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comparison yahs.xml @ 2:fc925f53cae7 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/yahs commit 73f497e595363dea7f041a4374c3a9518e7b9862
author iuc
date Wed, 27 Jul 2022 09:26:18 +0000
parents a3a92e30a727
children 39495e107274
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1:a3a92e30a727 2:fc925f53cae7
1 <tool id="yahs" name="YAHS" version="@VERSION@+galaxy@VERSION_SUFFIX@" profile="20.01"> 1 <tool id="yahs" name="YAHS" version="@VERSION@+galaxy@VERSION_SUFFIX@" profile="20.01">
2 <description>yet another HI-C scaffolding tool</description> 2 <description>yet another HI-C scaffolding tool</description>
3 <macros> 3 <macros>
4 <token name="@VERSION@">1.2a</token> 4 <token name="@VERSION@">1.2a</token>
5 <token name="@VERSION_SUFFIX@">0</token> 5 <token name="@VERSION_SUFFIX@">1</token>
6 </macros> 6 </macros>
7 <requirements> 7 <requirements>
8 <requirement type="package" version="@VERSION@">yahs</requirement> 8 <requirement type="package" version="@VERSION@">yahs</requirement>
9 <requirement type="package" version="1.11">samtools</requirement> 9 <requirement type="package" version="1.11">samtools</requirement>
10 <requirement type="package" version="3.9">python</requirement> 10 <requirement type="package" version="3.9">python</requirement>
51 #if $function.quality: 51 #if $function.quality:
52 -q $function.quality 52 -q $function.quality
53 #end if 53 #end if
54 $function.no_contig_ec 54 $function.no_contig_ec
55 $function.no_scaffold_ec 55 $function.no_scaffold_ec
56 -o yahs_out && 56 -o yahs_out
57 ls -lah && 57 #if $log_out
58 2> output.log
59 #end if
60 && ls -lah &&
58 python '$__tool_directory__/move_files.py' 61 python '$__tool_directory__/move_files.py'
59 && ls -lah ./* 62 && ls -lah ./*
60 #else: 63 #else:
61 ln -s '$function.fasta' input.fasta && 64 ln -s '$function.fasta' input.fasta &&
62 ln -s '$function.agp' input.agp && 65 ln -s '$function.agp' input.agp &&
63 agp_to_fasta input.agp input.fasta 66 agp_to_fasta input.agp input.fasta
64 #if $function.length: 67 #if $function.length:
65 -l $function.length 68 -l $function.length
66 #end if 69 #end if
67 -o output.fasta 70 -o output.fasta
71 #if $log_out:
72 2> output.log
73 #end if
68 #end if 74 #end if
69 ]]></command> 75 ]]></command>
70 <inputs> 76 <inputs>
71 <conditional name="function"> 77 <conditional name="function">
72 <param name="function_select" type="select" label="Which function would you like to run?"> 78 <param name="function_select" type="select" label="Which function would you like to run?">
83 <conditional name="enzyme_conditional"> 89 <conditional name="enzyme_conditional">
84 <param name="enzyme_options" type="select" label="Restriction enzyme used in Hi-C experiment" help="Hi-C experiments can use different restriction enzymes. 90 <param name="enzyme_options" type="select" label="Restriction enzyme used in Hi-C experiment" help="Hi-C experiments can use different restriction enzymes.
85 The enzyme frequency in contigs is used to normalize the Hi-C interaction frequency. Note that you need to specify the actual 91 The enzyme frequency in contigs is used to normalize the Hi-C interaction frequency. Note that you need to specify the actual
86 sequence of the cutting site for a restriction enzyme and not the enzyme name. You can also specify DNASE as an enzyme if you 92 sequence of the cutting site for a restriction enzyme and not the enzyme name. You can also specify DNASE as an enzyme if you
87 use an enzyme-free prep, e.g. Omin-C."> 93 use an enzyme-free prep, e.g. Omin-C.">
88 <option value="not_especified">Not especified</option> 94 <option value="not_specified">Not specified</option>
89 <option value="preconfigured">Preconfigured restriction enzymes</option> 95 <option value="preconfigured">Preconfigured restriction enzymes</option>
90 <option value="specific">Enter a specific sequence</option> 96 <option value="specific">Enter a specific sequence</option>
91 </param> 97 </param>
92 <when value="not_especified"/> 98 <when value="not_specified"/>
93 <when value="preconfigured"> 99 <when value="preconfigured">
94 <param name="preconfigured_enzymes" argument="-e" type="select" label="Preconfigured enzymes"> 100 <param name="preconfigured_enzymes" argument="-e" type="select" label="Preconfigured enzymes">
95 <option value="dovetail">Dovetail Chicago, Dovetail Hi-C or Phase: GATC</option> 101 <option value="dovetail">Dovetail Chicago, Dovetail Hi-C or Phase: GATC</option>
96 <option value="arima1">Arima Hi-C 1.0: GATC, GANTC</option> 102 <option value="arima1">Arima Hi-C 1.0: GATC, GANTC</option>
97 <option value="arima2">Arima Hi-C 2.0: GATC, GANTC, CTNAG, TTAA</option> 103 <option value="arima2">Arima Hi-C 2.0: GATC, GANTC, CTNAG, TTAA</option>
113 <param name="agp" type="data" format="agp" label="Input AGP file"/> 119 <param name="agp" type="data" format="agp" label="Input AGP file"/>
114 <param name="fasta" type="data" format="fasta" label="Contig fasta file"/> 120 <param name="fasta" type="data" format="fasta" label="Contig fasta file"/>
115 <param name="length" type='integer' label="Output fasta line length" value="60" min="1"/> 121 <param name="length" type='integer' label="Output fasta line length" value="60" min="1"/>
116 </when> 122 </when>
117 </conditional> 123 </conditional>
124 <param name="log_out" type="boolean" label="Output log file?" truevalue="yes" falsevalue="no"/>
118 </inputs> 125 </inputs>
119 <outputs> 126 <outputs>
120 <!-- INITIAL ROUNDS --> 127 <!-- INITIAL ROUNDS -->
121 <collection name="initial_agp_break" type="list" label="${tool.name} on ${on_string}: AGP initial break files"> 128 <collection name="initial_agp_break" type="list" label="${tool.name} on ${on_string}: AGP initial break files">
122 <filter>function['function_select'] == "yahs"</filter> 129 <filter>function['function_select'] == "yahs"</filter>
138 <filter>function['function_select'] == "yahs"</filter> 145 <filter>function['function_select'] == "yahs"</filter>
139 </data> 146 </data>
140 <data format="fasta" name="fasta_from_agp" label="${tool.name} on ${on_string}: agp to fasta" from_work_dir="output.fasta"> 147 <data format="fasta" name="fasta_from_agp" label="${tool.name} on ${on_string}: agp to fasta" from_work_dir="output.fasta">
141 <filter>function['function_select'] == "agp_to_fasta"</filter> 148 <filter>function['function_select'] == "agp_to_fasta"</filter>
142 </data> 149 </data>
150 <data format="txt" name="log_file" from_work_dir="output.log" label="${tool.name} ${on_string}, log file">
151 <filter>log_out</filter>
152 </data>
143 </outputs> 153 </outputs>
144 <tests> 154 <tests>
145 <test expect_num_outputs="5"> 155 <test expect_num_outputs="5">
146 <conditional name="function"> 156 <conditional name="function">
147 <param name="function_select" value="yahs"/> 157 <param name="function_select" value="yahs"/>
213 <param name="fasta" value="test.fasta"/> 223 <param name="fasta" value="test.fasta"/>
214 <param name="agp" value="test.agp"/> 224 <param name="agp" value="test.agp"/>
215 <param name="length" value="20"/> 225 <param name="length" value="20"/>
216 </conditional> 226 </conditional>
217 <output name="fasta_from_agp" file="test_05.fasta" ftype="fasta"/> 227 <output name="fasta_from_agp" file="test_05.fasta" ftype="fasta"/>
218 <!-- COMMAND: agp_to_fasta teast.fasta test.agp -l 20 -o test_4 --> 228 <!-- COMMAND: agp_to_fasta test.fasta test.agp -l 20 -o test_4 -->
229 </test>
230 <test expect_num_outputs="6">
231 <conditional name="function">
232 <param name="function_select" value="yahs"/>
233 <param name="fasta" value="test.fasta"/>
234 <param name="bfile" value="test.bed"/>
235 <param name="agp" value="test.agp"/>
236 <param name="res" value="50000,100000,150000,2000000,1000000"/>
237 </conditional>
238 <param name="log_out" value="yes"/>
239 <output name="final_agp_out" file="test_01_scaffolds_final.agp" ftype="agp"/>
240 <output name="final_fasta_out" file="test_01_scaffolds_final.fa" ftype="fasta"/>
241 <output name="log_file" ftype="txt">
242 <assert_contents>
243 <has_text text="[I::main] CMD: yahs"/>
244 </assert_contents>
245 </output>
246 <!-- COMMAND: yahs test.fasta test.bed -r 50000,100000,150000,2000000,1000000 -a test.agp -o test_1 -->
219 </test> 247 </test>
220 </tests> 248 </tests>
221 <help><![CDATA[ 249 <help><![CDATA[
222 YaHS is scaffolding tool using Hi-C data. It relies on a new algothrim for contig joining detection which considers the topological distribution of Hi-C signals aiming to distingush real interaction signals from mapping nosies. YaHS has been tested in a wide range of genome assemblies. Compared to other Hi-C scaffolding tools, it usually generates more contiguous scaffolds - especially with a higher N90 and L90 statistics. It is also super fast - takes less than 5 minutes to reconstruct the human genome from an assembly of 5,483 contigs with ~45X Hi-C data. 250 YaHS is scaffolding tool using Hi-C data. It relies on a new algothrim for contig joining detection which considers the topological distribution of Hi-C signals aiming to distingush real interaction signals from mapping nosies. YaHS has been tested in a wide range of genome assemblies. Compared to other Hi-C scaffolding tools, it usually generates more contiguous scaffolds - especially with a higher N90 and L90 statistics. It is also super fast - takes less than 5 minutes to reconstruct the human genome from an assembly of 5,483 contigs with ~45X Hi-C data.
223 ]]></help> 251 ]]></help>