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comparison yahs.xml @ 4:425e63adcc5d draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/yahs commit be65e1846c9d4d63e80c01625e6e5f0d613948fe
author iuc
date Thu, 09 Mar 2023 21:59:34 +0000
parents 39495e107274
children ff4031bfaa22
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3:39495e107274 4:425e63adcc5d
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.2</token> 4 <token name="@VERSION@">1.2a.2</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>
37 #if $function.enzyme_conditional.enzyme_options == 'preconfigured': 37 #if $function.enzyme_conditional.enzyme_options == 'preconfigured':
38 #if $function.enzyme_conditional.preconfigured_enzymes == 'dovetail' 38 #if $function.enzyme_conditional.preconfigured_enzymes == 'dovetail'
39 -e 'GATC' 39 -e 'GATC'
40 #else if $function.enzyme_conditional.preconfigured_enzymes == 'arima1' 40 #else if $function.enzyme_conditional.preconfigured_enzymes == 'arima1'
41 -e 'GATC,GANTC' 41 -e 'GATC,GANTC'
42 #else 42 #else if $function.enzyme_conditional.preconfigured_enzymes == 'arima2'
43 -e 'GATC,GANTC,CTNAG,TTAA' 43 -e 'GATC,GANTC,CTNAG,TTAA'
44 #else if $function.enzyme_conditional.preconfigured_enzymes == 'omnic'
45
44 #end if 46 #end if
45 #else if $function.enzyme_conditional.enzyme_options == 'specific': 47 #else if $function.enzyme_conditional.enzyme_options == 'specific':
46 -e '${function.enzyme_conditional.manual_enzyme}' 48 -e '${function.enzyme_conditional.manual_enzyme}'
47 #end if 49 #end if
48 #if $function.length: 50 #if $function.length:
99 <when value="preconfigured"> 101 <when value="preconfigured">
100 <param name="preconfigured_enzymes" argument="-e" type="select" label="Preconfigured enzymes"> 102 <param name="preconfigured_enzymes" argument="-e" type="select" label="Preconfigured enzymes">
101 <option value="dovetail">Dovetail Chicago, Dovetail Hi-C or Phase: GATC</option> 103 <option value="dovetail">Dovetail Chicago, Dovetail Hi-C or Phase: GATC</option>
102 <option value="arima1">Arima Hi-C 1.0: GATC, GANTC</option> 104 <option value="arima1">Arima Hi-C 1.0: GATC, GANTC</option>
103 <option value="arima2">Arima Hi-C 2.0: GATC, GANTC, CTNAG, TTAA</option> 105 <option value="arima2">Arima Hi-C 2.0: GATC, GANTC, CTNAG, TTAA</option>
106 <option value="omnic">Dovetail Omni-C: enzyme-free prep</option>
104 </param> 107 </param>
105 </when> 108 </when>
106 <when value="specific"> 109 <when value="specific">
107 <param name="manual_enzyme" argument="-e" type="text" label="Restriction enzyme sequence(s)" 110 <param name="manual_enzyme" argument="-e" type="text" label="Restriction enzyme sequence(s)"
108 help="Restriction enzyme sequence. If multiple were used, include all as a comma separated list without spaces (ex. 'GATC,AAGCTT')."> 111 help="Restriction enzyme sequence. If multiple were used, include all as a comma separated list without spaces (ex. 'GATC,AAGCTT').">
246 <has_text text="[I::main] CMD: yahs"/> 249 <has_text text="[I::main] CMD: yahs"/>
247 </assert_contents> 250 </assert_contents>
248 </output> 251 </output>
249 <!-- COMMAND: yahs test.fasta test.bed -r 50000,100000,150000,2000000,1000000 -a test.agp -o test_1 --> 252 <!-- COMMAND: yahs test.fasta test.bed -r 50000,100000,150000,2000000,1000000 -a test.agp -o test_1 -->
250 </test> 253 </test>
254 <!-- TEST 7: omnic prep -->
255 <test expect_num_outputs="6">
256 <conditional name="function">
257 <param name="function_select" value="yahs"/>
258 <param name="fasta" value="test.fasta"/>
259 <param name="bfile" value="test.bed"/>
260 </conditional>
261 <conditional name="enzyme_conditional">
262 <param name="enzyme_options" value="preconfigured"/>
263 <param name="preconfigured_enzymes" value="omnic"/>
264 </conditional>
265 <param name="log_out" value="yes"/>
266 <output name="log_file" ftype="txt">
267 <assert_contents>
268 <not_has_text text="-e"/>
269 </assert_contents>
270 </output>
271 </test>
251 </tests> 272 </tests>
252 <help><![CDATA[ 273 <help><![CDATA[
253 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. 274 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.
254 ]]></help> 275 ]]></help>
255 <citations> 276 <citations>