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1 <tool id="glytools_get_CFG_array" name="GAP Get CFG array" version="0.1.1">
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2
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3 <description> download glycan metadata (and xls) from CFG</description>
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4 <requirements>
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5 <requirement type="package" version="1.0">python_for_glycan_tools</requirement>
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6 </requirements>
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7 <stdio>
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8 <regex match="IOError"
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9 source="both"
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10 level="fatal"
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11 description="IOError" />
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12 <regex match="UserWarning: gzip transfer encoding is experimental"
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13 source="both"
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14 level="warning"
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15 description="Warning re use of gzip encoding" />
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16 <regex match="br.set_handle_gzip(True)"
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17 source="both"
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18 level="warning"
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19 description="Warning re use of gzip encoding" />
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20 <regex match="IOError"
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21 source="both"
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22 level="fatal"
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23 description="IOError" />
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24 </stdio>
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25
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26
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27 <command interpreter="python"><![CDATA[ cfg_get_glycan_array_data.py -s "$species" -g "$glycanarrayversion" -i -j "$json_file" -o "$html_file" -d --filepath "xls_output" ]]></command>
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28 <inputs>
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29 <param name="species" type="select" label="Species" >
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30 <option value="cTypeLectins" selected="true">cTypeLectins</option>
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31 <option value="iTypeLectins" selected="false">iTypeLectins</option>
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32 <option value="sTypeLectins" selected="false">sTypeLectins</option>
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33 <option value="otherAnimalLectins" selected="false">otherAnimalLectins</option>
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34 <option value="plantLectins" selected="false">plantLectins</option>
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35 <option value="antiBodies" selected="false">antiBodies</option>
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36 <option value="other" selected="false">other</option>
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37 <option value="cellsOrganisms" selected="false">cellsOrganisms</option>
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38 <option value="all" selected="false">all</option>
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39 </param>
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40 <param name="glycanarrayversion" type="select" label="Glycan Array Version">
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41 <option value="v1" selected="false">v1</option>
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42 <option value="v2" selected="false">v2</option>
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43 <option value="v3" selected="false">v3</option>
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44 <option value="pv1" selected="false">pv1</option>
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45 <option value="pv2" selected="false">pv2</option>
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46 <option value="pv21" selected="false">pv21</option>
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47 <option value="pv3" selected="false">pv3</option>
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48 <option value="pv31" selected="false">pv31</option>
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49 <option value="pv32" selected="false">pv32</option>
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50 <option value="pv4" selected="false">pv4</option>
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51 <option value="pv41" selected="false">pv41</option>
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52 <option value="pv42" selected="false">pv42</option>
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53 <option value="pv5" selected="false">pv5</option>
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54 <option value="pv51" selected="false">pv51</option>
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55 <option value="pv52" selected="false">pv52</option>
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56 <option value="bactv1" selected="false">bactv1</option>
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57 <option value="all" selected="true">all</option>
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58
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59 </param>
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60 </inputs>
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61 <outputs>
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62 <data format="html" name="html_file" label="Summary_${tool.name}.html"/>
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63 <data format="txt" name="json_file" label="Summary_${tool.name}.json"/>
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64 </outputs>
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65
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66 <help> <![CDATA[
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67 .. class:: infomark
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68
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69 **What this tool does**
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70
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71 This tool download the metadata from the glycan array data available at the CFG.
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72
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73 .. class:: infomark
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74
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75 **Input**
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76
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77 Your choice of Species and Glycan Array Type.
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78
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79 ----
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80
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81 .. class:: infomark
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82
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83 **Output**
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84
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85 HTML summary of retrieved information (Note links in html do not function within Galaxy).
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86
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87 JSON summary of glycan array metadata.
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88
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89 xls data (not yet available in Galaxy)
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90
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91
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92 ]]>
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93 </help>
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94
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95 </tool>
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