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comparison chainnet.xml @ 0:3d8635fc3e51 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/ucsc_chainnet commit 09ce055ec6cd95f6999cc680a707418cee25d42a
author iuc
date Fri, 30 Aug 2024 17:53:36 +0000
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-1:000000000000 0:3d8635fc3e51
1 <tool id="ucsc_chainnet" name="chainNet" version="@TOOL_VERSION@+galaxy0" profile="21.05" license="MIT">
2 <description>
3 make alignment nets out of alignment chains
4 </description>
5 <macros>
6 <token name="@TOOL_VERSION@">469</token>
7 </macros>
8 <xrefs>
9 <xref type="bio.tools">UCSC_Genome_Browser_Utilities</xref>
10 </xrefs>
11 <requirements>
12 <requirement type="package" version="@TOOL_VERSION@">ucsc-chainnet</requirement>
13 </requirements>
14 <version_command><![CDATA[ echo "@TOOL_VERSION@" ]]></version_command>
15 <command detect_errors="exit_code"><![CDATA[
16 chainNet
17 '$in_chain'
18 #if str( $target_reference_index_source.target_reference_index_source_selector ) == "history":
19 '${target_reference_index_source.in_tar_ref_index}'
20 #else:
21 '$target_reference_index_source.tar_ref_index_file.fields.path'
22 #end if
23 #if str( $query_reference_index_source.query_reference_index_source_selector ) == "history":
24 '${query_reference_index_source.in_que_ref_index}'
25 #else:
26 '$query_reference_index_source.que_ref_index_file.fields.path'
27 #end if
28 '$targetNet'
29 '$queryNet'
30 #if str($minSpace)
31 -minSpace=$minSpace
32 #end if
33 #if str($minFill)
34 -minFill=$minFill
35 #end if
36 #if str($minScore)
37 -minScore=$minScore
38 #end if
39 $inclHap
40 #if str($verbose)
41 -verbose=$verbose
42 #end if
43 ]]></command>
44 <inputs>
45 <param name="in_chain" format="chain" type="data" label="Chain dataset" help="Select chain dataset" />
46
47 <conditional name="target_reference_index_source">
48 <param name="target_reference_index_source_selector" type="select" label="Choose the source for the target reference genome index">
49 <option value="cached">Built-in</option>
50 <option value="history">From history</option>
51 </param>
52 <when value="cached">
53 <param name="tar_ref_index_file" type="select" label="Using reference genome index">
54 <options from_data_table="fasta_indexes" />
55 </param>
56 </when>
57 <when value="history">
58 <param name="in_tar_ref_index" format="tabular" type="data" label="Dataset with chrom sizes for target sequence. Typically a '.fai' file." />
59 </when>
60 </conditional>
61
62 <conditional name="query_reference_index_source">
63 <param name="query_reference_index_source_selector" type="select" label="Choose the source for the query reference genome index">
64 <option value="cached">Built-in</option>
65 <option value="history">From history</option>
66 </param>
67 <when value="cached">
68 <param name="que_ref_index_file" type="select" label="Using reference genome index">
69 <options from_data_table="fasta_indexes" />
70 </param>
71 </when>
72 <when value="history">
73 <param name="in_que_ref_index" format="tabular" type="data" label="Dataset with chrom sizes for query sequence. Typically a '.fai' file." />
74 </when>
75 </conditional>
76
77 <param argument="-minSpace" type="integer" optional="true" min="0" label="Minimum gap size to fill" help="default 25" />
78 <param argument="-minFill" type="integer" optional="true" min="0" label="Minimum fill to record" help="default half of minSpace" />
79 <param argument="-minScore" type="integer" optional="true" label="Minimum chain score to consider" help="default 2000" />
80 <param argument="-inclHap" type="boolean" optional="true" truevalue="-inclHap" falsevalue="" label="Include query sequences name in the form *_hap*|*_alt*. Normally these are excluded from nets as being haplotype pseudochromosomes." />
81 <param argument="-verbose" type="integer" optional="true" label="Verbosity" help="default 1" />
82
83 </inputs>
84 <outputs>
85 <data name="targetNet" format="ucsc.net" label="${tool.name} on ${on_string}: target.net"/>
86 <data name="queryNet" format="ucsc.net" label="${tool.name} on ${on_string}: query.net" />
87 </outputs>
88 <tests>
89 <test expect_num_outputs="2">
90 <param name="in_chain" value="input.chain" />
91 <conditional name="target_reference_index_source">
92 <param name="target_reference_index_source_selector" value="history" />
93 <param name="in_tar_ref_index" value="hg38.chr20.chunk.fasta.fai"/>
94 </conditional>
95 <conditional name="query_reference_index_source">
96 <param name="query_reference_index_source_selector" value="history" />
97 <param name="in_que_ref_index" value="mm39.chr2.chunk.fasta.fai"/>
98 </conditional>
99 <output name="targetNet" file="target.net"/>
100 <output name="queryNet" file="query.net"/>
101 </test>
102 <test expect_num_outputs="2">
103 <param name="in_chain" value="input.chain" />
104 <conditional name="target_reference_index_source">
105 <param name="target_reference_index_source_selector" value="cached" />
106 <param name="tar_ref_index_file" value="hg38.chr20.chunk"/>
107 </conditional>
108 <conditional name="query_reference_index_source">
109 <param name="query_reference_index_source_selector" value="cached" />
110 <param name="que_ref_index_file" value="mm39.chr2.chunk"/>
111 </conditional>
112 <output name="targetNet" file="target.net"/>
113 <output name="queryNet" file="query.net"/>
114 </test>
115 <test expect_num_outputs="2">
116 <param name="in_chain" value="input.chain" />
117 <param name="minScore" value="1200" />
118 <conditional name="target_reference_index_source">
119 <param name="target_reference_index_source_selector" value="cached" />
120 <param name="tar_ref_index_file" value="hg38.chr20.chunk"/>
121 </conditional>
122 <conditional name="query_reference_index_source">
123 <param name="query_reference_index_source_selector" value="history" />
124 <param name="in_que_ref_index" value="mm39.chr2.chunk.fasta.fai"/>
125 </conditional>
126 <output name="targetNet" file="target.1200.net"/>
127 <output name="queryNet" file="query.1200.net"/>
128 </test>
129 </tests>
130 <help><![CDATA[
131 **What it does**
132
133 `chainNet`_ is a tool that makes alignment nets out of `alignment chains`_.
134 It outputs two files in the `ucsc.net`_ format -- one for the target sequence and one for the query sequence.
135
136 For implementation details see ChainNet's `source code`_.
137
138 .. _chainNet: http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/FOOTER.txt
139 .. _ucsc.net: https://genome.ucsc.edu/goldenPath/help/net.html
140 .. _alignment chains: https://genome.ucsc.edu/goldenPath/help/chain.html
141 .. _source code: https://github.com/ucscGenomeBrowser/kent/blob/master/src/hg/mouseStuff/chainNet/chainNet.c
142 ]]> </help>
143 <citations>
144 <citation type="doi">10.1093/bib/bbs038</citation>
145 </citations>
146 </tool>