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comparison checkm2.xml @ 3:b8962c1bce40 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/main/tools/checkm2/ commit 1d1f552e49a0faf7eb16acd3ecdd8d05142aeaf9
author iuc
date Mon, 29 Sep 2025 19:35:47 +0000
parents 33096c8893c3
children f203425336f1
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2:33096c8893c3 3:b8962c1bce40
1 <tool id="checkm2" name="checkm2" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="23.1"> 1 <tool id="checkm2" name="checkm2" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="23.1">
2 <description>Rapid assessment of genome bin quality using machine learning</description> 2 <description>Rapid assessment of genome bin quality using machine learning</description>
3 <macros> 3 <macros>
4 <!-- enable tests and output assertions on update --> 4 <!-- enable tests and output assertions on update -->
5 <token name="@TOOL_VERSION@">1.0.2</token> 5 <token name="@TOOL_VERSION@">1.0.2</token>
6 <token name="@VERSION_SUFFIX@">1</token> 6 <token name="@VERSION_SUFFIX@">2</token>
7 <token name="@IDX_DATA_TABLE@">checkm2</token> 7 <token name="@IDX_DATA_TABLE@">checkm2</token>
8 </macros> 8 </macros>
9 <xrefs> 9 <xrefs>
10 <xref type="bio.tools">checkm</xref> 10 <xref type="bio.tools">checkm</xref>
11 </xrefs> 11 </xrefs>
14 </requirements> 14 </requirements>
15 <command detect_errors="exit_code"><![CDATA[ 15 <command detect_errors="exit_code"><![CDATA[
16 #import re 16 #import re
17 mkdir input_dir && 17 mkdir input_dir &&
18 #for $i, $file in enumerate($input): 18 #for $i, $file in enumerate($input):
19 #set $cleaned = re.sub('[^\s\w\-\\.]', '_', str($file.element_identifier)) 19 #set $cleaned = re.sub('[^\w\-\\.]', '_', str($file.element_identifier))
20 ln -s '$file' 'input_dir/${cleaned}.dat' && 20 ln -s '$file' 'input_dir/${cleaned}.dat' &&
21 #end for 21 #end for
22 checkm2 predict 22 checkm2 predict
23 --input input_dir 23 --input input_dir
24 $model 24 $model