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comparison axtchain.xml @ 0:7c25f4e9f358 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/axtchain commit b20df9521808e2519d001b390545667368111964
author iuc
date Mon, 26 Aug 2024 17:34:17 +0000
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children 5d9b51f7230a
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-1:000000000000 0:7c25f4e9f358
1 <tool id="ucsc_axtchain" name="axtChain" version="@TOOL_VERSION@+galaxy0" profile="21.05" license="MIT">
2 <description>
3 Chain together axt alignments
4 </description>
5 <macros>
6 <token name="@TOOL_VERSION@">455</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-axtchain</requirement>
13 </requirements>
14 <version_command><![CDATA[ echo "@TOOL_VERSION@" ]]></version_command>
15 <command detect_errors="exit_code"><![CDATA[
16 axtChain
17 -faQ
18 -faT
19 #if $minScore
20 -minScore='$minScore'
21 #end if
22 #if $scoreScheme
23 -scoreScheme='$scoreScheme'
24 #end if
25 #if str($linear_gap_options.linear_gap) == "linear_gap_file"
26 -linearGap='${linear_gap_options.lineargap_input}'
27 #else
28 -linearGap=$linear_gap_options.linear_gap
29 #end if
30 '$in_axt'
31 '$in_target'
32 '$in_query'
33 '$out'
34 ]]></command>
35 <inputs>
36 <param name="in_axt" format="axt" type="data" label="Alignments" />
37 <param name="in_target" format="fasta" type="data" label="Target sequence" help="Make sure you are using the same name in both alignment and source sequence e.g. hg38.chr1"/>
38 <param name="in_query" format="fasta" type="data" label="Query sequence" help="Make sure you are using the same name in both alignment and source sequence e.g. mm39.chr1"/>
39
40 <conditional name="linear_gap_options">
41 <param label="Specify type of linear gap costs to use" name="linear_gap" type="select">
42 <option selected="true" value="loose">loose (chicken/human linear gap costs)</option>
43 <option value="medium">medium (mouse/human linear gap costs)</option>
44 <option value="linear_gap_file">Provide a dataset with linear gap costs</option>
45 </param>
46 <when value="medium" />
47 <when value="loose" />
48 <when value="linear_gap_file">
49 <param name="lineargap_input" type="data" format="tabular" label="Read the linear gap costs from" help="See help for a sample file"/>
50 </when>
51 </conditional>
52
53 <param argument="-minScore" type="integer" optional="true" label="Minimum score for chain" help="Default 1000" />
54 <param argument="-scoreScheme" type="data" format="tabular" optional="true" label="Read the scoring matrix from a blastz-format file" />
55 </inputs>
56 <outputs>
57 <data name="out" format="chain" />
58 </outputs>
59 <tests>
60 <test>
61 <param name="in_axt" value="hg38.chrM.mm39.chrM.axt" />
62 <param name="in_target" value="hg38.chrM.fasta" />
63 <param name="in_query" value="mm39.chrM.fasta" />
64 <conditional name="linear_gap_options">
65 <param name="linear_gap" value="medium" />
66 </conditional>
67 <output name="out" file="hg38.chrM.mm39.chrM.chain" />
68 </test>
69 </tests>
70 <help><![CDATA[
71 **What it does**
72
73 `axtChain`_ is a tool to chain together alignments. The `chain`_ format describes a pairwise alignment that allow gaps in both sequences simultaneously.
74
75
76 sample linearGap file (loose)::
77
78 tablesize 11
79 smallSize 111
80 position 1 2 3 11 111 2111 12111 32111 72111 152111 252111
81 qGap 325 360 400 450 600 1100 3600 7600 15600 31600 56600
82 tGap 325 360 400 450 600 1100 3600 7600 15600 31600 56600
83 bothGap 625 660 700 750 900 1400 4000 8000 16000 32000 57000
84
85
86 .. _axtChain: http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/FOOTER.txt
87 .. _chain: https://genome.ucsc.edu/goldenPath/help/chain.html
88 ]]> </help>
89 <citations>
90 <citation type="doi">10.1093/bib/bbs038</citation>
91 </citations>
92 </tool>