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comparison fasterq_dump.xml @ 16:aad3885b3216 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit 2be63abd7e4db27fa32ecbbc10d48cacb0073115"
author iuc
date Fri, 20 Mar 2020 12:47:18 -0400
parents f5ea3ce9b9b0
children c441583adae5
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15:f5ea3ce9b9b0 16:aad3885b3216
1 <tool id="fasterq_dump" name="Faster Download and Extract Reads in FASTQ" version="@VERSION@.4" profile="16.01"> 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 <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
10 @SET_ACCESSIONS@ 9 @SET_ACCESSIONS@
11 #if $input.input_select == "file": 10 #if $input.input_select == "file":
12 acc='${input.file.name}' && 11 acc='${input.file.name}' &&
13 ln -s '${input.file}' "\$acc" && 12 ln -s '${input.file}' "\$acc" &&
14 #end if 13 #end if
15 14 @CONFIGURE_TIMEOUT@
16 fasterq-dump "\$acc" -e \${GALAXY_SLOTS:-1} 15 fasterq-dump "\$acc" -e \${GALAXY_SLOTS:-1}
17 $adv.split 16 $adv.split
18 #if str( $adv.minlen ) != "": 17 #if str( $adv.minlen ) != "":
19 --min-read-len "$adv.minlen" 18 --min-read-len "$adv.minlen"
20 #end if 19 #end if