18 ## the complete sra file. 18 ## the complete sra file.
19 #if ( str( $adv.region ) == "" ) and ( str( $adv.minID ) == "" ) and ( str( $adv.maxID ) == "" ): 19 #if ( str( $adv.region ) == "" ) and ( str( $adv.minID ) == "" ) and ( str( $adv.maxID ) == "" ):
20 prefetch -X 200000000 "\$acc" && 20 prefetch -X 200000000 "\$acc" &&
21 #end if 21 #end if
22 fastq-dump --accession "\$acc" 22 fastq-dump --accession "\$acc"
23 --split-files 23 #end if
24 #end if 24 --split-files
25 --defline-seq '$adv.defline_seq' 25 --defline-seq '$adv.defline_seq'
26 --defline-qual '+' 26 --defline-qual '+'
27 27
28 $adv.split 28 $adv.split
29 #if str( $adv.alignments ) == "aligned": 29 #if str( $adv.alignments ) == "aligned":
267 </assert_contents> 267 </assert_contents>
268 </element> 268 </element>
269 </element> 269 </element>
270 </output_collection> 270 </output_collection>
271 </test> 271 </test>
272 <test expect_num_outputs="2">
273 <param name="input_select" value="sra_file"/>
274 <param name="sra_file" value="SRR522874.sra"/>
275 <param name="split" value="True"/>
276 <param name="skip_technical" value="True"/>
277 <section name="adv">
278 <param name="defline_seq" value="@$sn/$ri"/>
279 </section>
280 <output_collection name="list_paired" type="list:paired" count="1">
281 <element name="SRR522874.sra">
282 <element name="forward" file="SRR522874.sra_2.fastq.gz" ftype="fastqsanger.gz" decompress="True"/>
283 <element name="reverse" file="SRR522874.sra_4.fastq.gz" ftype="fastqsanger.gz" decompress="True"/>
284 </element>
285 </output_collection>
286 </test>
272 </tests> 287 </tests>
273 <help><![CDATA[ 288 <help><![CDATA[
274 **What it does?** 289 **What it does?**
275 290
276 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. The following applies: 291 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. The following applies: