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comparison lineage_set.xml @ 0:b39999cdbf21 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
author iuc
date Fri, 29 Jul 2022 20:38:36 +0000
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-1:000000000000 0:b39999cdbf21
1 <tool id="checkm_lineage_set" name="CheckM lineage_set" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
2 <description>
3 Infer lineage-specific marker sets for each bin
4 </description>
5 <macros>
6 <import>macros.xml</import>
7 </macros>
8 <expand macro="biotools"/>
9 <expand macro="requirements"/>
10 <expand macro="version"/>
11 <command detect_errors="exit_code"><![CDATA[
12 @HMM_MARKER_STATS_INPUTS@
13 mkdir 'inputs/storage/tree' &&
14 ln -s '$concatenated_tre' 'inputs/storage/tree/concatenated.tre' &&
15
16 checkm lineage_set
17 'inputs'
18 '$marker'
19 --unique $unique
20 --multi $multi
21 $force_domain
22 $no_refinement
23 ]]></command>
24 <inputs>
25 <expand macro="hmm_marker_stats_inputs"/>
26 <param name="concatenated_tre" type="data" format="phyloxml" label="Concatenated tree" help="Output of the CheckM tree tool"/>
27 <expand macro="lineage_set_params" />
28 </inputs>
29 <outputs>
30 <expand macro="marker_output" />
31 </outputs>
32 <tests>
33 <test expect_num_outputs="1">
34 <param name="phylo_hmm_info" ftype="zip" value="phylo_hmm_info.pkl.gz"/>
35 <param name="bin_stats_tree" ftype="tabular" value="bin_stats.tree.tsv"/>
36 <param name="hmmer_tree">
37 <collection type="list">
38 <element name="637000110" ftype="txt" value="hmmer.tree.txt"/>
39 </collection>
40 </param>
41 <param name="concatenated_tre" ftype="phyloxml" value="concatenated.tre"/>
42 <param name="unique" value="10"/>
43 <param name="multi" value="10"/>
44 <param name="force_domain" value="false"/>
45 <param name="no_refinement" value="false"/>
46 <output name="marker" ftype="tabular">
47 <assert_contents>
48 <has_text text="637000110"/>
49 <has_text text="Lineage Marker File"/>
50 <has_text text="PF00203"/>
51 </assert_contents>
52 </output>
53 </test>
54 </tests>
55 <help><![CDATA[
56 @HELP_HEADER@
57
58 This command places bins in the genome tree.
59 ]]></help>
60 <expand macro="citations"/>
61 </tool>