Mercurial > repos > iuc > hal_halextract

comparison macros.xml @ 0:ea84fd77a2d2 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 10:34:37 +0000
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-1:000000000000 0:ea84fd77a2d2
1 <macros>
2 <xml name="requirements">
3 <requirements>
4 <requirement type="package" version="@TOOL_VERSION@">cactus</requirement>
5 </requirements>
6 </xml>
7 <token name="@TOOL_VERSION@">2.9.9</token>
8 <token name="@VERSION_SUFFIX@">0</token>
9 <token name="@PROFILE@">25.1</token>
10 <xml name="stdio">
11 <stdio>
12 <!-- Anything other than zero is an error -->
13 <exit_code range="1:"/>
14 <exit_code range=":-1"/>
15 <!-- In case the return code has not been set properly check stderr too -->
16 <regex source="stderr" match="Error:"/>
17 <regex source="stderr" match="Exception:"/>
18 <regex match="terminate called after throwing"/>
19 <regex match="hal_exception"/>
20 </stdio>
21 </xml>
22 <xml name="input_hal">
23 <param name="input_hal" type="data" format="hal" label="HAL file"/>
24 </xml>
25 <xml name="input_mapping">
26 <param name="input_mapping" type="data" format="txt,tsv" label="File for renaming" help="Tab-separated file. First column: existing name, second column: new name. Any names not provided will stay the same"/>
27 </xml>
28 <xml name="hal_backend_format">
29 <conditional name="backend">
30 <param name="format" type="select" label="Back-end storage format for new HAL file" help="Select the back-end storage format for the new HAL file (--format)">
31 <option value="hdf5" selected="true">HDF5</option>
32 <!--
33 At the moment, creating a HAL file in mmap format is disabled. The creation in HDF5 format is enforced.
34 <option value="mmap">mmap</option>
35 -->
36 </param>
37 <when value="hdf5"/>
38 <!--
39 <when value="mmap">
40 <param argument="- -mmapFileSize" type="integer" label="Initial file size" value="64" min="1" help="Initial mmap HAL file size in gigabytes"/>
41 </when>
42 -->
43 </conditional>
44 </xml>
45 <xml name="params_mmap_size">
46 <param argument="--mmapFileSize" type="integer" label="Initial file size" value="64" min="1" help="Initial mmap HAL file size in gigabytes"/>
47 </xml>
48 <xml name="params_start">
49 <param argument="--start" type="integer" value="0" label="Start coordinate" help="Coordinate within reference genome (or reference sequence if set) to start at"/>
50 </xml>
51 <xml name="params_length">
52 <param argument="--length" type="integer" min="0" value="0" label="Length to process" help="Length of the reference genome (or reference sequence if set) to process. If set to 0, the entire thing is processed"/>
53 </xml>
54 <xml name="params_onlySequenceNames">
55 <param argument="--onlySequenceNames" type="boolean" truevalue="--onlySequenceNames" falsevalue="" checked="false" label="Only sequence names" help="Use only sequence names for output names. By default, the UCSC convention of Genome.Sequence is used"/>
56 </xml>
57 <xml name="params_root_optional">
58 <param argument="--root" type="text" value="" optional="true" label="Root genome" help="Process only genomes belonging to the subtree rooted at the root genome">
59 <expand macro="sanitizer_default"/>
60 <expand macro="validator_trim"/>
61 </param>
62 </xml>
63 <xml name="params_refGenome">
64 <param name="refGenome" type="text" value="" label="Reference genome" help="Reference genome to process">
65 <expand macro="sanitizer_default"/>
66 <expand macro="validator_trim"/>
67 </param>
68 </xml>
69 <xml name="params_genomeNoRoot">
70 <param name="genome" type="text" value="" label="Genome name" help="Name of genome to process (can't be root)">
71 <expand macro="sanitizer_default"/>
72 <expand macro="validator_trim"/>
73 </param>
74 </xml>
75 <xml name="params_rootGenome">
76 <param name="rootGenome" type="text" value="" label="Root genome" help="Process only genomes belonging to the subtree rooted at the root genome">
77 <expand macro="sanitizer_default"/>
78 <expand macro="validator_trim"/>
79 </param>
80 </xml>
81 <xml name="params_rootGenome_optional">
82 <param argument="--rootGenome" type="text" value="" optional="true" label="Root genome" help="Process only genomes belonging to the subtree rooted at the root genome">
83 <expand macro="sanitizer_default"/>
84 <expand macro="validator_trim"/>
85 </param>
86 </xml>
87 <xml name="params_targetGenomes">
88 <param name="targetGenomes" type="text" value="" label="Target genomes" help="Comma-separated (no spaces) list of target genomes (others are excluded)">
89 <expand macro="sanitizer_default"/>
90 <expand macro="validator_comma_list"/>
91 </param>
92 </xml>
93 <xml name="params_targetGenomes_optional">
94 <param argument="--targetGenomes" type="text" value="" optional="true" label="Target genomes" help="Comma-separated (no spaces) list of target genomes (others are excluded) (vist all if empty)">
95 <expand macro="sanitizer_default"/>
96 <expand macro="validator_comma_list"/>
97 </param>
98 </xml>
99 <xml name="params_sequence">
100 <param name="sequence" type="text" value="" label="Reference sequence" help="Reference sequence in reference genome to process">
101 <expand macro="sanitizer_default"/>
102 <expand macro="validator_trim"/>
103 </param>
104 </xml>
105 <xml name="params_srcGenome">
106 <param name="srcGenome" type="text" label="Source genome" help="Source genome present in both input files from which coordinates should be mapped from">
107 <expand macro="sanitizer_default"/>
108 <expand macro="validator_trim"/>
109 </param>
110 </xml>
111 <xml name="params_tgtGenome">
112 <param name="tgtGenome" type="text" label="Target genome" help="Target genome present in HAL file to which coordinates should be mapped to">
113 <expand macro="sanitizer_default"/>
114 <expand macro="validator_trim"/>
115 </param>
116 </xml>
117 <xml name="params_conditional_refGenome">
118 <conditional name="genome">
119 <param name="reference" type="select" label="Reference genome" help="Select the genome to use as reference">
120 <option value="" selected="true">Use HAL tree root (default)</option>
121 <option value="custom">Specific reference genome (--refGenome)</option>
122 </param>
123 <when value=""/>
124 <when value="custom">
125 <param name="refGenome" type="text" value="" label="Reference genome">
126 <expand macro="sanitizer_default"/>
127 <expand macro="validator_trim"/>
128 </param>
129 <param argument="--noAncestors" type="boolean" truevalue="--noAncestors" falsevalue="" checked="false" label="Exclude ancestors" help="Should only be enabled when the chosen reference genome is a non-ancestral genome"/>
130 </when>
131 </conditional>
132 </xml>
133 <xml name="params_conditional_compression">
134 <conditional name="compression">
135 <param name="type" type="select" label="Compress output file">
136 <option value="" selected="true">Don't compress output file (default)</option>
137 <option value="gz">Compress output file to .gz</option>
138 <option value="bz2">Compress output file to .bz2</option>
139 </param>
140 <when value=""/>
141 <when value="gz"/>
142 <when value="bz2"/>
143 </conditional>
144 </xml>
145 <xml name="params_numSamples">
146 <param argument="--numSamples" type="integer" min="1" value="1000000" label="Number of bases" help="Number of bases to sample for calculation"/>
147 </xml>
148 <xml name="params_seed">
149 <param argument="--seed" type="integer" value="0" label="Random seed" help="Set a seed for reproducibility"/>
150 </xml>
151 <xml name="params_maxGap">
152 <param argument="--maxGap" type="integer" min="0" value="20" label="Max gap" help="Maximum indel length to be considered a gap. Gaps can be nested within other rearrangements"/>
153 </xml>
154 <xml name="params_maxNFraction">
155 <param argument="--maxNFraction" type="float" min="0" value="1" label="Maximum fraction of Ns" help="Maximum fraction of Ns in a rearranged segment for it to not be ignored as missing data"/>
156 </xml>
157 <xml name="params_noDupes">
158 <param argument="--noDupes" type="boolean" truevalue="--noDupes" falsevalue="" checked="false" label="No duplicates" help="Do not map between duplications in graph"/>
159 </xml>
160 <xml name="params_noMarkAncestors">
161 <param argument="--noMarkAncestors" type="boolean" truevalue="--noMarkAncestors" falsevalue="" checked="false" label="Don't mark ancestors" help="Don't mark ancestors for update"/>
162 </xml>
163 <xml name="sanitizer_default">
164 <sanitizer invalid_char="">
165 <valid initial="string.ascii_letters,string.digits,string.punctuation">
166 <add value=" "/>
167 </valid>
168 </sanitizer>
169 </xml>
170 <xml name="validator_trim">
171 <validator type="regex" message="Enter without leading or trailing spaces">^\S(?:.*\S)?$</validator>
172 </xml>
173 <xml name="validator_comma_list">
174 <validator type="regex" message="Enter a comma separated list of genomes, without leading or trailing spaces">^\S(?:[^,]*\S)?(?:,\S(?:[^,]*\S)?)*$</validator>
175 </xml>
176 <xml name="validator_newick">
177 <validator type="regex" message="Enter a Newick tree">^.*;$</validator>
178 </xml>
179 <xml name="creator">
180 <creator>
181 <person givenName="Niklas" familyName="Mayle" url="https://github.com/Maed0x"/>
182 <person givenName="Saim" familyName="Momin" url="https://github.com/SaimMomin12"/>
183 <organization name="Galaxy Europe" url="https://galaxyproject.org/eu/"/>
184 </creator>
185 </xml>
186 <xml name="citation">
187 <citations>
188 <citation type="doi">10.1093/bioinformatics/btt128</citation>
189 </citations>
190 </xml>
191 </macros>