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comparison shovill.xml @ 5:8d1af5db538d draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit da99aa8018e36c84fc4cbd7c73923fc710b3b31a"
author iuc
date Sun, 28 Jun 2020 04:16:16 -0400
parents d9f6a00b6db7
children 83ead2be47b2
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4:d9f6a00b6db7 5:8d1af5db538d
1 <tool id="shovill" name="Shovill" version="@TOOL_VERSION@+galaxy0"> 1 <tool id="shovill" name="Shovill" version="@TOOL_VERSION@+galaxy1">
2 <description>Faster SPAdes assembly of Illumina reads</description> 2 <description>Faster SPAdes assembly of Illumina reads</description>
3 <macros> 3 <macros>
4 <token name="@TOOL_VERSION@">1.0.4</token> 4 <token name="@TOOL_VERSION@">1.0.4</token>
5 </macros> 5 </macros>
6 <requirements> 6 <requirements>
17 #set r1_ext = $library.input1.forward.extension 17 #set r1_ext = $library.input1.forward.extension
18 #set r2_ext = $library.input1.reverse.extension 18 #set r2_ext = $library.input1.reverse.extension
19 ln -s '$library.input1.forward' fastq_r1.'$r1_ext' && 19 ln -s '$library.input1.forward' fastq_r1.'$r1_ext' &&
20 ln -s '$library.input1.reverse' fastq_r2.'$r2_ext' && 20 ln -s '$library.input1.reverse' fastq_r2.'$r2_ext' &&
21 #end if 21 #end if
22
23 ## Sets the memory used by Shovill according to the following conditions
24 ## (1) If SHOVILL_RAM is already set, use this value
25 ## (2) Otherwise, set based on GALAXY_MEMORY_MB
26 ## (3) Or default to 4 GB if GALAXY_MEMORY_MB is unset
27 GALAXY_MEMORY_GB=\$((\${GALAXY_MEMORY_MB:-4096}/1024)) &&
28 SHOVILL_RAM=\${SHOVILL_RAM:-\${GALAXY_MEMORY_GB}} &&
22 29
23 shovill 30 shovill
24 --outdir 'out' 31 --outdir 'out'
25 --cpus \${GALAXY_SLOTS:-1} 32 --cpus \${GALAXY_SLOTS:-1}
26 --ram \${SHOVILL_RAM:-4} 33 --ram \${SHOVILL_RAM:-4}