Mercurial > repos > cpt > cpt_gff_extract_seq

annotate macros.xml @ 8:759ba1430091 draft

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author cpt
date Fri, 01 Dec 2023 04:07:14 +0000
parents 706058e804d1
children 9264ac799feb
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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="0.6.4">bcbiogff</requirement>
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5 <requirement type="package" version="3.9">python</requirement>
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6 <requirement type="package" version="1.65">biopython</requirement>
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7 <requirement type="package" version="2.12.1">requests</requirement>
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8 <requirement type="package" version="1.2.2">cpt_gffparser</requirement>
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9 <yield/>
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10 </requirements>
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11 </xml>
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12 <token name="@WRAPPER_VERSION@">2.4.0</token>
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13 <xml name="citation/gepard">
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14 <citation type="doi">10.1093/bioinformatics/btm039</citation>
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15 </xml>
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16 <token name="@XMFA_INPUT@">
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17 '$xmfa'
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18 </token>
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19 <xml name="xmfa_input" token_formats="xmfa">
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20 <param type="data" format="@FORMATS@" name="xmfa" label="XMFA MSA"/>
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21 </xml>
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22 <token name="@XMFA_FA_INPUT@">
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23 '$sequences'
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24 </token>
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25 <xml name="xmfa_fa_input">
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26 <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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27 </xml>
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28 <xml name="genome_selector">
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29 <conditional name="reference_genome">
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30 <param name="reference_genome_source" type="select" label="Reference Genome">
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31 <option value="history" selected="True">From History</option>
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32 <option value="cached">Locally Cached</option>
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33 </param>
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34 <when value="cached">
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35 <param name="fasta_indexes" type="select" label="Source FASTA Sequence">
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36 <options from_data_table="all_fasta"/>
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37 </param>
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38 </when>
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39 <when value="history">
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40 <param name="genome_fasta" type="data" format="fasta" label="Source FASTA Sequence"/>
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41 </when>
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42 </conditional>
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43 </xml>
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44 <xml name="gff3_input">
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45 <param label="GFF3 Annotations" name="gff3_data" type="data" format="gff3"/>
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46 </xml>
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47 <xml name="input/gff3+fasta">
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48 <expand macro="gff3_input"/>
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49 <expand macro="genome_selector"/>
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50 </xml>
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51 <xml name="citation/mijalisrasche">
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52 <citation type="doi">10.1371/journal.pcbi.1008214</citation>
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53 <citation type="bibtex">@unpublished{galaxyTools,
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54 author = {E. Mijalis, H. Rasche},
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55 title = {CPT Galaxy Tools},
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56 year = {2013-2017},
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57 note = {https://github.com/tamu-cpt/galaxy-tools/}
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58 }
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59 </citation>
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60 </xml>
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61 <xml name="citations">
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62 <citations>
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63 <citation type="doi">10.1371/journal.pcbi.1008214</citation>
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64 <citation type="bibtex">
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65 @unpublished{galaxyTools,
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66 author = {E. Mijalis, H. Rasche},
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67 title = {CPT Galaxy Tools},
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68 year = {2013-2017},
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69 note = {https://github.com/tamu-cpt/galaxy-tools/}
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70 }
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71 </citation>
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72 <yield/>
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73 </citations>
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74 </xml>
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75 <xml name="citations-crr">
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76 <citations>
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77 <citation type="doi">10.1371/journal.pcbi.1008214</citation>
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78 <citation type="bibtex">
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79 @unpublished{galaxyTools,
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80 author = {C. Ross},
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81 title = {CPT Galaxy Tools},
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82 year = {2020-},
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83 note = {https://github.com/tamu-cpt/galaxy-tools/}
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84 }
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85 </citation>
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86 <yield/>
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87 </citations>
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88 </xml>
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89 <xml name="citations-2020">
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90 <citations>
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91 <citation type="doi">10.1371/journal.pcbi.1008214</citation>
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92 <citation type="bibtex">
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93 @unpublished{galaxyTools,
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94 author = {E. Mijalis, H. Rasche},
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95 title = {CPT Galaxy Tools},
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96 year = {2013-2017},
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97 note = {https://github.com/tamu-cpt/galaxy-tools/}
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98 }
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99 </citation>
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100 <citation type="bibtex">
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101 @unpublished{galaxyTools,
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102 author = {A. Criscione},
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103 title = {CPT Galaxy Tools},
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104 year = {2019-2021},
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105 note = {https://github.com/tamu-cpt/galaxy-tools/}
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106 }
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107 </citation>
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108 <yield/>
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109 </citations>
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110 </xml>
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111 <xml name="citations-2020-AJC-solo">
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112 <citations>
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113 <citation type="doi">10.1371/journal.pcbi.1008214</citation>
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114 <citation type="bibtex">
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115 @unpublished{galaxyTools,
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116 author = {A. Criscione},
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117 title = {CPT Galaxy Tools},
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118 year = {2019-2021},
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119 note = {https://github.com/tamu-cpt/galaxy-tools/}
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120 }
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121 </citation>
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122 <yield/>
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123 </citations>
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124 </xml>
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125 <xml name="citations-clm">
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126 <citations>
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127 <citation type="doi">10.1371/journal.pcbi.1008214</citation>
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128 <citation type="bibtex">
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129 @unpublished{galaxyTools,
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130 author = {C. Maughmer},
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131 title = {CPT Galaxy Tools},
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132 year = {2017-2020},
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133 note = {https://github.com/tamu-cpt/galaxy-tools/}
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134 }
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135 </citation>
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136 <yield/>
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137 </citations>
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138 </xml>
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139 <xml name="sl-citations-clm">
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140 <citation type="bibtex">
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141 @unpublished{galaxyTools,
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142 author = {C. Maughmer},
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143 title = {CPT Galaxy Tools},
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144 year = {2017-2020},
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145 note = {https://github.com/tamu-cpt/galaxy-tools/}
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146 }
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147 </citation>
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148 <yield/>
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149 </xml>
4
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150 <token name="@INPUT_GFF@">
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151 '$gff3_data'
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152 </token>
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153 <token name="@INPUT_FASTA@">
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154 #if str($reference_genome.reference_genome_source) == 'cached':
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155 '${reference_genome.fasta_indexes.fields.path}'
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156 #else if str($reference_genome.reference_genome_source) == 'history':
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157 genomeref.fa
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158 #end if
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159 </token>
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160 <token name="@GENOME_SELECTOR_PRE@">
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161 #if $reference_genome.reference_genome_source == 'history':
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162 ln -s '$reference_genome.genome_fasta' genomeref.fa;
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163 #end if
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164 </token>
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165 <token name="@GENOME_SELECTOR@">
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166 #if str($reference_genome.reference_genome_source) == 'cached':
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167 '${reference_genome.fasta_indexes.fields.path}'
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168 #else if str($reference_genome.reference_genome_source) == 'history':
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169 genomeref.fa
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170 #end if
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171 </token>
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172 </macros>