Mercurial > repos > bgruening > uniprot_rest_interface

annotate macros.xml @ 5:f7ebd1b4783b draft

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/uniprot_rest_interface commit f4fd11072886b30675afb8f8bb459eba9c4671bb
author bgruening
date Sat, 15 Sep 2018 10:23:35 -0400
parents 48522382b6a4
children bfdc6a7ffd3a
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48522382b6a4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/uniprot_rest_interface commit 2b8ad1bbfe098129ae32cd8311a755dff58ae97b-dirty
bgruening
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1 <macros>
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2 <token name="@EXECUTABLE@">1.0</token>
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3 <macro name="macro-category_FROM">
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4 <param name="category_FROM" type="select" label="Choose your database category (FROM):"
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5 help="Select a databse from which your ids are coming from">
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6 <option value="uniprot">UniProt</option>
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7 <option value="oseqdb">Other sequence databases</option>
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8 <option value="3Dstrdb">3D structure databases</option>
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9 <option value="ppidb">Protein-protein interaction databases</option>
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10 <option value="chemistry">Chemistry</option>
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11 <option value="protfgdb">Protein family/group databases</option>
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12 <option value="polymorphismANDmutation">Polymorphism and mutation databases</option>
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13 <option value="2DgelDB">2D gel databases</option>
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14 <option value="ProtocolsMaterialsDB">Protocols and materials databases</option>
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15 <option value="GenomeAnnotationDB">Genome annotation databases</option>
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16 <option value="OrganismSpecificGeneDB">Organism-specific gene databases</option>
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17 <option value="phylogenomic">Phylogenomic databases</option>
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18 <option value="EnzymePathwayDB">Enzyme and pathway databases</option>
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19 <option value="GeneExpression">Gene expression databases</option>
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20 <option value="other">Other</option>
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21 </param>
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22 </macro>
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23 <macro name="macro-category_TO">
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24 <param name="category_TO" type="select" label="Choose your database category (TO):"
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25 help="Select a database which will be used for mapping">
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26 <option value="uniprot">UniProt</option>
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27 <option value="oseqdb">Other sequence databases</option>
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28 <option value="3Dstrdb">3D structure databases</option>
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29 <option value="ppidb">Protein-protein interaction databases</option>
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30 <option value="chemistry">Chemistry</option>
48522382b6a4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/uniprot_rest_interface commit 2b8ad1bbfe098129ae32cd8311a755dff58ae97b-dirty
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31 <option value="protfgdb">Protein family/group databases</option>
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32 <option value="polymorphismANDmutation">Polymorphism and mutation databases</option>
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33 <option value="2DgelDB">2D gel databases</option>
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34 <option value="ProtocolsMaterialsDB">Protocols and materials databases</option>
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35 <option value="GenomeAnnotationDB">Genome annotation databases</option>
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36 <option value="OrganismSpecificGeneDB">Organism-specific gene databases</option>
48522382b6a4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/uniprot_rest_interface commit 2b8ad1bbfe098129ae32cd8311a755dff58ae97b-dirty
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37 <option value="phylogenomic">Phylogenomic databases</option>
48522382b6a4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/uniprot_rest_interface commit 2b8ad1bbfe098129ae32cd8311a755dff58ae97b-dirty
bgruening
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38 <option value="EnzymePathwayDB">Enzyme and pathway databases</option>
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39 <option value="GeneExpression">Gene expression databases</option>
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40 <option value="other">Other</option>
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41 </param>
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42 </macro>
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43 <macro name="macro-db_uniprot_FROM">
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44 <param name="db_uniprot_FROM" type="select" label="Choose a database:"
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45 help="">
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46 <option value="ACC+ID">UniProtKB AC/ID</option>
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47 <option value="ACC">UniProtKB AC</option>
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48 <option value="ID">UniProtKB ID</option>
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49 <option value="ACC">UniProtKB AC</option>
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50 <option value="UPARC">UniParc</option>
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51 <option value="NF50">UniRef50</option>
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52 <option value="NF90">UniRef90</option>
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53 <option value="NF100">UniRef100</option>
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54 <option value="GENENAME">Gene name</option>
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55 </param>
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56 </macro>
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57 <macro name="macro-db_uniprot_TO">
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58 <param name="db_uniprot_TO" type="select" label="Choose a database:"
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59 help="">
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60 <option value="ACC">UniProtKB AC</option>
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61 <option value="ID">UniProtKB ID</option>
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62 <option value="ACC">UniProtKB AC</option>
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63 <option value="UPARC">UniParc</option>
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64 <option value="NF50">UniRef50</option>
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65 <option value="NF90">UniRef90</option>
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66 <option value="NF100">UniRef100</option>
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67 <option value="GENENAME">Gene name</option>
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68 </param>
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69 </macro>
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70 <macro name="macro-db_oseqdb">
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71 <param name="db_oseqdb" type="select" label="Choose a database:"
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72 help="">
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73 <option value="EMBL_ID">EMBL/GenBank/DDBJ</option>
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74 <option value="EMBL">EMBL/GenBank/DDBJ CDS</option>
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75 <option value="PIR">PIR</option>
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76
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77 <option value="UNIGENE_ID">UniParc</option>
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78 <option value="P_ENTREZGENEID">Entrez Gene (GeneID)</option>
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79 <option value="P_GI">GI number</option>
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80 <option value="P_REFSEQ_AC">RefSeq Protein</option>
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81 <option value="REFSEQ_NT_ID">RefSeq Nucleotide</option>
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82 </param>
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83 </macro>
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bgruening
parents:
diff changeset
84 <macro name="macro-db_3Dstrdb">
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bgruening
parents:
diff changeset
85 <param name="db_3Dstrdb" type="select" label="Choose a database:"
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bgruening
parents:
diff changeset
86 help="">
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bgruening
parents:
diff changeset
87 <option value="PDB_ID">PDB</option>
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bgruening
parents:
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88 <option value="DISPROT_ID">DisProt</option>
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bgruening
parents:
diff changeset
89 </param>
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bgruening
parents:
diff changeset
90 </macro>
48522382b6a4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/uniprot_rest_interface commit 2b8ad1bbfe098129ae32cd8311a755dff58ae97b-dirty
bgruening
parents:
diff changeset
91 <macro name="macro-db_ppidb">
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bgruening
parents:
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92 <param name="db_ppidb" type="select" label="Choose a database:"
48522382b6a4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/uniprot_rest_interface commit 2b8ad1bbfe098129ae32cd8311a755dff58ae97b-dirty
bgruening
parents:
diff changeset
93 help="">
48522382b6a4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/uniprot_rest_interface commit 2b8ad1bbfe098129ae32cd8311a755dff58ae97b-dirty
bgruening
parents:
diff changeset
94 <option value="BIOGRID_ID">BioGrid</option>
48522382b6a4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/uniprot_rest_interface commit 2b8ad1bbfe098129ae32cd8311a755dff58ae97b-dirty
bgruening
parents:
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95 <option value="DIP_ID">DIP</option>
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bgruening
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96 <option value="MINT_ID">MINT</option>
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bgruening
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97 <option value="STRING_ID">STRING</option>
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bgruening
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98 </param>
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bgruening
parents:
diff changeset
99 </macro>
48522382b6a4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/uniprot_rest_interface commit 2b8ad1bbfe098129ae32cd8311a755dff58ae97b-dirty
bgruening
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100 <macro name="macro-db_chemistry">
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bgruening
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101 <param name="db_chemistry" type="select" label="Choose a database:"
48522382b6a4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/uniprot_rest_interface commit 2b8ad1bbfe098129ae32cd8311a755dff58ae97b-dirty
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102 help="">
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bgruening
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103 <option value="CHEMBL_ID">ChEMBL</option>
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104 <option value="DrugBank_ID">DrugBank</option>
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105 <option value="GUIDETOPHARMACOLOGY_ID">GuidetoPHARMACOLOGY</option>
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106 </param>
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bgruening
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107 </macro>
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108 <macro name="macro-db_protfgdb">
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109 <param name="db_protfgdb" type="select" label="Choose a database:"
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bgruening
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110 help="">
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bgruening
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111 <option value="ALLERGOME_ID">Allergome</option>
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bgruening
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112 <option value="MEROPS_ID">MEROPS</option>
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bgruening
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113 <option value="MYCOCLAP_ID">mycoCLAP</option>
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114 <option value="PEROXIBASE_ID">PeroxiBase</option>
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bgruening
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115 <option value="REBASE_ID">REBASE</option>
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116 <option value="TCDB_ID">TCDB</option>
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bgruening
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117 </param>
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bgruening
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118 </macro>
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bgruening
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119 <macro name="macro-db_polymorphismANDmutation">
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bgruening
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120 <param name="db_polymorphismANDmutation" type="select" label="Choose a database:"
48522382b6a4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/uniprot_rest_interface commit 2b8ad1bbfe098129ae32cd8311a755dff58ae97b-dirty
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121 help="">
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bgruening
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122 <option value="DMDM_ID">DMDM</option>
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bgruening
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123 </param>
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bgruening
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124 </macro>
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bgruening
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125 <macro name="macro-db_2DgelDB">
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bgruening
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126 <param name="db_2DgelDB" type="select" label="Choose a database:"
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127 help="">
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bgruening
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128 <option value="WORLD_2DPAGE_ID">World-2DPAGE</option>
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bgruening
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129 </param>
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bgruening
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130 </macro>
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bgruening
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131 <macro name="macro-db_ProtocolsMaterialsDB">
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132 <param name="db_ProtocolsMaterialsDB" type="select" label="Choose a database:"
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133 help="">
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134 <option value="DNASU_ID">DNASU</option>
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135 </param>
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bgruening
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136 </macro>
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bgruening
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137 <macro name="macro-db_GenomeAnnotationDB">
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bgruening
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138 <param name="db_GenomeAnnotationDB" type="select" label="Choose a database:"
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139 help="">
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140 <option value="ENSEMBL_ID">Ensembl</option>
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141 <option value="ENSEMBL_PRO_ID">Ensembl Protein</option>
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142 <option value="ENSEMBL_TRS_ID">Ensembl Transcript</option>
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bgruening
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143 <option value="ENSEMBLGENOME_ID">Ensembl Genomes</option>
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144 <option value="ENSEMBLGENOME_PRO_ID">Ensembl Genomes Protein</option>
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bgruening
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145 <option value="ENSEMBLGENOME_TRS_ID">Ensembl Genomes Transcript</option>
48522382b6a4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/uniprot_rest_interface commit 2b8ad1bbfe098129ae32cd8311a755dff58ae97b-dirty
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146 <option value="P_ENTREZGENEID">GeneID</option>
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147 <option value="KEGG_ID">KEGG</option>
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148 <option value="PATRIC_ID">PATRIC</option>
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149 <option value="UCSC_ID">UCSC</option>
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150 <option value="VECTORBASE_ID">VectorBase</option>
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151 </param>
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152 </macro>
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153 <macro name="macro-db_OrganismSpecificGeneDB">
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154 <param name="db_OrganismSpecificGeneDB" type="select" label="Choose a database:"
48522382b6a4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/uniprot_rest_interface commit 2b8ad1bbfe098129ae32cd8311a755dff58ae97b-dirty
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155 help="">
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156 <option value="ARACHNOSERVER_ID">ArachnoServer</option>
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157 <option value="CGD">CGD</option>
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158 <option value="CONOSERVER_ID">ConoServer</option>
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159 <option value="DICTYBASE_ID">dictyBase</option>
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160 <option value="ECHOBASE_ID">EchoBASE</option>
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161 <option value="ECOGENE_ID">EcoGene</option>
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162 <option value="EUHCVDB_ID">euHCVdb</option>
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163 <option value="EUPATHDB_ID">EuPathDB</option>
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164 <option value="FLYBASE_ID">FlyBase</option>
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165 <option value="GENECARDS_ID">GeneCards</option>
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166 <option value="GENEFARM_ID">GeneFarm</option>
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167 <option value="GENOLIST_ID">GenoList</option>
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168 <option value="H_INVDB_ID">H-InvDB</option>
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169 <option value="HGNC_ID">HGNC</option>
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170 <option value="HPA_ID">HPA</option>
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171 <option value="LEGIOLIST_ID">LegioList</option>
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172 <option value="MAIZEGDB_ID">MaizeGDB</option>
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173 <option value="MIM_ID">MIM</option>
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174 <option value="MGI_ID">MGI</option>
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175 <option value="NEXTPROT_ID">neXtProt</option>
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176 <option value="ORPHANET_ID">Orphanet</option>
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177 <option value="PHARMGKB_ID">PharmGKB</option>
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178 <option value="POMBASE_ID">PomBase</option>
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179 <option value="PSEUDOCAP_ID">PseudoCAP</option>
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180 <option value="RGD_ID">RGD</option>
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181 <option value="SGD_ID">SGD</option>
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182 <option value="TAIR_ID">TAIR</option>
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183 <option value="TUBERCULIST_ID">TubercuList</option>
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184 <option value="WORMBASE_ID">WormBase</option>
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185 <option value="WORMBASE_TRS_ID">WormBase Transcript</option>
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186 <option value="WORMBASE_PRO_ID">WormBase Protein</option>
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187 <option value="XENBASE_ID">Xenbase</option>
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188 <option value="ZFIN_ID">ZFIN</option>
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189 </param>
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190 </macro>
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191 <macro name="macro-db_phylogenomic">
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192 <param name="db_phylogenomic" type="select" label="Choose a database:"
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193 help="">
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194 <option value="EGGNOG_ID">eggNOG</option>
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195 <option value="GENETREE_ID">GeneTree</option>
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196 <option value="HOGENOM_ID">HOGENOM</option>
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197 <option value="HOVERGEN_ID">HOVERGEN</option>
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198 <option value="KO_ID">KO</option>
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199 <option value="OMA_ID">OMA</option>
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200 <option value="ORTHODB_ID">OrthoDB</option>
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201 <option value="PROTCLUSTDB_ID">ProtClustDB</option>
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202 <option value="TREEFAM_ID">TreeFam</option>
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203 </param>
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204 </macro>
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205 <macro name="macro-db_EnzymePathwayDB">
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206 <param name="db_EnzymePathwayDB" type="select" label="Choose a database:"
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207 help="">
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208 <option value="BIOCYC_ID">BioCyc</option>
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209 <option value="REACTOME_ID">Reactome</option>
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210 <option value="UNIPATHWAY_ID">UniPathWay</option>
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211 </param>
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212 </macro>
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213 <macro name="macro-db_GeneExpression">
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214 <param name="db_GeneExpression" type="select" label="Choose a database:"
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215 help="">
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216 <option value="CLEANEX_ID">CleanEx</option>
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217 </param>
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218 </macro>
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219 <macro name="macro-db_other">
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220 <param name="db_other" type="select" label="Choose a database:"
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221 help="">
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222 <option value="CHITARS_ID">ChiTaRS</option>
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223 <option value="GENOMERNAI_ID">GenomeRNAi</option>
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224 <option value="GENEWIKI_ID">GeneWiki</option>
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225 <option value="NEXTBIO_ID">NextBio</option>
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226 </param>
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227 </macro>
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228 </macros>