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comparison bin.xml @ 0:84b8e9bd88aa draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4
author iuc
date Fri, 14 Oct 2022 22:10:54 +0000
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children 897bb1b6c6c7
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-1:000000000000 0:84b8e9bd88aa
1 <tool id="semibin_bin" name="SemiBin: Group the contigs" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
2 <description>
3 into bins
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 #import re
13 @FASTA_FILES@
14 SemiBin bin
15 --input-fasta 'contigs.fasta'
16 --data '$data'
17 #if $mod.select == 'history'
18 --model '$mod.model'
19 #else
20 --environment '$mod.environment'
21 #end if
22 --output 'output'
23 --threads \${GALAXY_SLOTS:-1}
24 --minfasta-kbs $minfasta_kbs
25 $no_recluster
26 --max-node $max_node
27 --max-edges $max_edges
28 --random-seed $random_seed
29 @MIN_LEN@
30 --orf-finder '$orf_finder'
31 ]]></command>
32 <inputs>
33 <expand macro="mode_fasta"/>
34 <expand macro="data"/>
35 <conditional name="mod">
36 <param name="select" type="select" label="Model to use">
37 <option value="built-in" selected="true">Built-in model</option>
38 <option value="history">From history</option>
39 </param>
40 <when value="built-in">
41 <expand macro="environment"/>
42 </when>
43 <when value="history">
44 <param argument="--model" type="data" format="h5" label="Trained semi-supervised deep learning model"/>
45 </when>
46 </conditional>
47 <expand macro="min_len"/>
48 <expand macro="orf-finder"/>
49 <expand macro="random-seed"/>
50 <expand macro="max-node"/>
51 <expand macro="max-edges"/>
52 <expand macro="minfasta-kbs"/>
53 <expand macro="no-recluster"/>
54 </inputs>
55 <outputs>
56 <collection name="output_recluster_bins" type="list" label="${tool.name} on ${on_string}: Reconstructed bins after reclustering">
57 <filter>not no_recluster</filter>
58 <discover_datasets pattern=".*?\.(?P&lt;designation&gt;.*).fa" format="fasta" directory="output/output_recluster_bins" />
59 </collection>
60 <collection name="output_bins" type="list" label="${tool.name} on ${on_string}: Reconstructed bins before reclustering">
61 <discover_datasets pattern=".*?\.(?P&lt;designation&gt;.*).fa" format="fasta" directory="output/output_bins" />
62 </collection>
63 </outputs>
64 <tests>
65 <test expect_num_outputs="2">
66 <conditional name="mode">
67 <param name="select" value="single"/>
68 <param name="input_fasta" ftype="fasta" value="input_single.fasta"/>
69 </conditional>
70 <param name="data" ftype="csv" value="data.csv"/>
71 <conditional name="mod">
72 <param name="select" value="history"/>
73 <param name="model" ftype="h5" value="model.h5"/>
74 </conditional>
75 <conditional name="min_len">
76 <param name="method" value="min-len"/>
77 <param name="min_len" value="0" />
78 </conditional>
79 <param name="orf_finder" value="prodigal"/>
80 <param name="random-seed" value="0"/>
81 <param name="max_node" value="1"/>
82 <param name="max_edges" value="200"/>
83 <param name="minfasta_kbs" value="200"/>
84 <param name="no_recluster" value="false"/>
85 <output_collection name="output_recluster_bins" count="0"/>
86 <output_collection name="output_bins" count="3">
87 <element name="0" ftype="fasta">
88 <assert_contents>
89 <has_text text=">g1k_0"/>
90 <has_text text=">g4k_9"/>
91 </assert_contents>
92 </element>
93 <element name="1" ftype="fasta">
94 <assert_contents>
95 <has_text text=">g2k_0"/>
96 <has_text text=">g2k_9"/>
97 </assert_contents>
98 </element>
99 <element name="2" ftype="fasta">
100 <assert_contents>
101 <has_text text=">g3k_0"/>
102 <has_text text=">g3k_9"/>
103 </assert_contents>
104 </element>
105 </output_collection>
106 </test>
107 <test expect_num_outputs="1">
108 <conditional name="mode">
109 <param name="select" value="single"/>
110 <param name="input_fasta" ftype="fasta" value="input_single.fasta"/>
111 </conditional>
112 <param name="data" ftype="csv" value="data.csv"/>
113 <conditional name="mod">
114 <param name="select" value="built-in"/>
115 <param name="environment" value="human_gut"/>
116 </conditional>
117 <conditional name="min_len">
118 <param name="method" value="min-len"/>
119 <param name="min_len" value="0" />
120 </conditional>
121 <param name="orf_finder" value="prodigal"/>
122 <param name="random-seed" value="0"/>
123 <param name="max_node" value="1"/>
124 <param name="max_edges" value="200"/>
125 <param name="minfasta_kbs" value="200"/>
126 <param name="no_recluster" value="true"/>
127 <output_collection name="output_bins" count="3">
128 <element name="0" ftype="fasta">
129 <assert_contents>
130 <has_text text=">g1k_0"/>
131 <has_text text=">g4k_9"/>
132 </assert_contents>
133 </element>
134 <element name="1" ftype="fasta">
135 <assert_contents>
136 <has_text text=">g2k_0"/>
137 <has_text text=">g2k_9"/>
138 </assert_contents>
139 </element>
140 <element name="2" ftype="fasta">
141 <assert_contents>
142 <has_text text=">g3k_0"/>
143 <has_text text=">g3k_9"/>
144 </assert_contents>
145 </element>
146 </output_collection>
147 </test>
148 </tests>
149 <help><![CDATA[
150 @HELP_HEADER@
151
152 Inputs
153 ======
154
155 @HELP_INPUT_FASTA@
156 @HELP_INPUT_BAM@
157
158 Outputs
159 =======
160
161 @HELP_BINS@
162
163 ]]></help>
164 <expand macro="citations"/>
165 </tool>