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1 <tool id="vl_tools_query" name="VLT.query">
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2 <description>
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3 Provides a simplified environment to perform complex queries to
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4 BIOBANK.
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5 </description>
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6 <command interpreter="bash">
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7 launcher.sh
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8 --interpreter=python
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9 --runner=kb_query.py
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10 --host=$__user_omero_host__
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11 --user=$__user_omero_user__
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12 --passwd=$__user_omero_password__
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13 --operator=$__user_email__
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14 --ofile=${output1}
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15 --logfile=${logfile}
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16 query
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17 --group=$study
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18 --code-file=$code_file
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19 </command>
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20 <inputs>
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21 <param name="study" type="select" label="study label"
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22 help="Choose one of the available groups/studies.
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23 See below.">
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24 <options from_parameter="tool.app.known_studies"
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25 transform_lines="[ "%s%s%s:%s"
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26 % ( l[0], self.separator, l[0], l[1][:40] )
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27 for l in obj ]">
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28 <column name="value" index="0"/>
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29 <column name="name" index="1"/>
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30 <filter type="sort_by" column="0"/>
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31 </options>
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32 </param>
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33 <param name="query_code" type="text" area="True" size="10x60"
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34 optional="False"
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35 value=""
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36 />
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37 <!-- ************************************************** -->
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38
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39 </inputs>
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40
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41 <configfiles>
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42 <configfile name="code_file">${str($query_code).replace('__sq__', "'").replace('__cr____cn__', '\n')}</configfile>
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43 </configfiles>
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44
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45 <outputs>
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46 <data format="tabular" name="output1" label="${tool.name}.mapped"/>
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47 <data format="txt" name="logfile" label="${tool.name}.logfile"/>
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48 </outputs>
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49
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50 <help>
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51 The following is an example of a query that will dump family relations
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52 within the group::
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53
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54 writeheader('study', 'id', 'gender', 'father', 'mother')
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55 for i in Individuals(group):
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56 writerow(group.id, enum_label(i.gender),
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57 i.father.id if i.father else 'None',
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58 i.mother.id if i.mother else 'None')
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59
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60
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61 The next example will prepare a file that could be used to define a
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62 data collection and then as the input for a genotyping run::
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63
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64 writeheader('dc_id', 'gender', 'data_sample',
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65 'path', 'mimetype', 'size', 'sha1')
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66 for i in Individuals(group):
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67 for d in DataSamples(i, 'AffymetrixCel'):
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68 for o in DataObjects(d):
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69 writerow(group.id, enum_label(i.gender), d.id,
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70 o.path, o.mimetype, o.size, o.sha1)
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71
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72 In the examples above, '''group''' (actually a study) corresponds to
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73 the group whose label is assigned by the '''--group''' flag.
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74
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75 **Note** This is clearly an extremely dangerous tool.
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76
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77 </help>
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78
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79 </tool> |
