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comparison fasterq_dump.xml @ 20:b50c21c6e6bb draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit 3c5c7587a9e8f4177db5ff1390b7e29cb190eb72"
author iuc
date Thu, 20 Aug 2020 09:05:33 +0000
parents adc510b2288d
children 9828888fc245
comparison
equal deleted inserted replaced
19:adc510b2288d 20:b50c21c6e6bb
1 <tool id="fasterq_dump" name="Faster Download and Extract Reads in FASTQ" version="@VERSION@+galaxy1" profile="18.01"> 1 <tool id="fasterq_dump" name="Faster Download and Extract Reads in FASTQ" version="@VERSION@+galaxy0" profile="18.01">
2 <description>format from NCBI SRA</description> 2 <description>format from NCBI SRA</description>
3 <macros> 3 <macros>
4 <import>sra_macros.xml</import> 4 <import>sra_macros.xml</import>
5 </macros> 5 </macros>
6 <expand macro="requirements"/> 6 <expand macro="requirements"/>
7 <version_command>fasterq-dump --version</version_command> 7 <version_command>fasterq-dump --version</version_command>
8 <command detect_errors="exit_code"><![CDATA[ 8 <command detect_errors="exit_code"><![CDATA[
9 set -o | grep -q pipefail && set -o pipefail;
9 @COPY_CONFIGFILE@ 10 @COPY_CONFIGFILE@
10 @SET_ACCESSIONS@ 11 @SET_ACCESSIONS@
11 #if $input.input_select == "file": 12 #if $input.input_select == "file":
12 acc='${input.file.name}' && 13 acc='${input.file.name}' &&
13 ln -s '${input.file}' "\$acc" && 14 ln -s '${input.file}' "\$acc" &&
17 fasterq-dump "\$acc" -e \${GALAXY_SLOTS:-1} 18 fasterq-dump "\$acc" -e \${GALAXY_SLOTS:-1}
18 $adv.split 19 $adv.split
19 #if str( $adv.minlen ) != "": 20 #if str( $adv.minlen ) != "":
20 --min-read-len "$adv.minlen" 21 --min-read-len "$adv.minlen"
21 #end if 22 #end if
22 $adv.skip_technical >> $log 2>&1 ; 23 $adv.skip_technical 2>&1 | tee $log;
23 if [ \$? == 0 ] && [ \$(ls *.fastq | wc -l) -ge 1 ]; then 24 if [ \$? == 0 ] && [ \$(ls *.fastq | wc -l) -ge 1 ]; then
24 break ; 25 break ;
25 else 26 else
26 echo "Prefetch attempt \$SRA_PREFETCH_ATTEMPT of \$SRA_PREFETCH_RETRIES exited with code \$?" ; 27 echo "Prefetch attempt \$SRA_PREFETCH_ATTEMPT of \$SRA_PREFETCH_RETRIES exited with code \$?" ;
27 SRA_PREFETCH_ATTEMPT=`expr \$SRA_PREFETCH_ATTEMPT + 1` ; 28 SRA_PREFETCH_ATTEMPT=`expr \$SRA_PREFETCH_ATTEMPT + 1` ;