Mercurial > repos > iuc > ucsc_axtchain

annotate axtchain.xml @ 3:56132e3167a9 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/ucsc_axtchain commit 420bba1b6a3ac4747a282f4c183fcd985a1a9075
author iuc
date Fri, 24 Oct 2025 17:46:18 +0000
parents 0ad4e20ecce4
children
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rev   line source
3
56132e3167a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/ucsc_axtchain commit 420bba1b6a3ac4747a282f4c183fcd985a1a9075
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1 <tool id="ucsc_axtchain" name="axtChain" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05" license="MIT">
0
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2 <description>
7c25f4e9f358 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/axtchain commit b20df9521808e2519d001b390545667368111964
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3 Chain together axt alignments
7c25f4e9f358 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/axtchain commit b20df9521808e2519d001b390545667368111964
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4 </description>
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5 <macros>
3
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6 <token name="@TOOL_VERSION@">482</token>
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7 <token name="@VERSION_SUFFIX@">1</token>
0
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8 </macros>
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9 <xrefs>
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10 <xref type="bio.tools">UCSC_Genome_Browser_Utilities</xref>
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11 </xrefs>
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12 <requirements>
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13 <requirement type="package" version="@TOOL_VERSION@">ucsc-axtchain</requirement>
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14 </requirements>
7c25f4e9f358 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/axtchain commit b20df9521808e2519d001b390545667368111964
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15 <version_command><![CDATA[ echo "@TOOL_VERSION@" ]]></version_command>
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16 <command detect_errors="exit_code"><![CDATA[
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17 axtChain
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18 -faQ
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19 -faT
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20 #if $minScore
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21 -minScore='$minScore'
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22 #end if
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23 #if $scoreScheme
7c25f4e9f358 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/axtchain commit b20df9521808e2519d001b390545667368111964
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24 -scoreScheme='$scoreScheme'
7c25f4e9f358 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/axtchain commit b20df9521808e2519d001b390545667368111964
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25 #end if
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26 #if str($linear_gap_options.linear_gap) == "linear_gap_file"
7c25f4e9f358 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/axtchain commit b20df9521808e2519d001b390545667368111964
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27 -linearGap='${linear_gap_options.lineargap_input}'
7c25f4e9f358 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/axtchain commit b20df9521808e2519d001b390545667368111964
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28 #else
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29 -linearGap=$linear_gap_options.linear_gap
7c25f4e9f358 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/axtchain commit b20df9521808e2519d001b390545667368111964
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30 #end if
3
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31 <(gzip -cdfq '$in_axt')
0
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32 '$in_target'
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33 '$in_query'
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34 '$out'
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35 ]]></command>
7c25f4e9f358 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/axtchain commit b20df9521808e2519d001b390545667368111964
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36 <inputs>
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37 <param name="in_axt" format="axt" type="data" label="Alignments" />
7c25f4e9f358 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/axtchain commit b20df9521808e2519d001b390545667368111964
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38 <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"/>
7c25f4e9f358 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/axtchain commit b20df9521808e2519d001b390545667368111964
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39 <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"/>
7c25f4e9f358 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/axtchain commit b20df9521808e2519d001b390545667368111964
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40
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41 <conditional name="linear_gap_options">
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42 <param label="Specify type of linear gap costs to use" name="linear_gap" type="select">
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43 <option selected="true" value="loose">loose (chicken/human linear gap costs)</option>
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44 <option value="medium">medium (mouse/human linear gap costs)</option>
7c25f4e9f358 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/axtchain commit b20df9521808e2519d001b390545667368111964
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45 <option value="linear_gap_file">Provide a dataset with linear gap costs</option>
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46 </param>
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47 <when value="medium" />
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48 <when value="loose" />
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49 <when value="linear_gap_file">
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50 <param name="lineargap_input" type="data" format="tabular" label="Read the linear gap costs from" help="See help for a sample file"/>
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51 </when>
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52 </conditional>
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53
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54 <param argument="-minScore" type="integer" optional="true" label="Minimum score for chain" help="Default 1000" />
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55 <param argument="-scoreScheme" type="data" format="tabular" optional="true" label="Read the scoring matrix from a blastz-format file" />
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56 </inputs>
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57 <outputs>
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58 <data name="out" format="chain" />
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59 </outputs>
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60 <tests>
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61 <test>
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62 <param name="in_axt" value="hg38.chrM.mm39.chrM.axt" />
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63 <param name="in_target" value="hg38.chrM.fasta" />
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64 <param name="in_query" value="mm39.chrM.fasta" />
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65 <conditional name="linear_gap_options">
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66 <param name="linear_gap" value="medium" />
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67 </conditional>
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68 <output name="out" file="hg38.chrM.mm39.chrM.chain" />
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69 </test>
3
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70 <test>
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71 <param name="in_axt" value="hg38.chrM.mm39.chrM.axt.gz" />
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72 <param name="in_target" value="hg38.chrM.fasta" />
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73 <param name="in_query" value="mm39.chrM.fasta" />
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74 <conditional name="linear_gap_options">
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75 <param name="linear_gap" value="medium" />
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76 </conditional>
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77 <output name="out" file="hg38.chrM.mm39.chrM.chain" />
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78 </test>
0
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79 </tests>
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80 <help><![CDATA[
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81 **What it does**
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82
1
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83 `axtChain`_ is a tool to chain together alignments in `axt`_ format. The `chain`_ format describes a pairwise alignment that allow gaps in both sequences simultaneously.
0
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84
2
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85 For implementation details see axtChain's `source code`_.
0
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86
2
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87 linearGap defaults:
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88
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89 loose::
0
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90
2
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91 tablesize 11
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92 smallSize 111
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93 position 1 2 3 11 111 2111 12111 32111 72111 152111 252111
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94 qGap 325 360 400 450 600 1100 3600 7600 15600 31600 56600
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95 tGap 325 360 400 450 600 1100 3600 7600 15600 31600 56600
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96 bothGap 625 660 700 750 900 1400 4000 8000 16000 32000 57000
0
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97
2
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98 medium::
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99
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100 tableSize 11
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101 smallSize 111
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102 position 1 2 3 11 111 2111 12111 32111 72111 152111 252111
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103 qGap 350 425 450 600 900 2900 22900 57900 117900 217900 317900
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104 tGap 350 425 450 600 900 2900 22900 57900 117900 217900 317900
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105 bothGap 750 825 850 1000 1300 3300 23300 58300 118300 218300 318300
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106
0
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107
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108 .. _axtChain: http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/FOOTER.txt
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109 .. _chain: https://genome.ucsc.edu/goldenPath/help/chain.html
1
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110 .. _axt: https://genome.ucsc.edu/goldenPath/help/axt.html
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111 .. _source code: https://github.com/ucscGenomeBrowser/kent/blob/master/src/hg/mouseStuff/axtChain/axtChain.c
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112 ]]> </help>
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113 <citations>
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114 <citation type="doi">10.1093/bib/bbs038</citation>
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115 </citations>
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116 </tool>