Mercurial > repos > iuc > tbl2gff3

annotate tbl2gff3.xml @ 1:4a7f4b0cc0a3 draft default tip

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tbl2gff3 commit db75a8489a1f61ea30abe9b91f6febac8b34204f"
author iuc
date Thu, 03 Dec 2020 16:59:23 +0000
parents 965674d88d34
children
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1
4a7f4b0cc0a3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tbl2gff3 commit db75a8489a1f61ea30abe9b91f6febac8b34204f"
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1 <tool id="tbl2gff3" name="Table to GFF3" version="1.2">
0
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2 <description></description>
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
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6 <expand macro="requirements"/>
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7 <command detect_errors="exit_code">
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8 <![CDATA[
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9 python '$__tool_directory__/tbl2gff3.py'
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10 '$table'
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11 '$rid'
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12 '$begin'
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13 '$end'
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14
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15 #if $type:
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16 --type '$type'
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17 #end if
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18
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19 #if $score:
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20 --score '$score'
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21 #end if
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23 #if $source:
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24 --source '$source'
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25 #end if
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26
1
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27 #if str($strand.strand_select) == 'infer':
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28 --strand_infer
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29 #else if str($strand.strand_select) != "none":
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30 --strand_${strand.strand_select} '${strand.strand}'
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31 #end if
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32
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33 #for $a in $attributes
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34 -a '${a.key}:${a.val}'
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35 #end for
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36
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37 > '$output'
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38 ]]></command>
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39 <inputs>
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40 <param label="Table" name="table" type="data" format="tabular"/>
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41
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42 <param name="rid" type="text" value="1" label="Record ID column or value" optional="false" help="@HELP@"/>
1
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43 <param name="begin" type="text" value="" optional="false" label="Start column or value" help="@HELP@"/>
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44 <param name="end" type="text" value="" optional="false" label="End column or value" help="@HELP@"/>
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45 <param name="type" type="text" value="sequence_feature" label="Type column or value" help="@HELP@"/>
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46 <param name="score" type="text" value="" label="Score column or value" help="@HELP@"/>
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47 <param name="source" type="text" value="tbl2gff3" label="Source column or value" help="@HELP@"/>
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48
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49
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50 <conditional name="strand">
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51 <param name="strand_select" type="select" label="Strand">
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52 <option value="infer">Infer</option>
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53 <option value="none">Not specified</option>
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54 <option value="column">From Column</option>
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55 <option value="value">Specify Value</option>
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56 </param>
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57 <when value="none" />
1
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58 <when value="infer" />
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59 <when value="column" >
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60 <param name="strand" type="text" value="" label="Strand column" />
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61 </when>
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62 <when value="value">
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63 <param name="strand" type="integer" value="1" min="-1" max="1" label="Strand value" />
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64 </when>
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65 </conditional>
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66
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67 <repeat name="attributes" title="Qualifiers" help="Other columns can be turned into qualifiers with arbitrary keys and values">
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68 <param name="key" type="text" value="key" label="Name of the qualifier"/>
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69 <param name="val" type="text" value="" label="Qualifier value column or raw text" help="@HELP@"/>
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70 </repeat>
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71
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72 </inputs>
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73 <outputs>
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74 <data format="gff3" name="output"/>
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75 </outputs>
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76 <tests>
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77 <test>
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78 <param name="table" ftype="tabular" value="input.tab" />
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79 <param name="rid" value="1" />
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80 <param name="begin" value="5" />
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81 <param name="end" value="6" />
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82 <param name="score" value="14" />
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83 <conditional name="strand">
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84 <param name="strand_select" value="value"/>
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85 <param name="strand" value="1"/>
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86 </conditional>
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87 <repeat name="attributes">
965674d88d34 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tbl2gff3 commit 725ff8b6a4f01bf532052ce46400f529551a317d"
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88 <param name="key" value="e-value" />
965674d88d34 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tbl2gff3 commit 725ff8b6a4f01bf532052ce46400f529551a317d"
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89 <param name="val" value="7" />
965674d88d34 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tbl2gff3 commit 725ff8b6a4f01bf532052ce46400f529551a317d"
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90 </repeat>
965674d88d34 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tbl2gff3 commit 725ff8b6a4f01bf532052ce46400f529551a317d"
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91 <repeat name="attributes">
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92 <param name="key" value="hit" />
965674d88d34 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tbl2gff3 commit 725ff8b6a4f01bf532052ce46400f529551a317d"
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93 <param name="val" value="9" />
965674d88d34 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tbl2gff3 commit 725ff8b6a4f01bf532052ce46400f529551a317d"
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94 </repeat>
965674d88d34 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tbl2gff3 commit 725ff8b6a4f01bf532052ce46400f529551a317d"
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95 <repeat name="attributes">
965674d88d34 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tbl2gff3 commit 725ff8b6a4f01bf532052ce46400f529551a317d"
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96 <param name="key" value="GI" />
965674d88d34 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tbl2gff3 commit 725ff8b6a4f01bf532052ce46400f529551a317d"
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97 <param name="val" value="11" />
965674d88d34 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tbl2gff3 commit 725ff8b6a4f01bf532052ce46400f529551a317d"
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98 </repeat>
965674d88d34 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tbl2gff3 commit 725ff8b6a4f01bf532052ce46400f529551a317d"
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99 <repeat name="attributes">
965674d88d34 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tbl2gff3 commit 725ff8b6a4f01bf532052ce46400f529551a317d"
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100 <param name="key" value="test" />
965674d88d34 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tbl2gff3 commit 725ff8b6a4f01bf532052ce46400f529551a317d"
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101 <param name="val" value="one" />
965674d88d34 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tbl2gff3 commit 725ff8b6a4f01bf532052ce46400f529551a317d"
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102 </repeat>
965674d88d34 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tbl2gff3 commit 725ff8b6a4f01bf532052ce46400f529551a317d"
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103 <repeat name="attributes">
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104 <param name="key" value="test" />
965674d88d34 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tbl2gff3 commit 725ff8b6a4f01bf532052ce46400f529551a317d"
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105 <param name="val" value="two" />
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106 </repeat>
965674d88d34 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tbl2gff3 commit 725ff8b6a4f01bf532052ce46400f529551a317d"
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107
965674d88d34 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tbl2gff3 commit 725ff8b6a4f01bf532052ce46400f529551a317d"
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108 <output name="output" file="blast.gff3" />
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109
965674d88d34 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tbl2gff3 commit 725ff8b6a4f01bf532052ce46400f529551a317d"
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110 </test>
1
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111 <test>
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112 <param name="table" ftype="tabular" value="infer.tab" />
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113 <param name="rid" value="1" />
4a7f4b0cc0a3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tbl2gff3 commit db75a8489a1f61ea30abe9b91f6febac8b34204f"
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114 <param name="begin" value="2" />
4a7f4b0cc0a3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tbl2gff3 commit db75a8489a1f61ea30abe9b91f6febac8b34204f"
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115 <param name="end" value="3" />
4a7f4b0cc0a3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tbl2gff3 commit db75a8489a1f61ea30abe9b91f6febac8b34204f"
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116 <conditional name="strand">
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117 <param name="strand_select" value="infer"/>
4a7f4b0cc0a3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tbl2gff3 commit db75a8489a1f61ea30abe9b91f6febac8b34204f"
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118 </conditional>
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119 <output name="output" file="infer.gff3" />
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120
4a7f4b0cc0a3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tbl2gff3 commit db75a8489a1f61ea30abe9b91f6febac8b34204f"
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121 </test>
0
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122 </tests>
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123 <help><![CDATA[
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124 **What it does**
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125
965674d88d34 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tbl2gff3 commit 725ff8b6a4f01bf532052ce46400f529551a317d"
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126 Convert a table into GFF3. This is not a very complex or advanced tool, it won't produce GFF with hierarchy, just flat gff3 which may be sufficient for visualisation purposes.
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127
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128 ]]></help>
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129 <citations>
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130 </citations>
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131 </tool>
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132