Mercurial > repos > tduigou > parameters_maystro

annotate json_db_config_generating_boolean.xml @ 0:1a766d8d3883 draft

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author tduigou
date Fri, 11 Jul 2025 10:10:16 +0000
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1 <tool id="parameters_maystro" name="Parameters Maystro" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.09">
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2 <description>Store parameters of tools in a workflow to be used again</description>
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3 <macros>
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4 <token name="@VERSION_SUFFIX@">1</token>
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5 <token name="@TOOL_VERSION@">0.1.0</token>
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6 </macros>
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7 <command detect_errors="exit_code"><![CDATA[
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8 #set $json_files = ' '.join(['"%s"' % file for file in $json_from_workflow])
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9 #set $json_name_mapping = ",".join(["%s:%s" % (file.file_name, file.name) for file in $json_from_workflow])
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10 python '$__tool_directory__/maystro.py'
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11 --distribute_json '$distribute_json'
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12 --json_from_workflow $json_files
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13 --json_from_user '$json_from_user'
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14 --json_name_mapping $json_name_mapping
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15 --output_workflow '$output_workflow'
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16 --output_user '$output_user' && echo 'DEBUB' && cat '$output_user'
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17 ]]></command>
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18 <inputs>
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19 <param name="distribute_json" type="boolean" label="Input Your Parameters As JSON" checked ='false' help="If True user should set workflow parameters as json file" />
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20 <param name="json_from_workflow" type="data" format="json" multiple="true" optional="true" help='Only if Input Your Parameters As JSON is FALSE' />
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21 <param name="json_from_user" type="data" format="json" optional="true" help='Only if Input Your Parameters As JSON is TRUE' />
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22 </inputs>
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23 <outputs>
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24 <data name="output_workflow" format="json" label="workflow param"/>
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25 <data name="output_user" format="json" label="user_workflow param"/>
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26 </outputs>
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27 <tests>
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28 <!--distribute_json is false-->
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29 <test>
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30 <param name="distribute_json" value='false'/>
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31 <param name="json_from_workflow" value="seq_from_db_param.json,seq_to_db_param.json"/>
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32 <output name="output_user">
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33 <assert_contents>
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34 <has_n_lines n="17" />
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35 </assert_contents>
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36 </output>
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37 <output name="output_workflow">
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38 <assert_contents>
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39 <has_n_lines n="0" />
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40 </assert_contents>
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41 </output>
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42 </test>
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43 <!--distribute_json is true -->
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44 <test>
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45 <param name="distribute_json" value='true'/>
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46 <param name="json_from_workflow" value="seq_from_db_param.json,seq_to_db_param.json"/>
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47 <param name="json_from_user" value='merged_test.json'/>
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48 <output name="output_workflow">
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49 <assert_contents>
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50 <has_n_lines n="17" />
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51 </assert_contents>
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52 </output>
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53 <output name="output_user">
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54 <assert_contents>
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55 <has_n_lines n="0" />
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56 </assert_contents>
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57 </output>
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58 </test>
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59 </tests>
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60 <help><![CDATA[
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61 Parameters Maystro
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62 ===================
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63
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64 Store and Generate a JSON file to be used as a workflow configuration. This JSON file can later be used to pass workflow parameters
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65 This tool is recieve parameters from tools in workflow and return them as a JSON file that can be used later to pass thos parameters again.
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66 ]]></help>
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67 <citations>
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68 <citation type="bibtex">
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69 @unpublished{json_db_config_generating
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70 author = {Ramiz Khaled},
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71 title = {{json_db_config_generating}},
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72 url = {https://github.com/brsynth/},
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73 }
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74 </citation>
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75 </citations>
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76 </tool>