Mercurial > repos > cpt > cpt_intersect_adj
annotate macros.xml @ 0:923d2528480d draft
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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> |
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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> |