Mercurial > repos > earlhaminst > ensembl_get_genetree

annotate get_genetree.xml @ 8:935de83b470b draft default tip

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planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/Ensembl-REST commit 8f8808de862973aedbf87abd4dfa9d2dc7219322
author earlhaminst
date Mon, 17 Feb 2025 14:49:15 +0000
parents 515e7181d5e9
children
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1 <tool id="get_genetree" name="Get gene tree by Ensembl ID" version="1.0.0">
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2 <description>using REST API</description>
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3 <macros>
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4 <import>macros.xml</import>
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5 <xml name="sequence_conditional">
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6 <conditional name="sequence">
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7 <param name="sequence_selector" type="select" label="Sequence type" help="The type of sequences to bring back. If 'None', no sequence is returned">
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8 <option value="protein" selected="true">Protein</option>
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9 <option value="cdna">cDNA</option>
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10 <option value="none">None</option>
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11 </param>
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12 <when value="protein">
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13 <param name="aligned" type="boolean" truevalue="1" falsevalue="0" label="Return the aligned sequences instead of the original ones" help="The original sequences contain no insertions" />
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14 <yield />
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15 </when>
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16 <when value="cdna">
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17 <param name="aligned" type="boolean" truevalue="1" falsevalue="0" label="Return the aligned sequences instead of the original ones" help="The original sequences contain no insertions" />
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18 <yield />
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19 </when>
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20 <when value="none" />
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21 </conditional>
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22 </xml>
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23 </macros>
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24 <requirements>
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25 <requirement type="package" version="3.13">python</requirement>
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26 <requirement type="package" version="2.32.3">requests</requirement>
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27 </requirements>
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28 <command detect_errors="exit_code">
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29 <![CDATA[
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30 python3 '$__tool_directory__/get_genetree.py'
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31 --id_type ${input_type_conditional.input_type}
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32 #if $input_type_conditional.input_type == "gene_id"
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33 --species ${input_type_conditional.species}
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34 #end if
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35 -i '$input'
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36 --format ${output_format.output_format_selector}
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37 #if $output_format.output_format_selector == 'json'
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38 -s ${output_format.sequence.sequence_selector}
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39 #if $output_format.sequence.sequence_selector != 'none'
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40 -a ${output_format.sequence.aligned}
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41 -c ${output_format.sequence.cigar}
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42 #end if
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43 #elif $output_format.output_format_selector == 'phyloxml'
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44 -s ${output_format.sequence.sequence_selector}
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45 #if $output_format.sequence.sequence_selector != 'none'
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46 -a ${output_format.sequence.aligned}
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47 #end if
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48 #else
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49 --nh_format $output_format.nh_format
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50 #end if
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51 > '$output'
1
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52 ]]>
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53 </command>
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54
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55 <inputs>
8
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56 <conditional name="input_type_conditional">
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57 <param name="input_type" type="select" label="Input type">
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58 <option value="gene_id" selected="true">Ensembl gene ID</option>
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59 <option value="gene_tree_id">Ensembl genetree ID</option>
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60 </param>
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61 <when value="gene_id">
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62 <param name="species" type="text" label="Species name/alias">
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63 <validator type="empty_field" />
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64 </param>
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65 </when>
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66 <when value="gene_tree_id" />
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67 </conditional>
1
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68 <param name="input" type="text" label="Ensembl ID">
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69 <validator type="empty_field" />
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70 </param>
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71 <conditional name="output_format">
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72 <param name="output_format_selector" type="select" label="Output format">
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73 <option value="json" selected="true">JSON</option>
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74 <!-- <option value="orthoxml">OrthoXML</option> -->
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75 <option value="phyloxml">phyloXML</option>
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76 <option value="nh">Newick</option>
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77 </param>
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78 <when value="json">
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79 <expand macro="sequence_conditional">
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80 <param name="cigar" type="boolean" truevalue="1" falsevalue="0" label="Output the sequences also in CIGAR format" />
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81 </expand>
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82 </when>
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earlhaminst
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83 <when value="phyloxml">
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earlhaminst
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84 <expand macro="sequence_conditional" />
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earlhaminst
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85 </when>
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earlhaminst
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86 <when value="nh">
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earlhaminst
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87 <param name="nh_format" type="select" label="NH format" help="The format of a NH (New Hampshire) request">
98aba0efe77a planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/Ensembl-REST commit aaf8d501c3a92ed415fdf9293a65468c72aae984-dirty
earlhaminst
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88 <option value="simple" selected="true">simple</option>
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earlhaminst
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89 <option value="full">full</option>
98aba0efe77a planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/Ensembl-REST commit aaf8d501c3a92ed415fdf9293a65468c72aae984-dirty
earlhaminst
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90 <option value="display_label_composite">display_label_composite</option>
98aba0efe77a planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/Ensembl-REST commit aaf8d501c3a92ed415fdf9293a65468c72aae984-dirty
earlhaminst
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91 <option value="species">species</option>
98aba0efe77a planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/Ensembl-REST commit aaf8d501c3a92ed415fdf9293a65468c72aae984-dirty
earlhaminst
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92 <option value="species_short_name">species_short_name</option>
98aba0efe77a planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/Ensembl-REST commit aaf8d501c3a92ed415fdf9293a65468c72aae984-dirty
earlhaminst
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93 <option value="ncbi_taxon">ncbi_taxon</option>
98aba0efe77a planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/Ensembl-REST commit aaf8d501c3a92ed415fdf9293a65468c72aae984-dirty
earlhaminst
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94 <option value="ncbi_name">ncbi_name</option>
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earlhaminst
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95 <option value="njtree">njtree</option>
98aba0efe77a planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/Ensembl-REST commit aaf8d501c3a92ed415fdf9293a65468c72aae984-dirty
earlhaminst
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96 <option value="phylip">phylip</option>
98aba0efe77a planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/Ensembl-REST commit aaf8d501c3a92ed415fdf9293a65468c72aae984-dirty
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97 </param>
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98 </when>
98aba0efe77a planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/Ensembl-REST commit aaf8d501c3a92ed415fdf9293a65468c72aae984-dirty
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99 </conditional>
98aba0efe77a planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/Ensembl-REST commit aaf8d501c3a92ed415fdf9293a65468c72aae984-dirty
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100 </inputs>
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101
98aba0efe77a planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/Ensembl-REST commit aaf8d501c3a92ed415fdf9293a65468c72aae984-dirty
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102 <outputs>
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103 <data name="output" format="json" label="$(tool.name) on ${input_type} ${input}">
98aba0efe77a planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/Ensembl-REST commit aaf8d501c3a92ed415fdf9293a65468c72aae984-dirty
earlhaminst
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104 <change_format>
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earlhaminst
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105 <when input="output_format.output_format_selector" value="phyloxml" format="phyloxml" />
98aba0efe77a planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/Ensembl-REST commit aaf8d501c3a92ed415fdf9293a65468c72aae984-dirty
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106 <when input="output_format.output_format_selector" value="nh" format="nhx" />
98aba0efe77a planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/Ensembl-REST commit aaf8d501c3a92ed415fdf9293a65468c72aae984-dirty
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107 </change_format>
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108 </data>
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109 </outputs>
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110
98aba0efe77a planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/Ensembl-REST commit aaf8d501c3a92ed415fdf9293a65468c72aae984-dirty
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111 <tests>
98aba0efe77a planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/Ensembl-REST commit aaf8d501c3a92ed415fdf9293a65468c72aae984-dirty
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112 <test>
8
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earlhaminst
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113 <conditional name="input_type_conditional">
935de83b470b planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/Ensembl-REST commit 8f8808de862973aedbf87abd4dfa9d2dc7219322
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114 <param name="input_type" value="gene_id" />
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115 <param name="species" value="Chicken" />
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116 </conditional>
7
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117 <param name="input" value="ENSGALP00010009242" />
1
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118 <param name="output_format_selector" value="json" />
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119 <param name="sequence_selector" value="protein" />
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120 <param name="aligned" value="0" />
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121 <param name="cigar" value="0" />
4
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earlhaminst
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122 <output name="output" ftype="json">
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123 <assert_contents>
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earlhaminst
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124 <has_text text="tree" />
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earlhaminst
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125 <has_text text="Euteleostomi" />
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earlhaminst
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126 <has_text text="ENSG00000139618" />
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earlhaminst
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127 <has_text text="ENSMUSG00000041147" />
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128 </assert_contents>
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129 </output>
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130 </test>
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131 <test>
8
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132 <conditional name="input_type_conditional">
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133 <param name="input_type" value="gene_id" />
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134 <param name="species" value="Chicken" />
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135 </conditional>
7
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earlhaminst
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136 <param name="input" value="ENSGALP00010009242" />
4
0602dcf02768 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/Ensembl-REST commit 95bab1105cf8a7b07c668f08f712399e8775a4ae
earlhaminst
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137 <param name="output_format_selector" value="nh" />
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earlhaminst
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138 <param name="nh_format" value="simple" />
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earlhaminst
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139 <output name="output" ftype="nhx">
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140 <assert_contents>
7
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141 <has_text text="ENSGALP00010009242" />
4
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earlhaminst
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142 <has_text text="ENSP00000369497" />
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143 </assert_contents>
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144 </output>
1
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145 </test>
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146 <test>
8
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147 <conditional name="input_type_conditional">
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148 <param name="input_type" value="gene_tree_id" />
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149 </conditional>
1
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150 <param name="input" value="ENSGT00390000003602" />
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151 <param name="output_format_selector" value="json" />
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152 <param name="sequence_selector" value="protein" />
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153 <param name="aligned" value="0" />
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154 <param name="cigar" value="0" />
4
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155 <output name="output" ftype="json">
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156 <assert_contents>
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earlhaminst
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157 <has_text text="tree" />
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158 <has_text text="Euteleostomi" />
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earlhaminst
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159 <has_text text="ENSG00000139618" />
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160 <has_text text="ENSMUSG00000041147" />
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161 </assert_contents>
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162 </output>
1
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163 </test>
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164 <test>
8
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165 <conditional name="input_type_conditional">
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166 <param name="input_type" value="gene_tree_id" />
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167 </conditional>
1
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168 <param name="input" value="ENSGT00390000003602" />
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169 <param name="output_format_selector" value="phyloxml" />
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170 <param name="sequence_selector" value="protein" />
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171 <param name="aligned" value="0" />
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172 <output name="output" ftype="phyloxml">
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173 <assert_contents>
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174 <has_text text="Euteleostomi" />
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175 <has_text text="ENSG00000139618" />
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176 <has_text text="ENSMUSG00000041147" />
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177 <has_text text="&lt;/phyloxml&gt;" />
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178 </assert_contents>
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179 </output>
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180 </test>
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181 </tests>
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182
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183 <help>
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184 <![CDATA[
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185 **What it does**
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186
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187 Retrieve a gene tree from Ensembl using its REST API.
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188
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189 Uses the `"GET genetree/id/:id"`_ and `"GET genetree/member/id/:species/:id"`_ API endpoints.
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190
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191 .. _"GET genetree/id/:id": https://rest.ensembl.org/documentation/info/genetree
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192 .. _"GET genetree/member/id/:species/:id": https://rest.ensembl.org/documentation/info/genetree_species_member_id
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193 ]]>
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194 </help>
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195 <expand macro="citations" />
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196 </tool>