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comparison metabat2.xml @ 3:55a1b03696bf draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/ commit 37e664b4211a39ac3dba2adb871c0b0ec80a4215
author iuc
date Sat, 25 Jan 2025 21:15:49 +0000
parents 4a4a2b21a89c
children
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2:4a4a2b21a89c 3:55a1b03696bf
1 <tool id="metabat2" name="MetaBAT2" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@"> 1 <tool id="metabat2" name="MetaBAT2" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
2 <description>metagenome binning</description> 2 <description>metagenome binning</description>
3 <macros> 3 <macros>
4 <import>macros.xml</import> 4 <import>macros.xml</import>
5 </macros> 5 </macros>
6 <expand macro="biotools"/>
6 <expand macro="requirements"/> 7 <expand macro="requirements"/>
7 <command detect_errors="exit_code"><![CDATA[ 8 <command detect_errors="exit_code"><![CDATA[
8 mkdir bins && 9 mkdir bins &&
9 metabat2 10 metabat2
10 --inFile '$inFile' 11 --inFile '$inFile'
75 <option value="log">Process log file</option> 76 <option value="log">Process log file</option>
76 </param> 77 </param>
77 </section> 78 </section>
78 </inputs> 79 </inputs>
79 <outputs> 80 <outputs>
80 <collection name="bins" type="list" label="${tool.name} on ${on_string}: Bins"> 81 <collection name="bins" type="list" label="${tool.name} on ${on_string}: Bin sequences">
81 <filter>not out['saveCls'] and not out['onlyLabel']</filter> 82 <filter>not out['saveCls'] and not out['onlyLabel']</filter>
82 <discover_datasets pattern="bin\.(?P&lt;designation&gt;\d*)\.fa" format="fasta" directory="bins"/> 83 <discover_datasets pattern="bin\.(?P&lt;designation&gt;\d*)\.fa" format="fasta" directory="bins"/>
83 </collection> 84 </collection>
84 <data name="bin_saveCls" format="tabular" from_work_dir="bins/bin" label="${tool.name} on ${on_string}: Bins"> 85 <data name="bin_saveCls" format="tabular" from_work_dir="bins/bin" label="${tool.name} on ${on_string}: Bins with cluster memberships">
85 <filter>out['saveCls'] and not out['onlyLabel']</filter> 86 <filter>out['saveCls'] and not out['onlyLabel']</filter>
86 </data> 87 </data>
87 <collection name="bin_onlyLabel" type="list" label="${tool.name} on ${on_string}: Bins"> 88 <collection name="bin_onlyLabel" type="list" label="${tool.name} on ${on_string}: Bin labels">
88 <filter>not out['saveCls'] and out['onlyLabel']</filter> 89 <filter>not out['saveCls'] and out['onlyLabel']</filter>
89 <discover_datasets pattern="bin\.(?P&lt;designation&gt;\d*)" format="tabular" directory="bins"/> 90 <discover_datasets pattern="bin\.(?P&lt;designation&gt;\d*)" format="tabular" directory="bins"/>
90 </collection> 91 </collection>
91 <data name="lowDepth" format="fasta" from_work_dir="bins/bin.lowDepth.fa" label="${tool.name} on ${on_string}: Low depth bins"> 92 <data name="lowDepth" format="fasta" from_work_dir="bins/bin.lowDepth.fa" label="${tool.name} on ${on_string}: Low depth bins">
92 <filter>not out['saveCls'] and not out['onlyLabel'] and 'lowDepth' in out['extra_outputs']</filter> 93 <filter>not out['saveCls'] and not out['onlyLabel'] and 'lowDepth' in out['extra_outputs']</filter>