Mercurial > repos > iuc > exonerate

annotate exonerate.xml @ 4:37f3a8c3c694 draft default tip

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/exonerate commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
author iuc
date Tue, 31 Aug 2021 08:06:32 +0000
parents 0d6a5769f901
children
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0d6a5769f901 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/exonerate commit a141c63903d1a598569985e400125d4e7de42801"
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1 <tool id="exonerate" name="Exonerate" profile="16.04" version="@VERSION@+galaxy2">
0
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2 <description>pairwise sequence comparison</description>
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37f3a8c3c694 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/exonerate commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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3 <xrefs>
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4 <xref type="bio.tools">exonerate</xref>
37f3a8c3c694 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/exonerate commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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5 </xrefs>
0
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6 <macros>
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7 <import>macros.xml</import>
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8 </macros>
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9 <expand macro="requirements"/>
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10 <command><![CDATA[
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11 exonerate
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12
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13 --query '$query'
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15 #if str( $ref_seq.ref_seq_selector ) == "personal"
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16 --target '${ref_seq.input_fasta}'
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17 #else
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18 --target '${ref_seq.input_fasta.fields.path}'
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19 #end if
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21 --score $score
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22 --percent $percent
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23 --bestn $bestn
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24 --verbose 0
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25
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26 #if str($model) != "ungapped"
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27 --model '${model}'
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28 #end if
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29
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30 #if str($model) == "est2genome"
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31 --querytype dna --targettype dna
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32 #elif str($model) == "protein2genome"
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33 --querytype protein --targettype dna
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34 #elif str($model) == "coding2coding"
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35 --querytype dna --targettype dna
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36 #end if
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37
3
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38 #if $minintron
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39 --minintron ${minintron}
0d6a5769f901 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/exonerate commit a141c63903d1a598569985e400125d4e7de42801"
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40 #end if
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0d6a5769f901 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/exonerate commit a141c63903d1a598569985e400125d4e7de42801"
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42 #if $maxintron
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43 --maxintron ${maxintron}
0d6a5769f901 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/exonerate commit a141c63903d1a598569985e400125d4e7de42801"
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44 #end if
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0d6a5769f901 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/exonerate commit a141c63903d1a598569985e400125d4e7de42801"
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46 --cores \${GALAXY_SLOTS:-1}
0d6a5769f901 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/exonerate commit a141c63903d1a598569985e400125d4e7de42801"
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47
0
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48 #if str($outformat) == "alignment"
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49 --showalignment yes --showvulgar no > '${output_ali}'
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50 #elif str($outformat) == "targetgff"
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51 --showalignment no --showvulgar no --showtargetgff yes --showquerygff no > '${output_gff}'
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52 #elif str($outformat) == "querygff"
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53 --showalignment no --showvulgar no --showtargetgff no --showquerygff yes > '${output_gff}'
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54 #end if
2
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55
3
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56 ## Produce a more standard GFF3
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57 #if str($outformat) in ["targetgff", "querygff"]
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58 && python '$__tool_directory__/exonerategff_to_gff3.py' '${output_gff}' > '${output_gff3}'
0d6a5769f901 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/exonerate commit a141c63903d1a598569985e400125d4e7de42801"
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59 #end if
0
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60 ]]></command>
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61
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62 <inputs>
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63 <param argument="--query" type="data" format="fasta" label="Select the query sequence(s) in fasta" />
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64
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65 <conditional name="ref_seq">
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66 <param name="ref_seq_selector" type="select" label="Reference sequence(s)">
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67 <option selected="True" value="database">Use a built-in genome</option>
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68 <option value="personal">Use a genome from history</option>
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69 </param>
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70 <when value="database">
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71 <param
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72 help="If your genome of interest is not listed, contact the Galaxy server administrators"
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73 label="Reference sequence(s)"
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74 name="input_fasta"
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75 type="select"
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76 >
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77 <options from_data_table="all_fasta">
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78 <filter column="2" type="sort_by" />
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79 <validator message="No sequences are available" type="no_options" />
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80 </options>
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81 </param>
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82 </when>
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83 <when value="personal">
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84 <param name="input_fasta" type="data" format="fasta" label="Reference sequence(s)" />
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85 </when>
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86 </conditional>
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87
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88 <param name='model' type='select' label="Alignment method">
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89 <option value="ungapped" selected="true">Simple ungapped alignment</option>
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90 <option value="est2genome">est2genome: align cDNA to a genome</option>
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91 <option value="protein2genome">protein2genome: align proteins to a genome</option>
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92 <option value="coding2coding">coding2coding: 6-frame translated alignment of DNA sequences</option>
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93 </param>
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94 <param name='outformat' type='select' label="Output format">
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95 <option value="targetgff" selected="true">GFF on target sequence(s)</option>
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96 <option value="querygff">GFF on query sequence(s)</option>
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97 <option value="alignment">Human readable alignment</option>
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98 </param>
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iuc
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99 <param name='score' type='integer' min="0" max="10000" value="100" label="Score threshold for gapped alignment"/>
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iuc
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100 <param name='percent' type='float' min="0" max="100" value="0.0" label="Report alignment over a percentage of the maximum score attainable by each query"/>
b1fd74cb7cb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/exonerate commit e02d20338ee01ed58265d93e9cc5b0695a322d47
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101 <param name='bestn' type='integer' min="0" max="10000" value="0" label="Report best N results per query (0 to report all)"/>
3
0d6a5769f901 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/exonerate commit a141c63903d1a598569985e400125d4e7de42801"
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102 <param argument='--minintron' type='integer' optional="true" label="Minimum intron length limit" help="This is not a hard limit - it only affects size of introns which are sought during heuristic alignment."/>
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103 <param argument='--maxintron' type='integer' optional="true" label="Maximum intron length limit" help="This is not a hard limit - it only affects size of introns which are sought during heuristic alignment."/>
0
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104 </inputs>
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105 <outputs>
3
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106 <data name="output_gff" format="gff" label="${tool.name} on $on_string - Raw GFF">
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107 <filter>outformat != 'alignment'</filter>
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108 </data>
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109 <data name="output_gff3" format="gff3" label="${tool.name} on $on_string - GFF3">
0
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110 <filter>outformat != 'alignment'</filter>
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111 </data>
1
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112 <data name="output_ali" format="txt" label="${tool.name} on $on_string">
0
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113 <filter>outformat == 'alignment'</filter>
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114 </data>
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115 </outputs>
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116 <tests>
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117 <test>
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118 <param name="query" value="genome.fa"/>
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119 <conditional name="ref_seq">
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120 <param name="ref_seq_selector" value="personal"/>
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121 <param name="input_fasta" value="genome.fa"/>
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122 </conditional>
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123 <param name="outformat" value="targetgff"/>
1
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124 <output name="output_gff" file="out_target.gff" lines_diff="8"/>
3
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125 <output name="output_gff3" file="out_target.gff3" lines_diff="8"/>
0
b1fd74cb7cb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/exonerate commit e02d20338ee01ed58265d93e9cc5b0695a322d47
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126 </test>
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127 <test>
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128 <param name="query" value="genome.fa"/>
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129 <conditional name="ref_seq">
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130 <param name="ref_seq_selector" value="database"/>
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iuc
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131 <param name="input_fasta" value="merlin"/>
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132 </conditional>
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133 <param name="outformat" value="targetgff"/>
1
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134 <output name="output_gff" file="out_target.gff" lines_diff="8"/>
3
0d6a5769f901 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/exonerate commit a141c63903d1a598569985e400125d4e7de42801"
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135 <output name="output_gff3" file="out_target.gff3" lines_diff="8"/>
0
b1fd74cb7cb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/exonerate commit e02d20338ee01ed58265d93e9cc5b0695a322d47
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136 </test>
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137 <test>
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iuc
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138 <param name="query" value="genome.fa"/>
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iuc
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139 <conditional name="ref_seq">
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iuc
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140 <param name="ref_seq_selector" value="personal"/>
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iuc
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141 <param name="input_fasta" value="genome.fa"/>
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142 </conditional>
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iuc
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143 <param name="outformat" value="querygff"/>
1
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144 <output name="output_gff" file="out_query.gff" lines_diff="8"/>
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0d6a5769f901 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/exonerate commit a141c63903d1a598569985e400125d4e7de42801"
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145 <output name="output_gff3" file="out_query.gff3" lines_diff="8"/>
0
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146 </test>
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147 <test>
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148 <param name="query" value="genome.fa"/>
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149 <conditional name="ref_seq">
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150 <param name="ref_seq_selector" value="personal"/>
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151 <param name="input_fasta" value="genome.fa"/>
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152 </conditional>
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153 <param name="outformat" value="alignment"/>
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154 <output name="output_ali" file="out.txt"/>
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155 </test>
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156 <test>
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157 <param name="query" value="transcriptome.fa"/>
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158 <conditional name="ref_seq">
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159 <param name="ref_seq_selector" value="personal"/>
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160 <param name="input_fasta" value="genome.fa"/>
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161 </conditional>
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162 <param name="model" value="est2genome"/>
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163 <param name="outformat" value="targetgff"/>
1
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164 <output name="output_gff" file="est2genome.gff" lines_diff="4"/>
3
0d6a5769f901 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/exonerate commit a141c63903d1a598569985e400125d4e7de42801"
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165 <output name="output_gff3" file="est2genome.gff3" lines_diff="4"/>
0
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166 </test>
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167 <test>
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168 <param name="query" value="proteome.fa"/>
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169 <conditional name="ref_seq">
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170 <param name="ref_seq_selector" value="personal"/>
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171 <param name="input_fasta" value="genome.fa"/>
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172 </conditional>
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173 <param name="model" value="protein2genome"/>
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174 <param name="outformat" value="targetgff"/>
1
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175 <output name="output_gff" file="protein2genome.gff" lines_diff="2"/>
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176 <output name="output_gff3" file="protein2genome.gff3" lines_diff="2"/>
0
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177 </test>
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178 <test>
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179 <param name="query" value="genome.fa"/>
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180 <conditional name="ref_seq">
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181 <param name="ref_seq_selector" value="personal"/>
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182 <param name="input_fasta" value="genome.fa"/>
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183 </conditional>
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184 <param name="model" value="coding2coding"/>
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185 <param name="outformat" value="targetgff"/>
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186 <output name="output_gff" file="coding2coding.gff" lines_diff="4"/>
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187 <output name="output_gff3" file="coding2coding.gff3" lines_diff="4"/>
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188 </test>
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189 <test>
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190 <param name="query" value="transcriptome.fa"/>
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191 <conditional name="ref_seq">
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192 <param name="ref_seq_selector" value="personal"/>
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193 <param name="input_fasta" value="genome.fa"/>
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194 </conditional>
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195 <param name="model" value="est2genome"/>
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196 <param name="outformat" value="targetgff"/>
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197 <param name="minintron" value="100"/>
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198 <param name="maxintron" value="200"/>
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199 <output name="output_gff" file="est2genome_introns.gff" lines_diff="6"/>
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200 <output name="output_gff3" file="est2genome_introns.gff3" lines_diff="4"/>
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201 </test>
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202 </tests>
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203 <help><![CDATA[
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204 Exonerate is a generic tool for pairwise sequence comparison.
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205 It allows you to align sequences using a many alignment models, using either exhaustive dynamic programming, or a variety of heuristics.
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206
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207 .. _Exonerate website: https://www.ebi.ac.uk/about/vertebrate-genomics/software/exonerate
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208 ]]></help>
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209 <expand macro="citations"/>
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210 </tool>