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comparison fasterq_dump.xml @ 36:1ec814014652 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit cb858cbf5d9e307b663105f674f1acaa4f90a1fb
author iuc
date Thu, 14 Mar 2024 15:21:59 +0000
parents 734abc7ac21d
children f8054ea1c365
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35:de0f7e0a3896 36:1ec814014652
1 <tool id="fasterq_dump" name="Faster Download and Extract Reads in FASTQ" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@"> 1 <tool id="fasterq_dump" name="Faster Download and Extract Reads in FASTQ" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
2 <description>format from NCBI SRA</description> 2 <description>format from NCBI SRA</description>
3 <macros> 3 <macros>
4 <import>macros.xml</import> 4 <import>macros.xml</import>
5 <token name="VERSION_SUFFIX">1</token>
5 </macros> 6 </macros>
6 <expand macro="edam_ontology"/> 7 <expand macro="edam_ontology"/>
7 <expand macro="bio_tools"/> 8 <expand macro="bio_tools"/>
8 <expand macro="requirements"/> 9 <expand macro="requirements"/>
9 <version_command>fasterq-dump --version | tr -d $'\n'</version_command> 10 <version_command>fasterq-dump --version | tr -d $'\n'</version_command>
11 set -o | grep -q pipefail && set -o pipefail; 12 set -o | grep -q pipefail && set -o pipefail;
12 @COPY_CONFIGFILE@ 13 @COPY_CONFIGFILE@
13 @CONFIGURE_RETRY@ 14 @CONFIGURE_RETRY@
14 @SET_ACCESSIONS@ 15 @SET_ACCESSIONS@
15 while [ \$SRA_PREFETCH_ATTEMPT -le \$SRA_PREFETCH_RETRIES ] ; do 16 while [ \$SRA_PREFETCH_ATTEMPT -le \$SRA_PREFETCH_RETRIES ] ; do
16 fasterq-dump "\$acc" -e \${GALAXY_SLOTS:-1} 17 fasterq-dump "\$acc"
18 -e \${GALAXY_SLOTS:-1}
19 -t \${TMPDIR}
17 --seq-defline '$adv.seq_defline' 20 --seq-defline '$adv.seq_defline'
18 --qual-defline '+' 21 --qual-defline '+'
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"