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comparison hapog.xml @ 2:ee0d6e789958 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hapog commit 0da1ca313d02ca780a671247e434a424fa67887b
author iuc
date Sun, 28 Jan 2024 23:46:07 +0000
parents 7d56a813fd24
children 5287036a797a
comparison
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1:7d56a813fd24 2:ee0d6e789958
1 <tool id="hapog" name="Hapo-G" profile="21.05" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@"> 1 <tool id="hapog" name="Hapo-G" profile="21.05" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
2 <description>genome polishing</description> 2 <description>genome polishing</description>
3 <macros> 3 <macros>
4 <token name="@TOOL_VERSION@">1.3.6</token> 4 <token name="@TOOL_VERSION@">1.3.7</token>
5 <token name="@VERSION_SUFFIX@">0</token> 5 <token name="@VERSION_SUFFIX@">0</token>
6 </macros> 6 </macros>
7 <xrefs>
8 <xref type="bio.tools">hapog</xref>
9 </xrefs>
7 <requirements> 10 <requirements>
8 <requirement type="package" version="@TOOL_VERSION@">hapog</requirement> 11 <requirement type="package" version="@TOOL_VERSION@">hapog</requirement>
9 </requirements> 12 </requirements>
10 <command detect_errors="exit_code"><![CDATA[ 13 <command detect_errors="exit_code"><![CDATA[
14 ##Compute samtools memory settings like in samtools_sort
15 ##use only 75% of available: https://github.com/samtools/samtools/issues/831
16 addmemory=\${GALAXY_MEMORY_MB_PER_SLOT:-768} &&
17 ((addmemory=addmemory*75/100)) &&
11 hapog 18 hapog
12 --genome '${genome}' 19 --genome '${genome}'
13 --output output/ 20 --output output/
14 21
15 ## setting default threads to 2 until 22 --threads \${GALAXY_SLOTS:-1}
16 ## https://github.com/institut-de-genomique/HAPO-G/issues/34 23 --samtools-mem \$addmemory"M"
17 ## gets addressed, at least
18 --threads \${GALAXY_SLOTS:-2}
19 24
20 #if str( $reads.type ) == "short": 25 #if str( $reads.type ) == "short":
21 #for $i in $reads.pe1 26 #for $i in $reads.pe1
22 --pe1 '${i}' 27 --pe1 '${i}'
23 #end for 28 #end for