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comparison bin.xml @ 2:1bd3c93f565f draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit a9fc83e0029266f910b549d5d1eef6a9bc3e3f7b
author iuc
date Tue, 25 Mar 2025 15:51:24 +0000
parents 897bb1b6c6c7
children b8dab9f6d5f7
comparison
equal deleted inserted replaced
1:897bb1b6c6c7 2:1bd3c93f565f
9 <expand macro="requirements"/> 9 <expand macro="requirements"/>
10 <expand macro="version"/> 10 <expand macro="version"/>
11 <command detect_errors="exit_code"><![CDATA[ 11 <command detect_errors="exit_code"><![CDATA[
12 #import re 12 #import re
13 @FASTA_FILES@ 13 @FASTA_FILES@
14 SemiBin bin 14 SemiBin2 bin
15 --input-fasta 'contigs.fasta' 15 --input-fasta 'contigs.fasta'
16 --data '$data' 16 --data '$data'
17 #if $mod.select == 'history' 17 #if $mod.select == 'history'
18 --model '$mod.model' 18 --model '$mod.model'
19 #else 19 #else
20 --environment '$mod.environment' 20 --environment '$mod.environment'
21 #end if 21 #end if
22 --output 'output' 22 --output 'output'
23 --threads \${GALAXY_SLOTS:-1} 23 --threads \${GALAXY_SLOTS:-1}
24 --minfasta-kbs $minfasta_kbs 24 --minfasta-kbs $minfasta_kbs
25 $no_recluster 25 #if $mode.select == 'single' or $mode_fasta.mode_select == 'co'
26 $write_pre_reclustering_bins
27 #end if
26 --max-node $max_node 28 --max-node $max_node
27 --max-edges $max_edges 29 --max-edges $max_edges
28 --random-seed $random_seed 30 --random-seed $random_seed
31 --compression none
29 @MIN_LEN@ 32 @MIN_LEN@
30 --orf-finder '$orf_finder' 33 --orf-finder '$orf_finder'
31 ]]></command> 34 ]]></command>
32 <inputs> 35 <inputs>
33 <expand macro="mode_fasta"/> 36 <expand macro="mode_fasta"/>
48 <expand macro="orf-finder"/> 51 <expand macro="orf-finder"/>
49 <expand macro="random-seed"/> 52 <expand macro="random-seed"/>
50 <expand macro="max-node"/> 53 <expand macro="max-node"/>
51 <expand macro="max-edges"/> 54 <expand macro="max-edges"/>
52 <expand macro="minfasta-kbs"/> 55 <expand macro="minfasta-kbs"/>
53 <expand macro="no-recluster"/> 56 <expand macro="write_pre_reclustering_bins"/>
54 </inputs> 57 </inputs>
55 <outputs> 58 <outputs>
56 <collection name="output_recluster_bins" type="list" label="${tool.name} on ${on_string}: Reconstructed bins after reclustering"> 59 <collection name="output_bins" type="list" label="${tool.name} on ${on_string}: Reconstructed bins after reclustering">
57 <filter>not no_recluster</filter> 60 <filter>not write_pre_reclustering_bins</filter>
58 <discover_datasets pattern=".*?\.(?P&lt;designation&gt;.*).fa" format="fasta" directory="output/output_recluster_bins" /> 61 <discover_datasets pattern="(?P&lt;designation&gt;.*).fa" format="fasta" directory="output/output_bins" />
59 </collection> 62 </collection>
60 <collection name="output_prerecluster_bins" type="list" label="${tool.name} on ${on_string}: Reconstructed bins before reclustering"> 63 <collection name="output_recluster_bins" type="list" label="${tool.name} on ${on_string}: Reclustered bins?">
61 <filter>not no_recluster</filter> 64 <filter>write_pre_reclustering_bins</filter>
62 <discover_datasets pattern=".*?\.(?P&lt;designation&gt;.*).fa" format="fasta" directory="output/output_prerecluster_bins" /> 65 <discover_datasets pattern="(?P&lt;designation&gt;.*).fa" format="fasta" directory="output/output_recluster_bins" />
63 </collection> 66 </collection>
64 <collection name="output_bins" type="list" label="${tool.name} on ${on_string}: Reconstructed bins without reeclustering"> 67 <collection name="output_prerecluster_bins" type="list" label="${tool.name} on ${on_string}: Pre reclustered bins">
65 <filter>no_recluster</filter> 68 <filter>write_pre_reclustering_bins</filter>
66 <discover_datasets pattern=".*?\.(?P&lt;designation&gt;.*).fa" format="fasta" directory="output/output_bins" /> 69 <discover_datasets pattern="(?P&lt;designation&gt;.*).fa" format="fasta" directory="output/output_prerecluster_bins" />
67 </collection> 70 </collection>
68 </outputs> 71 </outputs>
69 <tests> 72 <tests>
70 <test expect_num_outputs="2"> 73 <test expect_num_outputs="2">
71 <conditional name="mode"> 74 <conditional name="mode">
80 <conditional name="min_len"> 83 <conditional name="min_len">
81 <param name="method" value="min-len"/> 84 <param name="method" value="min-len"/>
82 <param name="min_len" value="0" /> 85 <param name="min_len" value="0" />
83 </conditional> 86 </conditional>
84 <param name="orf_finder" value="prodigal"/> 87 <param name="orf_finder" value="prodigal"/>
85 <param name="random-seed" value="0"/> 88 <param name="random_seed" value="0"/>
86 <param name="max_node" value="1"/> 89 <param name="max_node" value="1"/>
87 <param name="max_edges" value="200"/> 90 <param name="max_edges" value="200"/>
88 <param name="minfasta_kbs" value="200"/> 91 <param name="minfasta_kbs" value="200"/>
89 <param name="no_recluster" value="false"/> 92 <param name="write_pre_reclustering_bins" value="true"/>
90 <output_collection name="output_recluster_bins" count="0"/>
91 <output_collection name="output_prerecluster_bins" count="3"> 93 <output_collection name="output_prerecluster_bins" count="3">
92 <element name="0" ftype="fasta"> 94 <element name="SemiBin_0" ftype="fasta">
93 <assert_contents> 95 <assert_contents>
94 <has_text text=">g1k_0"/> 96 <has_text text=">g1k_0"/>
95 <has_text text=">g4k_9"/> 97 <has_text text=">g4k_9"/>
96 </assert_contents> 98 </assert_contents>
97 </element> 99 </element>
98 <element name="1" ftype="fasta"> 100 <element name="SemiBin_1" ftype="fasta">
99 <assert_contents> 101 <assert_contents>
100 <has_text text=">g2k_0"/> 102 <has_text text=">g2k_0"/>
101 <has_text text=">g2k_9"/> 103 <has_text text=">g2k_9"/>
102 </assert_contents> 104 </assert_contents>
103 </element> 105 </element>
104 <element name="2" ftype="fasta"> 106 <element name="SemiBin_2" ftype="fasta">
105 <assert_contents> 107 <assert_contents>
106 <has_text text=">g3k_0"/> 108 <has_text text=">g3k_0"/>
107 <has_text text=">g3k_9"/> 109 <has_text text=">g3k_9"/>
108 </assert_contents> 110 </assert_contents>
109 </element> 111 </element>
122 <conditional name="min_len"> 124 <conditional name="min_len">
123 <param name="method" value="min-len"/> 125 <param name="method" value="min-len"/>
124 <param name="min_len" value="0" /> 126 <param name="min_len" value="0" />
125 </conditional> 127 </conditional>
126 <param name="orf_finder" value="prodigal"/> 128 <param name="orf_finder" value="prodigal"/>
127 <param name="random-seed" value="0"/> 129 <param name="random_seed" value="0"/>
128 <param name="max_node" value="1"/> 130 <param name="max_node" value="1"/>
129 <param name="max_edges" value="200"/> 131 <param name="max_edges" value="200"/>
130 <param name="minfasta_kbs" value="200"/> 132 <param name="minfasta_kbs" value="200"/>
131 <param name="no_recluster" value="true"/> 133 <param name="write_pre_reclustering_bins" value="false"/>
132 <output_collection name="output_bins" count="3"> 134 <output_collection name="output_bins" count="0"/>
133 <element name="0" ftype="fasta"> 135 </test>
134 <assert_contents> 136 <test expect_num_outputs="2">
135 <has_text text=">g1k_0"/> 137 <conditional name="mode">
136 <has_text text=">g4k_9"/> 138 <param name="select" value="single"/>
137 </assert_contents> 139 <param name="input_fasta" ftype="fasta" value="input_single.fasta"/>
138 </element> 140 </conditional>
139 <element name="1" ftype="fasta"> 141 <param name="data" ftype="csv" value="data.csv"/>
140 <assert_contents> 142 <conditional name="mod">
141 <has_text text=">g2k_0"/> 143 <param name="select" value="history"/>
142 <has_text text=">g2k_9"/> 144 <param name="model" ftype="h5" value="model.h5"/>
143 </assert_contents> 145 </conditional>
144 </element> 146 <conditional name="min_len">
145 <element name="2" ftype="fasta"> 147 <param name="method" value="min-len"/>
146 <assert_contents> 148 <param name="min_len" value="0" />
147 <has_text text=">g3k_0"/> 149 </conditional>
148 <has_text text=">g3k_9"/> 150 <param name="orf_finder" value="prodigal"/>
149 </assert_contents> 151 <param name="random_seed" value="0"/>
150 </element> 152 <param name="max_node" value="1"/>
151 </output_collection> 153 <param name="max_edges" value="200"/>
154 <param name="minfasta_kbs" value="200"/>
155 <param name="write_pre_reclustering_bins" value="true"/>
156 <output_collection name="output_prerecluster_bins" count="3"/>
152 </test> 157 </test>
153 </tests> 158 </tests>
154 <help><![CDATA[ 159 <help><![CDATA[
155 @HELP_HEADER@ 160 @HELP_HEADER@
156 161