Mercurial > repos > dchristiany > data_manager_proteore

annotate data_manager/resource_building.xml @ 2:1f1fb404255a draft

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author dchristiany
date Fri, 19 Oct 2018 03:50:20 -0400
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1 <tool id="data_manager_proteore" name="Get source files for proteore tools" version="0.1" tool_type="manage_data">
0
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2 <description>
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3 to create or update reference files for proteore tools
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4 </description>
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5 <requirements>
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6 </requirements>
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7 <stdio>
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8 <exit_code range="1:" />
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9 </stdio>
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10 <command><![CDATA[
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11
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12 python $__tool_directory__/resource_building.py
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13 #if $database.database == "human_protein_atlas"
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14 --hpa "$database.tissues"
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15 #else if $database.database == "peptide_atlas"
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16 --peptideatlas "$database.tissues"
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17 #else if $database.database == "id_mapping"
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18 --id_mapping="$database.species"
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19 #end if
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20 --output "$output"
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21
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22 ]]></command>
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23
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24 <inputs>
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25 <conditional name="database">
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26 <param name="database" type="select">
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27 <option value="human_protein_atlas">Human Protein Atlas</option>
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28 <option value="peptide_atlas">Peptide Atlas</option>
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29 <option value="id_mapping">ID mapping</option>
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30 </param>
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31 <when value="human_protein_atlas">
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32 <param name="tissues" type="select" multiple="false" label="Please select tissue">
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33 <option value="HPA_normal_tissue">Normal tissue</option>
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34 <option value="HPA_pathology">Pathology</option>
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35 <option value="HPA_full_atlas">Full Atlas</option>
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36 </param>
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37 </when>
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38 <when value="peptide_atlas">
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39 <param name="tissues" type="select" multiple="false" label="Please select the tissue">
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40 <option value="1-Human_Liver">Human liver</option>
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41 <option value="2-Human_Brain">Human brain</option>
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42 <option value="4-Human_Heart">Human heart</option>
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43 <option value="5-Human_Kidney">Human kidney</option>
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44 <option value="10-Human_Plasma">Human blood plasma</option>
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45 <option value="13-Human_Urine">Human urine</option>
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46 <option value="24-Human_CSF">Human cerebrospinal fluid</option>
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47 </param>
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48 </when>
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49 <when value="id_mapping">
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50 <param name="species" type="select" multiple="false" label="Please select the species">
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51 <option value="human">Homo sapiens</option>
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52 <option value="mouse">Mus musculus</option>
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53 <option value="rat">Rattus norvegicus</option>
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54 </param>
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55 </when>
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56 </conditional>
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57 </inputs>
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58
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59 <outputs>
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60 <!--data format="tabular" name="output">
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61 <discover_datasets pattern="(?P&lt;designation&gt;.+).tsv" ext="tabular" visible="true" assign_primary_output="true" />
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62 </data-->
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63 <data name="output" format="data_manager_json"/>
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64 </outputs>
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65
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66 <tests>
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67 </tests>
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68
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69 <help><![CDATA[
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70
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71 TODO
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72
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73 -----
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74
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75 .. class:: infomark
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76
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77 **Authors**
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78
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79 Lisa Peru, T.P. Lien Nguyen, Florence Combes, Yves Vandenbrouck CEA, INSERM, CNRS, Grenoble-Alpes University, BIG Institute, FR
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80
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81 Sandra Dérozier, Olivier Rué, Christophe Caron, Valentin Loux INRA, Paris-Saclay University, MAIAGE Unit, Migale Bioinformatics platform
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82
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83 This work has been partially funded through the French National Agency for Research (ANR) IFB project.
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84
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85 Contact support@proteore.org for any questions or concerns about the Galaxy implementation of this tool.
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86
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87 ]]></help>
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88 <citations>
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89 </citations>
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90
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91 </tool>