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comparison hal_hal2maf.xml @ 0:a3ff8225d554 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/haltools commit 6244b9d15a5ad97ae20191e2f8fbafe2050c3cac
author iuc
date Fri, 06 Feb 2026 10:38:29 +0000
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-1:000000000000 0:a3ff8225d554
1 <tool id="hal_hal2maf" name="hal2maf" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
2 <description>converts HAL to MAF</description>
3 <macros>
4 <import>macros.xml</import>
5 </macros>
6 <expand macro="requirements"/>
7 <expand macro="stdio"/>
8 <command detect_errors="aggressive"><![CDATA[
9 #if $file.append == 'true':
10 ## If an input MAF file is provided to append to, ensure that it is not modified.
11 cp '$input_maf' writable_maf.maf &&
12 #end if
13 hal2maf
14 #if $file.append == 'true':
15 --append
16 #end if
17 #if $genome.reference == 'custom':
18 --refGenome '$genome.refGenome'
19 $genome.noAncestors
20 #end if
21 #if $filter.option == '--targetGenomes':
22 --targetGenomes '$filter.targetGenomes'
23 #else if $filter.option == '--rootGenome':
24 --rootGenome '$filter.rootGenome'
25 #end if
26 #if $convert.mode == 'sequence':
27 --refSequence '$convert.sequence'
28 --start $convert.start
29 --length $convert.length
30 #else if $convert.mode == 'target':
31 --refTargets '$convert.refTargets'
32 #else if $convert.mode == 'global':
33 --global
34 #end if
35 --maxRefGap $maxRefGap
36 --maxBlockLen $maxBlockLen
37 $noDupes
38 $onlySequenceNames
39 $unique
40 $printTree
41 $onlyOrthologs
42 $keepEmptyRefBlocks
43 '$input_hal' writable_maf.maf
44 #if $compression.type == 'gz':
45 && gzip -c writable_maf.maf > '$output_file'
46 #else if $compression.type == 'bz2':
47 && bzip2 -c writable_maf.maf > '$output_file'
48 #else:
49 && mv writable_maf.maf '$output_file'
50 #end if
51 ]]></command>
52 <inputs>
53 <expand macro="input_hal"/>
54 <expand macro="params_conditional_refGenome"/>
55 <conditional name="filter">
56 <param name="option" type="select" label="Genomes to include in the output">
57 <option value="" selected="true">All genomes (default)</option>
58 <option value="--targetGenomes">Specific target genomes (--targetGenomes)</option>
59 <option value="--rootGenome">Only genomes in the subtree to a root (--rootGenome)</option>
60 </param>
61 <when value=""/>
62 <when value="--targetGenomes">
63 <expand macro="params_targetGenomes"/>
64 </when>
65 <when value="--rootGenome">
66 <expand macro="params_rootGenome"/>
67 </when>
68 </conditional>
69 <conditional name="convert">
70 <param name="mode" type="select" label="Convert options">
71 <option value="" selected="true">All sequences (default)</option>
72 <option value="sequence">A reference sequence (--refSequence)</option>
73 <option value="target">Using reference intervals from a BED file (--refTargets)</option>
74 <option value="global">All columns in alignment, ignoring reference-based filters (--global)</option>
75 </param>
76 <when value=""/>
77 <when value="sequence">
78 <expand macro="params_sequence"/>
79 <expand macro="params_start"/>
80 <expand macro="params_length"/>
81 </when>
82 <when value="target">
83 <param name="refTargets" type="data" format="bed" label="BED file" help="BED file with reference genome intervals to convert. Only alignment columns overlapping these intervals are included"/>
84 </when>
85 <when value="global"/>
86 </conditional>
87 <conditional name="file">
88 <param name="append" type="select" label="Append new alignment to an existing MAF file">
89 <option value="false" selected="true">No, create a new MAF file (default)</option>
90 <option value="true">Yes, append to an existing MAF file (--append)</option>
91 </param>
92 <when value="true">
93 <param name="input_maf" type="data" format="maf" label="MAF file"/>
94 </when>
95 <when value="false"/>
96 </conditional>
97 <param argument="--maxRefGap" type="integer" min="0" value="0" label="Maximum gap length" help="Maximum gap length in reference genome"/>
98 <param argument="--maxBlockLen" type="integer" min="0" value="1000" label="Maximum block length" help="Maximum length of MAF block in output"/>
99 <param argument="--noDupes" type="boolean" truevalue="--noDupes" falsevalue="" checked="false" label="Ignore paralogy edges" help="Ignore paralogy edges"/>
100 <expand macro="params_onlySequenceNames"/>
101 <param argument="--unique" type="boolean" truevalue="--unique" falsevalue="" checked="false" label="Unique" help="Only write column whose left-most reference coordinate is in the specified range. This is used to ensure that the same column isn't sampled twice (due to duplications) by MAFs generated on distinct ranges"/>
102 <param argument="--printTree" type="boolean" truevalue="--printTree" falsevalue="" checked="false" label="Print Tree" help="Print a gene tree for every block"/>
103 <param argument="--onlyOrthologs" type="boolean" truevalue="--onlyOrthologs" falsevalue="" checked="false" label="Only Orthologs" help="Make only orthologs to the reference appear in the MAF blocks"/>
104 <param argument="--keepEmptyRefBlocks" type="boolean" truevalue="--global" falsevalue="" checked="false" label="Keep empty reference blocks" help="Keep blocks that contain no reference sequence"/>
105 <expand macro="params_conditional_compression"/>
106 </inputs>
107 <outputs>
108 <data name="output_file" format="maf" label="${tool.name} on ${on_string}: MAF file">
109 <change_format>
110 <when input="compression.type" value="gz" format="maf.gz"/>
111 <when input="compression.type" value="bz2" format="maf.bz2"/>
112 </change_format>
113 </data>
114 </outputs>
115 <tests>
116 <test expect_num_outputs="1">
117 <param name="input_hal" value="halTest.hal"/>
118 <conditional name="filter">
119 <param name="option" value=""/>
120 </conditional>
121 <output name="output_file" ftype="maf">
122 <assert_contents>
123 <has_line line="##maf version=1 scoring=N/A"/>
124 <has_line line="# hal (Genome_1:1,Genome_2:1,Genome_3:1)Genome_0;"/>
125 <has_line line="a"/>
126 <has_text text="s&#009;Genome_0.Genome_0_seq&#009;293&#009;293&#009;+&#009;1758"/>
127 <has_text text="s&#009;Genome_1.Genome_1_seq&#009;4571&#009;117&#009;+&#009;5472"/>
128 <has_n_lines n="90"/>
129 </assert_contents>
130 </output>
131 </test>
132 <test expect_num_outputs="1">
133 <param name="input_hal" value="halTest.hal"/>
134 <conditional name="filter">
135 <param name="option" value=""/>
136 </conditional>
137 <conditional name="compression">
138 <param name="type" value="gz"/>
139 </conditional>
140 <output name="output_file" ftype="maf.gz" file="hal2maf_output.maf.gz"/>
141 </test>
142 <test expect_num_outputs="1">
143 <param name="input_hal" value="halTest.hal"/>
144 <conditional name="filter">
145 <param name="option" value=""/>
146 </conditional>
147 <conditional name="compression">
148 <param name="type" value="bz2"/>
149 </conditional>
150 <output name="output_file" ftype="maf.bz2" file="hal2maf_output.maf.bz2"/>
151 </test>
152 <test expect_num_outputs="1">
153 <param name="input_hal" value="halTest.hal"/>
154 <conditional name="filter">
155 <param name="option" value="--rootGenome"/>
156 <param name="rootGenome" value="Genome_1"/>
157 </conditional>
158 <param name="printTree" value="true"/>
159 <param name="onlySequenceNames" value="true"/>
160 <output name="output_file" ftype="maf">
161 <assert_contents>
162 <has_line line="##maf version=1 scoring=N/A"/>
163 <has_line line="# hal (Genome_1:1,Genome_2:1,Genome_3:1)Genome_0;"/>
164 <has_text text="a tree="/>
165 <has_text text="Genome_1_seq,Genome_1_seq,Genome_2,Genome_3,Genome_3)Genome_0_seq;"/>
166 <has_text text="Genome_0_seq&#009;293&#009;293&#009;+&#009;1758"/>
167 <has_text text="s&#009;Genome_1_seq&#009;4864&#009;117&#009;+&#009;5472"/>
168 <has_n_lines n="52"/>
169 </assert_contents>
170 </output>
171 </test>
172 <test expect_num_outputs="1">
173 <param name="input_hal" value="halTest.hal"/>
174 <param name="maxBlockLen" value="200"/>
175 <param name="noDupes" value="true"/>
176 <output name="output_file" ftype="maf">
177 <assert_contents>
178 <has_line line="##maf version=1 scoring=N/A"/>
179 <has_line line="# hal (Genome_1:1,Genome_2:1,Genome_3:1)Genome_0;"/>
180 <has_line line="a"/>
181 <has_text text="s&#009;Genome_3.Genome_3_seq&#009;4102&#009;200&#009;+&#009;6139"/>
182 <has_text text="s&#009;Genome_1.Genome_1_seq&#009;3130&#009;93&#009;+&#009;5472"/>
183 <has_text text="s&#009;Genome_0.Genome_0_seq&#009;1748&#009;10&#009;+&#009;1758&#009;CGCGTCGGCG"/>
184 <has_n_lines n="69"/>
185 </assert_contents>
186 </output>
187 </test>
188 <test expect_num_outputs="1">
189 <param name="input_hal" value="halTest.hal"/>
190 <conditional name="genome">
191 <param name="reference" value="custom"/>
192 <param name="refGenome" value="Genome_1"/>
193 <param name="noAncestors" value="true"/>
194 </conditional>
195 <param name="onlyOrthologs" value="true"/>
196 <output name="output_file" ftype="maf">
197 <assert_contents>
198 <has_line line="##maf version=1 scoring=N/A"/>
199 <has_line line="# hal (Genome_1:1,Genome_2:1,Genome_3:1)Genome_0;"/>
200 <has_line line="a"/>
201 <has_text text="s&#009;Genome_1.Genome_1_seq&#009;5135&#009;337&#009;+&#009;5472"/>
202 <has_text text="s&#009;Genome_2.Genome_2_seq&#009;2498&#009;139&#009;+&#009;4270"/>
203 <has_text text="s&#009;Genome_3.Genome_3_seq&#009;4571&#009;117&#009;+&#009;6139"/>
204 <has_n_lines n="230"/>
205 </assert_contents>
206 </output>
207 </test>
208 <test expect_num_outputs="1">
209 <param name="input_hal" value="halTest.hal"/>
210 <conditional name="genome">
211 <param name="reference" value="custom"/>
212 <param name="refGenome" value="Genome_1"/>
213 </conditional>
214 <param name="unique" value="true"/>
215 <output name="output_file" ftype="maf">
216 <assert_contents>
217 <has_line line="##maf version=1 scoring=N/A"/>
218 <has_line line="# hal (Genome_1:1,Genome_2:1,Genome_3:1)Genome_0;"/>
219 <has_line line="a"/>
220 <has_text text="s&#009;Genome_3.Genome_3_seq&#009;1033&#009;139&#009;+&#009;6139"/>
221 <has_text text="s&#009;Genome_0.Genome_0_seq&#009;1348&#009;117&#009;+&#009;1758"/>
222 <has_text text="s&#009;Genome_1.Genome_1_seq&#009;5274&#009;198&#009;+&#009;5472&#009;NNNNNNNNNNNNNNNN"/>
223 <has_n_lines n="96"/>
224 </assert_contents>
225 </output>
226 </test>
227 <test expect_num_outputs="1">
228 <param name="input_hal" value="halTest.hal"/>
229 <conditional name="genome">
230 <param name="reference" value="custom"/>
231 <param name="refGenome" value="Genome_1"/>
232 </conditional>
233 <param name="maxRefGap" value="2000"/>
234 <output name="output_file" ftype="maf">
235 <assert_contents>
236 <has_line line="##maf version=1 scoring=N/A"/>
237 <has_line line="# hal (Genome_1:1,Genome_2:1,Genome_3:1)Genome_0;"/>
238 <has_line line="a"/>
239 <has_text text="s&#009;Genome_2.Genome_2_seq&#009;2344&#009;154&#009;+&#009;4270"/>
240 <has_text text="s&#009;Genome_1.Genome_1_seq&#009;1465&#009;293&#009;+&#009;5472&#009;----------------"/>
241 <has_text text="s&#009;Genome_1.Genome_1_seq&#009;3516&#009;293&#009;+&#009;5472&#009;NNNNNNNNNNNNNNNN"/>
242 <has_n_lines n="101"/>
243 </assert_contents>
244 </output>
245 </test>
246 <test expect_num_outputs="1">
247 <param name="input_hal" value="halTest.hal"/>
248 <conditional name="convert">
249 <param name="mode" value="sequence"/>
250 <param name="sequence" value="Genome_0_seq"/>
251 <param name="start" value="4"/>
252 <param name="length" value="10"/>
253 </conditional>
254 <output name="output_file" ftype="maf">
255 <assert_contents>
256 <has_line line="##maf version=1 scoring=N/A"/>
257 <has_line line="# hal (Genome_1:1,Genome_2:1,Genome_3:1)Genome_0;"/>
258 <has_line line="a"/>
259 <has_line line="s&#009;Genome_0.Genome_0_seq&#009;4&#009;10&#009;+&#009;1758&#009;TCGGGGGGGA"/>
260 <has_line line="s&#009;Genome_2.Genome_2_seq&#009;4&#009;10&#009;+&#009;4270&#009;TCGGGGGGGA"/>
261 <has_line line="s&#009;Genome_3.Genome_3_seq&#009;4&#009;10&#009;+&#009;6139&#009;TCGGGGGGGA"/>
262 <has_n_lines n="11"/>
263 </assert_contents>
264 </output>
265 </test>
266 <test expect_num_outputs="1">
267 <param name="input_hal" value="halTest.hal"/>
268 <conditional name="file">
269 <param name="append" value="true"/>
270 <param name="input_maf" value="hal2maf_append.maf"/>
271 </conditional>
272 <conditional name="filter">
273 <param name="option" value="--targetGenomes"/>
274 <param name="targetGenomes" value="Genome_2,Genome_3"/>
275 </conditional>
276 <output name="output_file" ftype="maf">
277 <assert_contents>
278 <has_line line="##maf version=1 scoring=N/A"/>
279 <has_line line="# hal (Genome_1:1,Genome_2:1,Genome_3:1)Genome_0;"/>
280 <has_line line="a"/>
281 <has_text text="s&#009;Genome_1.Genome_1_seq&#009;0&#009;293&#009;+&#009;5472"/>
282 <has_text text="s&#009;Genome_3.Genome_3_seq&#009;4395&#009;176&#009;+&#009;6139"/>
283 <has_text text="s&#009;Genome_1.Genome_1_seq&#009;3223&#009;176&#009;+&#009;5472"/>
284 <has_n_lines n="152"/>
285 </assert_contents>
286 </output>
287 </test>
288 <test expect_num_outputs="1">
289 <param name="input_hal" value="halTest.hal"/>
290 <conditional name="convert">
291 <param name="mode" value="global"/>
292 </conditional>
293 <output name="output_file" ftype="maf">
294 <assert_contents>
295 <has_line line="##maf version=1 scoring=N/A"/>
296 <has_line line="# hal (Genome_1:1,Genome_2:1,Genome_3:1)Genome_0;"/>
297 <has_line line="a"/>
298 <has_text text="s&#009;Genome_1.Genome_1_seq&#009;3516&#009;293&#009;+&#009;5472&#009;NNNNNNNNNNNN"/>
299 <has_text text="s&#009;Genome_2.Genome_2_seq&#009;1465&#009;293&#009;+&#009;4270&#009;------------"/>
300 <has_text text="s&#009;Genome_3.Genome_3_seq&#009;4571&#009;117&#009;+&#009;6139"/>
301 <has_n_lines n="113"/>
302 </assert_contents>
303 </output>
304 </test>
305 <test expect_num_outputs="1">
306 <param name="input_hal" value="halTest.hal"/>
307 <conditional name="convert">
308 <param name="mode" value="target"/>
309 <param name="refTargets" value="hal2maf.bed"/>
310 </conditional>
311 <output name="output_file" ftype="maf">
312 <assert_contents>
313 <has_line line="##maf version=1 scoring=N/A"/>
314 <has_line line="# hal (Genome_1:1,Genome_2:1,Genome_3:1)Genome_0;"/>
315 <has_line line="a"/>
316 <has_text text="s&#009;Genome_0.Genome_0_seq&#009;0&#009;293&#009;+&#009;1758"/>
317 <has_text text="s&#009;Genome_2.Genome_2_seq&#009;3516&#009;293&#009;+&#009;4270"/>
318 <has_text text="s&#009;Genome_3.Genome_3_seq&#009;586&#009;293&#009;+&#009;6139"/>
319 <has_n_lines n="24"/>
320 </assert_contents>
321 </output>
322 </test>
323 </tests>
324 <help><![CDATA[
325 hal2maf converts an input HAL alignment into a MAF file as output.
326 The tool supports converting the full alignment or restricting output to a selected reference genome, reference sequence, a set of target genomes, or only genomes belonging to the subtree rooted at a root genome.
327
328 Additional controls allow filtering for orthologs, excluding ancestral sequences, keeping empty reference blocks, limiting block size, and controlling reference gaps.
329 MAF blocks can also include gene tree annotations if requested.
330 ]]></help>
331 <expand macro="citation"/>
332 <expand macro="creator"/>
333 </tool>