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comparison das_tool.xml @ 0:57e7d0b1681c draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/das_tool commit 151c0e625ce20fb3ea75aa5043486e41b1da48de
author iuc
date Mon, 27 Jun 2022 12:39:41 +0000
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children 2134c6475514
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-1:000000000000 0:57e7d0b1681c
1 <tool id="das_tool" name="DAS Tool" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
2 <description>
3 for genome resolved metagenomics
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 #set $bins = ""
13 #set $labels = ""
14 #set $sep = ""
15 #for $i, $s in enumerate($binning)
16 #set $bins += "%s%s" %($sep, $s.bins)
17 #set $labels += "%s%s" %($sep, $s.labels)
18 #set $sep = ","
19 #end for
20
21 #if $adv.proteins
22 ln -s $adv.proteins 'proteins' &&
23 #end if
24
25 DAS_Tool
26 --contigs '$contigs'
27 --outputbasename 'outputs'
28 --bins '$bins'
29 --labels '$labels'
30 --search_engine '$adv.search_engine'
31 #if $adv.proteins
32 --proteins 'proteins'
33 #end if
34 --score_threshold $adv.score_threshold
35 --duplicate_penalty $adv.duplicate_penalty
36 --megabin_penalty $adv.megabin_penalty
37 $output.write_bin_evals
38 $output.write_bins.write_bins
39 #if str($output.write_bins.write_bins) != ''
40 $output.write_bins.write_unbinned
41 #end if
42 $output.debug
43 --threads \${GALAXY_SLOTS:-1}
44 ]]></command>
45 <inputs>
46 <param argument="--contigs" type="data" format="fasta" label="Contig sequences"/>
47 <repeat name="binning" title="Bins" min="1">
48 <param argument="--bins" type="data" format="tabular" label="Contigs-to-bin table" help="Tabular with two columns: contig-IDs and bin-IDs. Fasta_to_Contigs2Bin can be used to Converts genome bins in fasta format to Contigs-to-bin table"/>
49 <param argument="--labels" type="text" value="" label="Name of binning prediction tool used to generate the table"/>
50 </repeat>
51 <section name="adv" title="Advanced options">
52 <param argument="--search_engine" type="select" label="Engine used for single copy gene identification">
53 <option value="diamond" selected="true">diamond</option>
54 <option value="blastp">blastp</option>
55 </param>
56 <param argument="--proteins" type="data" format="fasta" optional="true" label="Predicted proteins" help="The file should be prodigal fasta format: >contigID_geneNo"/>
57 <param argument="--score_threshold" type="float" min="0" max="1" value="0.5" label="Score threshold until selection algorithm will keep selecting bins"/>
58 <param argument="--duplicate_penalty" type="float" min="0" max="3" value="0.6" label="Penalty for duplicate single copy genes per bin (weight b)" help="Only change if you know what you are doing"/>
59 <param argument="--megabin_penalty" type="float" min="0" max="3" value="0.5" label="Penalty for megabins (weight c)" help="Only change if you know what you are doing"/>
60 </section>
61 <section name="output" title="Outputs">
62 <param name="proteins" type="boolean" checked="false" label="Output predicted proteins?"/>
63 <param argument="--write_bin_evals" type="boolean" truevalue="--write_bin_evals" falsevalue="" checked="false" label="Write evaluation of input bin sets?"/>
64 <conditional name="write_bins">
65 <param argument="--write_bins" type="select" label="Export bins as fasta files?">
66 <option value="--write_bins" selected="true">Yes</option>
67 <option value="">No</option>
68 </param>
69 <when value="--write_bins">
70 <param argument="--write_unbinned" type="boolean" truevalue="--write_unbinned" falsevalue="" checked="false" label="Export unbinned contigs as fasta file?"/>
71 </when>
72 <when value=""/>
73 </conditional>
74 <param argument="--debug" type="boolean" truevalue="--debug" falsevalue="" checked="false" label="Write debug information to log file?"/>
75 </section>
76 </inputs>
77 <outputs>
78 <data name="summary" format="tabular" from_work_dir="outputs_DASTool_summary.tsv" label="${tool.name} on ${on_string}: Summary of output bins" />
79 <data name="contigs2bin" format="tabular" from_work_dir="outputs_DASTool_contig2bin.tsv" label="${tool.name} on ${on_string}: Contigs to bin file for the output bins" />
80 <data name="log" format="txt" from_work_dir="outputs_DASTool.log" label="${tool.name} on ${on_string}: Log" />
81 <data name="eval" format="tabular" from_work_dir="outputs_allBins.eval" label="${tool.name} on ${on_string}: Quality and completeness estimates of input bin sets" >
82 <filter>output['write_bin_evals']</filter>
83 </data>
84 <collection name="bins" type="list" label="${tool.name} on ${on_string}: Bins">
85 <filter>output['write_bins']['write_bins'] != ""</filter>
86 <discover_datasets pattern=".*?\.(?P&lt;designation&gt;.*)\.fa" format="fasta" directory="outputs_DASTool_bins" />
87 </collection>
88 <data name="unbinned_contigs" format="fasta" from_work_dir="outputs_DASTool_bins/unbinned.fa" label="${tool.name} on ${on_string}: Unbinned contigs" >
89 <filter>output['write_bins']['write_bins'] != "" and output['write_bins']['write_unbinned']</filter>
90 </data>
91 <data name="proteins" format="fasta" from_work_dir="outputs_proteins.faa" label="${tool.name} on ${on_string}: Proteins" >
92 <filter>output['proteins']</filter>
93 </data>
94 </outputs>
95 <tests>
96 <test expect_num_outputs="4">
97 <param name="contigs" value="contigs.fasta"/>
98 <repeat name="binning">
99 <param name="bins" value="metabat.tabular"/>
100 <param name="labels" value="metabat"/>
101 </repeat>
102 <section name="adv">
103 <param name="search_engine" value="diamond"/>
104 <param name="proteins" value="proteins.fasta"/>
105 <param name="score_threshold" value="0.5"/>
106 <param name="duplicate_penalty" value="0.6"/>
107 <param name="megabin_penalty" value="0.5" />
108 </section>
109 <section name="output">
110 <param name="write_bin_evals" value="true"/>
111 <conditional name="write_bins">
112 <param name="write_bins" value=""/>
113 </conditional>
114 <param name="debug" value="true"/>
115 </section>
116 <output name="summary" ftype="tabular">
117 <assert_contents>
118 <has_text text="unique_SCGs"/>
119 <has_text text="metabat.8"/>
120 <has_text text="bacteria"/>
121 </assert_contents>
122 </output>
123 <output name="contigs2bin" ftype="tabular">
124 <assert_contents>
125 <has_text text="Ley3_66761_scaffold_6"/>
126 </assert_contents>
127 </output>
128 <output name="log" ftype="txt">
129 <assert_contents>
130 <has_text text="Skipping gene prediction"/>
131 <has_text text="#Target sequences to report alignments for: 1"/>
132 </assert_contents>
133 </output>
134 <output name="eval" ftype="tabular">
135 <assert_contents>
136 <has_text text="unique_SCGs"/>
137 <has_text text="metabat.8"/>
138 </assert_contents>
139 </output>
140 </test>
141 <test expect_num_outputs="6">
142 <param name="contigs" value="contigs.fasta"/>
143 <repeat name="binning">
144 <param name="bins" value="metabat.tabular"/>
145 <param name="labels" value="metabat"/>
146 </repeat>
147 <section name="adv">
148 <param name="search_engine" value="diamond"/>
149 <param name="score_threshold" value="0.5"/>
150 <param name="duplicate_penalty" value="0.6"/>
151 <param name="megabin_penalty" value="0.5" />
152 </section>
153 <section name="output">
154 <param name="proteins" value="true"/>
155 <param name="write_bin_evals" value="false"/>
156 <conditional name="write_bins">
157 <param name="write_bins" value="--write_bins"/>
158 <param name="write_unbinned" value="true"/>
159 </conditional>
160 <param name="debug" value="true"/>
161 </section>
162 <output name="summary" ftype="tabular">
163 <assert_contents>
164 <has_text text="unique_SCGs"/>
165 <has_text text="metabat.8"/>
166 <has_text text="bacteria"/>
167 </assert_contents>
168 </output>
169 <output name="contigs2bin" ftype="tabular">
170 <assert_contents>
171 <has_text text="Ley3_66761_scaffold_6"/>
172 </assert_contents>
173 </output>
174 <output name="log" ftype="txt">
175 <assert_contents>
176 <has_text text="Parameters"/>
177 <has_text text="Predicting genes"/>
178 </assert_contents>
179 </output>
180 <output_collection name="bins" count="1">
181 <element name="8" ftype="fasta">
182 <assert_contents>
183 <has_text text=">Ley3_66761_scaffold_6"/>
184 </assert_contents>
185 </element>
186 </output_collection>
187 <output name="unbinned_contigs" ftype="fasta">
188 <assert_contents>
189 <has_text text=">Ley3_66761_scaffold_505"/>
190 </assert_contents>
191 </output>
192 <output name="proteins" ftype="fasta">
193 <assert_contents>
194 <has_text text="Ley3_66761_scaffold_6_1 # 1 # 786 # 1 #"/>
195 </assert_contents>
196 </output>
197 </test>
198 </tests>
199 <help><![CDATA[
200 @HELP_HEADER@
201
202 Inputs
203 ======
204
205 - Bins: Tab separated files of contig-IDs and bin-IDs. Contigs to bin file example: ::
206
207 Contig_1 bin.01
208 Contig_8 bin.01
209 Contig_42 bin.02
210 Contig_49 bin.03
211
212 - Contigs: Assembled contigs in fasta format: ::
213
214 >Contig_1
215 ATCATCGTCCGCATCGACGAATTCGGCGAACGAGTACCCCTGACCATCTCCGATTA...
216 >Contig_2
217 GATCGTCACGCAGGCTATCGGAGCCTCGACCCGCAAGCTCTGCGCCTTGGAGCAGG...
218
219 - [Optional] Proteins: Predicted proteins in prodigal fasta format. Header contains contig-ID and gene number: ::
220
221 >Contig_1_1
222 MPRKNKKLPRHLLVIRTSAMGDVAMLPHALRALKEAYPEVKVTVATKSLFHPFFEG...
223 >Contig_1_2
224 MANKIPRVPVREQDPKVRATNFEEVCYGYNVEEATLEASRCLNCKNPRCVAACPVN...
225
226 Outputs
227 =======
228
229 - Summary of output bins including quality and completeness estimates
230 - Contigs to bin file of output bins
231 - [Optional] Quality and completeness estimates of input bin sets
232 - [Optional] Bins in fasta format
233 - [Optional] Unbinned contigs
234
235 ]]></help>
236 <expand macro="citations"/>
237 </tool>