Mercurial > repos > tomnl > submit_to_mogi

annotate submit_to_mogi.xml @ 5:821627b6ad6f draft

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planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 1800a3818988f21ef129e500818c9a087fce5875-dirty
author tomnl
date Tue, 28 Aug 2018 07:13:51 -0400
parents 58ee3687f776
children 187641a876b9
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1 <tool id="submit_to_mogi" name="submit_to_mogi" version="0.0.2">
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2 <description>
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3 Submit Galaxy datasets to MOGI django database
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4 </description>
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7 <macros>
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8 <import>macros.xml</import>
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9 </macros>
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11 <expand macro="requirements">
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13 </expand>
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16 <stdio>
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17 <exit_code range="1:" />
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18 </stdio>
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19 <command>
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20 #set $galaxy_data_id=$__app__.security.encode_id($mogi_data.id)
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21 #set $galaxy_history_id=$__app__.security.encode_id($mogi_data.creating_job.history.id)
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22 #set $galaxy_history_name=$mogi_data.creating_job.history.name
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23 curl -X POST --insecure $mogi_url/mogi/rest/incoming_galaxy_data/ -d galaxy_data_id=$galaxy_data_id
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24 -d galaxy_history_id=$galaxy_history_id -d galaxy_history_name='$galaxy_history_name'
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25 -d galaxy_name=$galaxy_name -d investigation_name=$investigation_name -d galaxy_url=$galaxy_url > curl_out.txt;
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26 </command>
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27 <inputs>
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30 <param type="data" name="mogi_data" label="Data to submit to MOGI" format="sqlite"
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31 help="SQLite database to submit to MOGI" />
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34 <param type="text" name="mogi_url" label="MOGI URL"
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35 help="URL for MOGI" />
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37 <param type="text" name="galaxy_name" label="Name of Galaxy instance in MOGI"
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38 help="Should be lower cases with no white spaces or non alphnumeric characters except _ or -" />
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40 <param type="text" name="investigation_name" label="Name of the investigation in submit to in MOGI"
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41 help="Should be lower cases with no white spaces or non alphnumeric characters except _ or -" />
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43 <param type="text" name="galaxy_url" label="Galaxy URL"
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44 help="URL of the Galaxy site (not required, but useful for a reference)" />
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48 </inputs>
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49 <outputs>
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50 <data name="curl_out" format="json" label="${tool.name} on ${on_string}: submit to MOGI (json if successful)"
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51 from_work_dir="curl_out.txt" />
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53 </outputs>
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54 <tests>
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55 <test>
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57 <param name="mogi_data" value="alldata.sqlite"/>
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58 <param name="mogi_url" value="https://www.djangoproject.com/"/>
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60 <output name="curl_out" >
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61 <assert_contents>
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62 <has_text_matching expression=".*django.*" />
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63 </assert_contents>
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64 </output>
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65 </test>
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66 </tests>
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68 <help><![CDATA[
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69 =============================================================
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70 Submit SQLite Database to MOGI
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71 =============================================================
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74 -----------
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75 Output
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76 -----------
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77 * out.json: The JSON request sent to MOGI
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79 ]]></help>
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80 <expand macro="citations" />
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81 </tool>