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annotate macros.xml @ 8:b5c1b167df3c draft

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author cpt
date Fri, 20 Sep 2024 03:03:00 +0000
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1 <macros>
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2 <xml name="requirements">
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3 <requirements>
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4 <requirement type="package" version="3.9">python</requirement>
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5 <requirement type="package" version="1.81">biopython</requirement>
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6 <requirement type="package" version="1.2.2">cpt_gffparser</requirement>
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7 <yield/>
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8 </requirements>
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9 </xml>
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10 <token name="@WRAPPER_VERSION@">2.4.0</token>
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11 <xml name="citation/gepard">
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12 <citation type="doi">10.1093/bioinformatics/btm039</citation>
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13 </xml>
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14 <token name="@XMFA_INPUT@">
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15 '$xmfa'
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16 </token>
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17 <xml name="xmfa_input" token_formats="xmfa">
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18 <param type="data" format="@FORMATS@" name="xmfa" label="XMFA MSA"/>
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19 </xml>
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20 <token name="@XMFA_FA_INPUT@">
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21 '$sequences'
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22 </token>
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23 <xml name="xmfa_fa_input">
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24 <param type="data" format="fasta" name="sequences" label="Sequences in alignment" help="These sequences should be the SAME DATASET that was used in the progressiveMauve run. Failing that, they should be provided in the same order as in original progressiveMauve run"/>
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25 </xml>
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26 <xml name="genome_selector">
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27 <conditional name="reference_genome">
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28 <param name="reference_genome_source" type="select" label="Reference Genome">
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29 <option value="history" selected="True">From History</option>
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30 <option value="cached">Locally Cached</option>
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31 </param>
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32 <when value="cached">
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33 <param name="fasta_indexes" type="select" label="Source FASTA Sequence">
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34 <options from_data_table="all_fasta"/>
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35 </param>
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36 </when>
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37 <when value="history">
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38 <param name="genome_fasta" type="data" format="fasta" label="Source FASTA Sequence"/>
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39 </when>
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40 </conditional>
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41 </xml>
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42 <xml name="gff3_input">
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43 <param label="GFF3 Annotations" name="gff3_data" type="data" format="gff3"/>
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44 </xml>
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45 <xml name="input/gff3+fasta">
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46 <expand macro="gff3_input"/>
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47 <expand macro="genome_selector"/>
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48 </xml>
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49 <xml name="citation/mijalisrasche">
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50 <citation type="doi">10.1371/journal.pcbi.1008214</citation>
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51 <citation type="bibtex">@unpublished{galaxyTools,
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52 author = {E. Mijalis, H. Rasche},
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53 title = {CPT Galaxy Tools},
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54 year = {2013-2017},
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55 note = {https://github.com/tamu-cpt/galaxy-tools/}
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56 }
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57 </citation>
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58 </xml>
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59 <xml name="citations">
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60 <citations>
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61 <citation type="doi">10.1371/journal.pcbi.1008214</citation>
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62 <citation type="bibtex">
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63 @unpublished{galaxyTools,
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64 author = {E. Mijalis, H. Rasche},
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65 title = {CPT Galaxy Tools},
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66 year = {2013-2017},
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67 note = {https://github.com/tamu-cpt/galaxy-tools/}
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68 }
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69 </citation>
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70 <yield/>
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71 </citations>
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72 </xml>
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73 <xml name="citations-crr">
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74 <citations>
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75 <citation type="doi">10.1371/journal.pcbi.1008214</citation>
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76 <citation type="bibtex">
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77 @unpublished{galaxyTools,
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78 author = {C. Ross},
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79 title = {CPT Galaxy Tools},
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80 year = {2020-},
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81 note = {https://github.com/tamu-cpt/galaxy-tools/}
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82 }
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83 </citation>
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84 <yield/>
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85 </citations>
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86 </xml>
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87 <xml name="citations-2020">
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88 <citations>
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89 <citation type="doi">10.1371/journal.pcbi.1008214</citation>
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90 <citation type="bibtex">
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91 @unpublished{galaxyTools,
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92 author = {E. Mijalis, H. Rasche},
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93 title = {CPT Galaxy Tools},
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94 year = {2013-2017},
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95 note = {https://github.com/tamu-cpt/galaxy-tools/}
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96 }
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97 </citation>
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98 <citation type="bibtex">
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99 @unpublished{galaxyTools,
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100 author = {A. Criscione},
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101 title = {CPT Galaxy Tools},
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102 year = {2019-2021},
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103 note = {https://github.com/tamu-cpt/galaxy-tools/}
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104 }
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105 </citation>
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106 <yield/>
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107 </citations>
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108 </xml>
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109 <xml name="citations-2020-AJC-solo">
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110 <citations>
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111 <citation type="doi">10.1371/journal.pcbi.1008214</citation>
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112 <citation type="bibtex">
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113 @unpublished{galaxyTools,
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114 author = {A. Criscione},
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115 title = {CPT Galaxy Tools},
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116 year = {2019-2021},
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117 note = {https://github.com/tamu-cpt/galaxy-tools/}
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118 }
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119 </citation>
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120 <yield/>
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121 </citations>
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122 </xml>
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123 <xml name="citations-clm">
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124 <citations>
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125 <citation type="doi">10.1371/journal.pcbi.1008214</citation>
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126 <citation type="bibtex">
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127 @unpublished{galaxyTools,
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128 author = {C. Maughmer},
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129 title = {CPT Galaxy Tools},
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130 year = {2017-2020},
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131 note = {https://github.com/tamu-cpt/galaxy-tools/}
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132 }
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133 </citation>
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134 <yield/>
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135 </citations>
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136 </xml>
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137 <xml name="sl-citations-clm">
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138 <citation type="bibtex">
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139 @unpublished{galaxyTools,
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140 author = {C. Maughmer},
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141 title = {CPT Galaxy Tools},
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142 year = {2017-2020},
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143 note = {https://github.com/tamu-cpt/galaxy-tools/}
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144 }
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145 </citation>
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146 <yield/>
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147 </xml>
1
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148 <token name="@INPUT_GFF@">
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149 '$gff3_data'
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150 </token>
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151 <token name="@INPUT_FASTA@">
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152 #if str($reference_genome.reference_genome_source) == 'cached':
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153 '${reference_genome.fasta_indexes.fields.path}'
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154 #else if str($reference_genome.reference_genome_source) == 'history':
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155 genomeref.fa
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156 #end if
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157 </token>
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158 <token name="@GENOME_SELECTOR_PRE@">
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159 #if $reference_genome.reference_genome_source == 'history':
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160 ln -s '$reference_genome.genome_fasta' genomeref.fa;
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161 #end if
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162 </token>
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163 <token name="@GENOME_SELECTOR@">
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164 #if str($reference_genome.reference_genome_source) == 'cached':
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165 '${reference_genome.fasta_indexes.fields.path}'
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166 #else if str($reference_genome.reference_genome_source) == 'history':
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167 genomeref.fa
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168 #end if
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169 </token>
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170 </macros>