Mercurial > repos > earlhaminst > ensembl_get_genetree

annotate get_genetree.xml @ 6:0618e3bd5138 draft

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"planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/Ensembl-REST commit 17c65045b726d0695814bfe761e534f6521786f1"
author earlhaminst
date Tue, 20 Oct 2020 15:06:37 +0000
parents 675fd774314e
children 515e7181d5e9
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1 <tool id="get_genetree" name="Get gene tree by Ensembl ID" version="0.1.2">
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2 <description>using REST API</description>
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3 <macros>
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4 <xml name="sequence_conditional">
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5 <conditional name="sequence">
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6 <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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7 <option value="protein" selected="true">Protein</option>
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8 <option value="cdna">cDNA</option>
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9 <option value="none">None</option>
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10 </param>
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11 <when value="protein">
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12 <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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13 <yield />
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14 </when>
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15 <when value="cdna">
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16 <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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17 <yield />
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18 </when>
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19 <when value="none" />
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20 </conditional>
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21 </xml>
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22 </macros>
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23 <requirements>
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24 <requirement type="package" version="2.12.4">requests</requirement>
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25 <requirement type="package" version="1.10.0">six</requirement>
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26 </requirements>
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27 <command detect_errors="exit_code">
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28 <![CDATA[
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29 python '$__tool_directory__/get_genetree.py'
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30 --id_type $input_type
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31 -i '$input'
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32 --format ${output_format.output_format_selector}
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33 #if $output_format.output_format_selector == 'json'
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34 -s ${output_format.sequence.sequence_selector}
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35 #if $output_format.sequence.sequence_selector != 'none'
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36 -a ${output_format.sequence.aligned}
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37 -c ${output_format.sequence.cigar}
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38 #end if
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39 #elif $output_format.output_format_selector == 'phyloxml'
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40 -s ${output_format.sequence.sequence_selector}
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41 #if $output_format.sequence.sequence_selector != 'none'
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42 -a ${output_format.sequence.aligned}
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43 #end if
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44 #else
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45 --nh_format $output_format.nh_format
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46 #end if
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47 > '$output'
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48 ]]>
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49 </command>
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50
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51 <inputs>
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52 <param name="input_type" type="select" label="Input type">
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53 <option value="gene_id" selected="true">Ensembl gene ID</option>
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54 <option value="gene_tree_id">Ensembl genetree ID</option>
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55 </param>
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56 <param name="input" type="text" label="Ensembl ID">
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57 <validator type="empty_field" />
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58 </param>
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59 <conditional name="output_format">
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60 <param name="output_format_selector" type="select" label="Output format">
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61 <option value="json" selected="true">JSON</option>
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62 <!-- <option value="orthoxml">OrthoXML</option> -->
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63 <option value="phyloxml">phyloXML</option>
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64 <option value="nh">Newick</option>
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65 </param>
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66 <when value="json">
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67 <expand macro="sequence_conditional">
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68 <param name="cigar" type="boolean" truevalue="1" falsevalue="0" label="Output the sequences also in CIGAR format" />
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69 </expand>
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70 </when>
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71 <when value="phyloxml">
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72 <expand macro="sequence_conditional" />
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73 </when>
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74 <when value="nh">
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75 <param name="nh_format" type="select" label="NH format" help="The format of a NH (New Hampshire) request">
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76 <option value="simple" selected="true">simple</option>
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77 <option value="full">full</option>
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78 <option value="display_label_composite">display_label_composite</option>
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79 <option value="species">species</option>
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80 <option value="species_short_name">species_short_name</option>
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81 <option value="ncbi_taxon">ncbi_taxon</option>
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82 <option value="ncbi_name">ncbi_name</option>
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83 <option value="njtree">njtree</option>
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84 <option value="phylip">phylip</option>
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85 </param>
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86 </when>
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87 </conditional>
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88 </inputs>
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89
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90 <outputs>
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91 <data name="output" format="json" label="$(tool.name) on ${input_type} ${input}">
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92 <change_format>
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93 <when input="output_format.output_format_selector" value="phyloxml" format="phyloxml" />
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94 <when input="output_format.output_format_selector" value="nh" format="nhx" />
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95 </change_format>
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96 </data>
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97 </outputs>
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98
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99 <tests>
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100 <test>
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101 <param name="input_type" value="gene_id" />
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102 <param name="input" value="ENSGALP00000027524" />
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103 <param name="output_format_selector" value="json" />
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104 <param name="sequence_selector" value="protein" />
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105 <param name="aligned" value="0" />
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106 <param name="cigar" value="0" />
4
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107 <output name="output" ftype="json">
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108 <assert_contents>
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109 <has_text text="tree" />
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110 <has_text text="Euteleostomi" />
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111 <has_text text="ENSG00000139618" />
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112 <has_text text="ENSMUSG00000041147" />
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113 </assert_contents>
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114 </output>
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115 </test>
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116 <test>
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117 <param name="input_type" value="gene_id" />
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118 <param name="input" value="ENSGALP00000027524" />
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119 <param name="output_format_selector" value="nh" />
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120 <param name="nh_format" value="simple" />
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121 <output name="output" ftype="nhx">
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122 <assert_contents>
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123 <has_text text="ENSGALP00000027524" />
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124 <has_text text="ENSP00000369497" />
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125 </assert_contents>
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126 </output>
1
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127 </test>
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128 <test>
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129 <param name="input_type" value="gene_tree_id" />
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130 <param name="input" value="ENSGT00390000003602" />
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131 <param name="output_format_selector" value="json" />
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132 <param name="sequence_selector" value="protein" />
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133 <param name="aligned" value="0" />
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134 <param name="cigar" value="0" />
4
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135 <output name="output" ftype="json">
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136 <assert_contents>
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137 <has_text text="tree" />
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138 <has_text text="Euteleostomi" />
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139 <has_text text="ENSG00000139618" />
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140 <has_text text="ENSMUSG00000041147" />
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141 </assert_contents>
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142 </output>
1
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143 </test>
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144 <test>
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145 <param name="input_type" value="gene_tree_id" />
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146 <param name="input" value="ENSGT00390000003602" />
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147 <param name="output_format_selector" value="phyloxml" />
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148 <param name="sequence_selector" value="protein" />
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149 <param name="aligned" value="0" />
4
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150 <output name="output" ftype="phyloxml">
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151 <assert_contents>
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152 <has_text text="Euteleostomi" />
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153 <has_text text="ENSG00000139618" />
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154 <has_text text="ENSMUSG00000041147" />
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155 <has_text text="&lt;/phyloxml&gt;" />
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156 </assert_contents>
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157 </output>
1
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158 </test>
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159 </tests>
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160
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161 <help>
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162 <![CDATA[
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163 **What it does**
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164
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165 Retrieve a gene tree from Ensembl using its REST API.
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166
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167 Uses the `"GET genetree/id"`_ and `"GET genetree/member/id"`_ API endpoint.
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168
6
0618e3bd5138 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/Ensembl-REST commit 17c65045b726d0695814bfe761e534f6521786f1"
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169 .. _"GET genetree/id": https://rest.ensembl.org/documentation/info/genetree
0618e3bd5138 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/Ensembl-REST commit 17c65045b726d0695814bfe761e534f6521786f1"
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170 .. _"GET genetree/member/id": https://rest.ensembl.org/documentation/info/genetree_member_id
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98aba0efe77a planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/Ensembl-REST commit aaf8d501c3a92ed415fdf9293a65468c72aae984-dirty
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171 ]]>
98aba0efe77a planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/Ensembl-REST commit aaf8d501c3a92ed415fdf9293a65468c72aae984-dirty
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172 </help>
98aba0efe77a planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/Ensembl-REST commit aaf8d501c3a92ed415fdf9293a65468c72aae984-dirty
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173 <citations>
98aba0efe77a planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/Ensembl-REST commit aaf8d501c3a92ed415fdf9293a65468c72aae984-dirty
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174 </citations>
98aba0efe77a planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/Ensembl-REST commit aaf8d501c3a92ed415fdf9293a65468c72aae984-dirty
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175 </tool>