Mercurial > repos > iuc > hal_maf2hal

comparison hal_maf2hal.xml @ 0:2900728b299a draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/haltools commit 6244b9d15a5ad97ae20191e2f8fbafe2050c3cac
author iuc
date Fri, 06 Feb 2026 10:37:03 +0000
parents
children
comparison
equal deleted inserted replaced
-1:000000000000 0:2900728b299a
1 <tool id="hal_maf2hal" name="maf2hal" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
2 <description>imports MAF into HAL database</description>
3 <macros>
4 <import>macros.xml</import>
5 </macros>
6 <expand macro="requirements"/>
7 <expand macro="stdio"/>
8 <command detect_errors="aggressive">
9 <![CDATA[
10 #if $mode.append == 'true':
11 ## If an input HAL file is provided to append to, ensure that it is not modified.
12 cp '$mode.input_hal' writable_hal.hal &&
13 #end if
14 ## Uncompress input
15 #if $input_maf.ext.endswith('.gz'):
16 gunzip -c '$input_maf' > uncompressed_input.maf &&
17 #else if $input_maf.ext.endswith('.bz2'):
18 bunzip2 -c '$input_maf' > uncompressed_input.maf &&
19 #else
20 cp '$input_maf' uncompressed_input.maf &&
21 #end if
22 maf2hal
23 #if $refGenome:
24 --refGenome '$refGenome'
25 #end if
26 #if $targetGenomes:
27 --targetGenomes '$targetGenomes'
28 #end if
29 #if $mode.append == 'true':
30 --append
31 #else if $mode.backend.format == 'mmap':
32 --format 'mmap'
33 --mmapFileSize $mode.backend.mmapFileSize
34 #end if
35 uncompressed_input.maf writable_hal.hal
36 ]]></command>
37 <inputs>
38 <param name="input_maf" type="data" format="maf,maf.gz,maf.bz2" label="MAF file"/>
39 <param argument="--refGenome" type="text" value="" optional="true" label="Reference genome" help="Name of the reference genome in the MAF file (first found if empty)">
40 <expand macro="sanitizer_default"/>
41 <expand macro="validator_trim"/>
42 </param>
43 <expand macro="params_targetGenomes_optional"/>
44 <conditional name="mode">
45 <param name="append" type="select" label="Output options">
46 <option value="false" selected="true">Create a new HAL file (default)</option>
47 <option value="true">Append MAF as subtree to an existing HAL file (--append)</option>
48 </param>
49 <when value="false">
50 <expand macro="hal_backend_format"/>
51 </when>
52 <when value="true">
53 <expand macro="input_hal"/>
54 </when>
55 </conditional>
56 </inputs>
57 <outputs>
58 <data name="output_file" format="hal" label="${tool.name} on ${on_string}: HAL file" from_work_dir="writable_hal.hal"/>
59 </outputs>
60 <tests>
61 <test expect_num_outputs="1">
62 <param name="input_maf" value="maf2halTest.maf"/>
63 <output name="output_file" ftype="hal">
64 <assert_contents>
65 <has_size min="50000"/>
66 </assert_contents>
67 </output>
68 <assert_stdout>
69 <has_text text="Total Number of blocks in maf: 6"/>
70 </assert_stdout>
71 </test>
72 <test expect_num_outputs="1">
73 <param name="input_maf" value="maf2halTest.maf.gz"/>
74 <output name="output_file" ftype="hal">
75 <assert_contents>
76 <has_size min="50000"/>
77 </assert_contents>
78 </output>
79 <assert_stdout>
80 <has_text text="Total Number of blocks in maf: 6"/>
81 </assert_stdout>
82 </test>
83 <test expect_num_outputs="1">
84 <param name="input_maf" value="maf2halTest.maf.bz2"/>
85 <output name="output_file" ftype="hal">
86 <assert_contents>
87 <has_size min="50000"/>
88 </assert_contents>
89 </output>
90 <assert_stdout>
91 <has_text text="Total Number of blocks in maf: 6"/>
92 </assert_stdout>
93 </test>
94 <test expect_num_outputs="1">
95 <param name="input_maf" value="maf2halTestAppend.maf"/>
96 <conditional name="mode">
97 <param name="append" value="true"/>
98 <param name="input_hal" value="maf2halTestAppend.hal"/>
99 </conditional>
100 <output name="output_file" ftype="hal">
101 <assert_contents>
102 <has_size min="70000"/>
103 </assert_contents>
104 </output>
105 <assert_stdout>
106 <has_text text="Total Number of blocks in maf: 1"/>
107 </assert_stdout>
108 </test>
109 <!--
110 Disabled until mmap HAL format is allowed
111 <test expect_num_outputs="1">
112 <param name="input_maf" value="maf2halTest.maf"/>
113 <conditional name="mode">
114 <param name="append" value="false"/>
115 <conditional name="inputFormat">
116 <param name="type" value="mmap"/>
117 <param name="mmapFileSize" value="1"/>
118 </conditional>
119 </conditional>
120 <assert_stdout>
121 <has_text text="Total Number of blocks in maf: 6"/>
122 </assert_stdout>
123 </test>
124 -->
125 </tests>
126 <help><![CDATA[
127 maf2hal takes a MAF alignment as input and produces a HAL database as output.
128 It can build a new HAL file or attach the MAF as a subtree if the reference genome already exists as a leaf.
129 You can specify the reference genome and limit import to selected target genomes.
130
131 -----
132
133 .. class:: warningmark
134
135 Creating or importing a HAL file in mmap format can result in a corrupted HAL file. Run halValidate on the output HAL file before further analysis.
136
137 .. class:: warningmark
138
139 At the moment, creating a HAL file in mmap format is disabled. The creation in HDF5 format is enforced.
140 ]]></help>
141 <expand macro="citation"/>
142 <expand macro="creator"/>
143 </tool>