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comparison cactus_cactus.xml @ 6:a74dbfee5a86 draft

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planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 1eadd6f869c4d28462ccf888008f21acdd00a91d
author galaxy-australia
date Thu, 12 Jan 2023 02:00:52 +0000
parents 48c13389050d
children 6ae5a7b5a0a2
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5:48c13389050d 6:a74dbfee5a86
1 <tool id="cactus_cactus" name="Cactus" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@" license="MIT"> 1 <tool id="cactus_cactus" name="Cactus" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@" license="MIT">
2 <description>whole-genome multiple sequence alignment.</description> 2 <description>whole-genome multiple sequence alignment</description>
3 <macros> 3 <macros>
4 <import>macros.xml</import> 4 <import>macros.xml</import>
5 </macros> 5 </macros>
6 <expand macro="xrefs"/> 6 <expand macro="xrefs"/>
7 <expand macro="requirements"/> 7 <expand macro="requirements"/>
59 pangenome.paf 59 pangenome.paf
60 alignment.hal 60 alignment.hal
61 && 61 &&
62 cactus-graphmap-join 62 cactus-graphmap-join
63 --binariesMode local 63 --binariesMode local
64 --gfaffix
65 --giraffe 64 --giraffe
66 --maxCores \${GALAXY_SLOTS:-4} 65 --maxCores \${GALAXY_SLOTS:-4}
67 --maxMemory \${GALAXY_MEMORY_MB:-8192}M 66 --maxMemory \${GALAXY_MEMORY_MB:-8192}M
68 --outDir ./
69 --outName alignment 67 --outName alignment
70 --reference $aln_mode.ref_level 68 --reference $aln_mode.ref_level
71 --vg alignment.vg 69 --vg alignment.vg
72 --wlineSep "." 70 --outDir ./
73 ./jobStore 71 ./jobStore
74 #else if $aln_mode.aln_mode_select == 'interspecies': 72 #else if $aln_mode.aln_mode_select == 'interspecies':
75 ## Run cactus normally 73 ## Run cactus normally
76 cactus 74 cactus
77 --binariesMode local 75 --binariesMode local
90 </param> 88 </param>
91 <when value="interspecies"> 89 <when value="interspecies">
92 <param name="in_tree" type="data" format="nhx" label="Guide tree" help="Phylogenetic tree in Newick format. Required by Cactus to achieve linear scaling with number of input genomes" /> 90 <param name="in_tree" type="data" format="nhx" label="Guide tree" help="Phylogenetic tree in Newick format. Required by Cactus to achieve linear scaling with number of input genomes" />
93 </when> 91 </when>
94 <when value="intraspecies"> 92 <when value="intraspecies">
95 <param name="ref_level" type="text" value="" label="Reference genome" help="Pangenomes from Minigraph-Cactus depend on a predetermined reference genome. Specify one of the Input Genomes as the reference genome. This must match the label used in 'Genome Label'." /> 93 <param name="ref_level" type="text" value="" label="Reference genome" help="Pangenomes from Minigraph-Cactus depend on a predetermined reference genome. Specify one of the Input Genomes as the reference genome. This must match the label used in 'Genome Label'.">
94 <sanitizer invalid_char="">
95 <valid initial="string.letters,string.digits">
96 <add value="_" />
97 </valid>
98 </sanitizer>
99 <validator type="regex">[0-9a-zA-Z_]+</validator>
100 </param>
96 </when> 101 </when>
97 </conditional> 102 </conditional>
98 <repeat name="in_seqs" title="Input genome"> 103 <repeat name="in_seqs" title="Input genome">
99 <param name="label" type="text" value="" label="Genome Label" help="NO SPACES. Must match a label in the guide tree."> 104 <param name="label" type="text" value="" label="Genome label" help="NO SPACES. Must match a label in the guide tree.">
105 <sanitizer invalid_char="">
106 <valid initial="string.letters,string.digits">
107 <add value="_" />
108 </valid>
109 </sanitizer>
110 <validator type="regex">[0-9a-zA-Z_]+</validator>
100 </param> 111 </param>
101 <param name="fasta" type="data" format="fasta,fasta.gz" label="Genome Sequence" help="Input genome"/> 112 <param name="fasta" type="data" format="fasta,fasta.gz" label="Genome Sequence" help="Input genome"/>
102 </repeat> 113 </repeat>
114
103 <!-- add an option for root --> 115 <!-- add an option for root -->
104 <!-- root mr --> 116 <!-- root mr -->
105 </inputs> 117 </inputs>
106 <outputs> 118 <outputs>
107 <data name="out_hal" format="h5" from_work_dir="alignment.hal" label="${tool.name} on ${on_string} (HAL file)" /> 119 <data name="out_hal" format="h5" from_work_dir="alignment.hal" label="${tool.name} on ${on_string} (HAL file)" />
136 <param name="label" value="simRat_chr6"/> 148 <param name="label" value="simRat_chr6"/>
137 <param name="fasta" value="simRat_chr6.fasta"/> 149 <param name="fasta" value="simRat_chr6.fasta"/>
138 </repeat> 150 </repeat>
139 <output name="out_hal"> 151 <output name="out_hal">
140 <assert_contents> 152 <assert_contents>
141 <has_size value="4783905" delta="200000" /> 153 <has_size value="4472551" delta="200000" />
142 </assert_contents> 154 </assert_contents>
143 </output> 155 </output>
144 </test> 156 </test>
145 <!-- within-species mode --> 157 <!-- within-species mode -->
146 <test expect_num_outputs="2"> 158 <test expect_num_outputs="2">
233 </assert_contents> 245 </assert_contents>
234 </output> 246 </output>
235 </test> 247 </test>
236 </tests> 248 </tests>
237 <help><![CDATA[ 249 <help><![CDATA[
250
251 .. class:: infomark
252
238 **What it does** 253 **What it does**
239 254
240 `Cactus <https://github.com/ComparativeGenomicsToolkit/cactus>`__ is a 255 `Cactus <https://github.com/ComparativeGenomicsToolkit/cactus>`__ is a
241 reference-free whole-genome multiple alignment program. It can be used 256 reference-free whole-genome multiple alignment program. It can be used
242 to progressively align a large number of genomes. 257 to progressively align a large number of genomes.
258
259 -----
260
261 .. class:: infomark
243 262
244 **Usage** 263 **Usage**
245 264
246 **Between-species mode (Progressive Cactus)** 265 **Between-species mode (Progressive Cactus)**
247 266
251 possible pairs of genomes. 270 possible pairs of genomes.
252 271
253 A Newick-formatted tree for human, chimp and gorilla genomes looks like 272 A Newick-formatted tree for human, chimp and gorilla genomes looks like
254 this: 273 this:
255 274
256 :: 275 ::
257 276
258 (((human:0.006,chimp:0.006667):0.0022,gorilla:0.008825):0.0096,orang:0.01831); 277 (((human:0.006,chimp:0.006667):0.0022,gorilla:0.008825):0.0096,orang:0.01831);
259 278
260 The numbers are the branch lengths. 279 The numbers are the branch lengths.
261 280
262 **Within-species mode (Minigraph-Cactus)** 281 **Within-species mode (Minigraph-Cactus)**
263 282
268 `minigraph <https://github.com/lh3/minigraph>`__ to generate a graph of 287 `minigraph <https://github.com/lh3/minigraph>`__ to generate a graph of
269 the input genomes and then use the graph to order the alignments. To use 288 the input genomes and then use the graph to order the alignments. To use
270 pangenome mode, select ‘Within-species’ in the ‘Alignment mode’ 289 pangenome mode, select ‘Within-species’ in the ‘Alignment mode’
271 dropdown. 290 dropdown.
272 291
273 Unlike Between-species mode, Within-species mode depends on a predetermined reference genome 292 Unlike Between-species mode, Within-species mode depends on a predetermined reference genome.
293
294 -----
295
296 .. class:: infomark
274 297
275 **Input** 298 **Input**
276 299
277 The developers recommend soft-masking your genomes with RepeatMasker 300 The developers recommend soft-masking your genomes with RepeatMasker
278 before running Cactus. RepeatMasker is available on Galaxy. 301 before running Cactus. RepeatMasker is available on Galaxy.
279 302
280 If you’re using Between-species mode, you need to provide labels for the 303 If you’re using Between-species mode, you need to provide labels for the
281 fasta files that match the leaves on the guide tree. In the example 304 fasta files that match the leaves on the guide tree. In the example
282 above, you would use the label ‘human’ for the human fasta file. 305 above, you would use the label ‘human’ for the human fasta file.
306
307 -----
308
309 .. class:: infomark
283 310
284 **Output** 311 **Output**
285 312
286 The main output of Cactus is in `HAL 313 The main output of Cactus is in `HAL
287 format <https://github.com/ComparativeGenomicsToolkit/cactus#using-the-output>`__. 314 format <https://github.com/ComparativeGenomicsToolkit/cactus#using-the-output>`__.