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comparison analyze.xml @ 0:7ce554541b5c 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 20:20:18 +0000
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children d5c2aa105c2e
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-1:000000000000 0:7ce554541b5c
1 <tool id="checkm_analyze" name="CheckM analyze" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
2 <description>
3 Identify marker genes in bins and calculate genome statistics
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 @BIN_INPUTS@
13
14 checkm analyze
15 '$marker_file'
16 'bins'
17 'output'
18 $ali
19 $nt
20 $genes
21 --extension 'fasta'
22 --threads \${GALAXY_SLOTS:-1}
23 ]]></command>
24 <inputs>
25 <expand macro="bin_inputs" />
26 <expand macro="marker_file" />
27 <expand macro="analyze_params"/>
28 <param name="extra_outputs" type="select" multiple="true" optional="true" label="Extra outputs">
29 <expand macro="analyze_extra_output_options" />
30 </param>
31 </inputs>
32 <outputs>
33 <collection name="hmmer_analyze" type="list" label="${tool.name} on ${on_string}: Marker gene HMM hits to each bin">
34 <discover_datasets pattern="(?P&lt;designation&gt;.*)/hmmer\.analyze\.txt" format="txt" directory="output/bins/" recurse="true" match_relative_path="true"/>
35 </collection>
36 <data name="bin_stats_analyze" format="tabular" from_work_dir="output/storage/bin_stats.analyze.tsv" label="${tool.name} on ${on_string}: Marker gene bin stats" />
37 <data name="checkm_hmm_info" format="zip" from_work_dir="output/storage/checkm_hmm_info.pkl.gz" label="${tool.name} on ${on_string}: Marker gene HMM info for each bin" />
38 <collection name="hmmer_analyze_ali" type="list" label="${tool.name} on ${on_string}: HMMER alignment file for each bin">
39 <filter>ali and 'hmmer_analyze_ali' in extra_outputs</filter>
40 <discover_datasets pattern="(?P&lt;designation&gt;.*)/hmmer\.analyze\.ali\.txt" format="txt" directory="output/bins/" recurse="true" match_relative_path="true"/>
41 </collection>
42 </outputs>
43 <tests>
44 <test expect_num_outputs="3">
45 <conditional name="bins">
46 <param name="select" value="collection"/>
47 <param name="bins_coll">
48 <collection type="list">
49 <element name="637000110" ftype="fasta" value="637000110.fna"/>
50 </collection>
51 </param>
52 </conditional>
53 <param name="marker_file" ftype="tabular" value="lineage_marker_set"/>
54 <param name="ali" value="false"/>
55 <param name="nt" value="false"/>
56 <param name="genes" value="false"/>
57 <param name="extra_outputs" value=""/>
58 <output_collection name="hmmer_analyze" count="1">
59 <element name="637000110" ftype="txt">
60 <assert_contents>
61 <has_text text="target name"/>
62 <has_text text="AC_000091_859"/>
63 </assert_contents>
64 </element>
65 </output_collection>
66 <output name="bin_stats_analyze" ftype="tabular">
67 <assert_contents>
68 <has_text text="637000110"/>
69 <has_text text="GC"/>
70 <has_text text="GC std"/>
71 </assert_contents>
72 </output>
73 <output name="checkm_hmm_info" ftype="zip">
74 <assert_contents>
75 <has_size value="99600" delta="500"/>
76 </assert_contents>
77 </output>
78 </test>
79 <test expect_num_outputs="4">
80 <conditional name="bins">
81 <param name="select" value="collection"/>
82 <param name="bins_coll">
83 <collection type="list">
84 <element name="637000110" ftype="fasta" value="637000110.fna"/>
85 </collection>
86 </param>
87 </conditional>
88 <param name="marker_file" ftype="tabular" value="lineage_marker_set"/>
89 <param name="ali" value="true"/>
90 <param name="nt" value="true"/>
91 <param name="genes" value="false"/>
92 <param name="extra_outputs" value="hmmer_analyze_ali"/>
93 <output_collection name="hmmer_analyze" count="1">
94 <element name="637000110" ftype="txt">
95 <assert_contents>
96 <has_text text="target name"/>
97 <has_text text="AC_000091_859"/>
98 </assert_contents>
99 </element>
100 </output_collection>
101 <output name="bin_stats_analyze" ftype="tabular">
102 <assert_contents>
103 <has_text text="637000110"/>
104 <has_text text="GC"/>
105 <has_text text="GC std"/>
106 </assert_contents>
107 </output>
108 <output name="checkm_hmm_info" ftype="zip">
109 <assert_contents>
110 <has_size value="99600" delta="500"/>
111 </assert_contents>
112 </output>
113 <output_collection name="hmmer_analyze_ali" count="1">
114 <element name="637000110" ftype="txt">
115 <assert_contents>
116 <has_text text="hmmsearch"/>
117 <has_text text="Query"/>
118 <has_text text="ACCA"/>
119 </assert_contents>
120 </element>
121 </output_collection>
122 </test>
123 </tests>
124 <help><![CDATA[
125 @HELP_HEADER@
126
127 This command identifies marker genes in bins and calculates genome statistics
128 ]]></help>
129 <expand macro="citations"/>
130 </tool>