Mercurial > repos > tomnl > submit_to_mogi

annotate submit_to_mogi.xml @ 0:58ee3687f776 draft

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planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0c9e55ffdc126b76e52d083d24c8f18ac1a901de
author tomnl
date Tue, 05 Jun 2018 06:44:50 -0400
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58ee3687f776 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0c9e55ffdc126b76e52d083d24c8f18ac1a901de
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1 <tool id="submit_to_mogi" name="submit_to_mogi" version="0.0.1">
58ee3687f776 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0c9e55ffdc126b76e52d083d24c8f18ac1a901de
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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)
58ee3687f776 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0c9e55ffdc126b76e52d083d24c8f18ac1a901de
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21 #set $galaxy_history_id=$__app__.security.encode_id($mogi_data.creating_job.history.id)
58ee3687f776 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0c9e55ffdc126b76e52d083d24c8f18ac1a901de
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22 #set $galaxy_history_name=$mogi_data.creating_job.history.name
58ee3687f776 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0c9e55ffdc126b76e52d083d24c8f18ac1a901de
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23 curl -X POST --insecure $mogi_url/rest/incoming_galaxy_data/ -d galaxy_data_id=$galaxy_data_id
58ee3687f776 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0c9e55ffdc126b76e52d083d24c8f18ac1a901de
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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=$galaxy_name -d galaxy_url=$galaxy_url > curl_out.txt;
58ee3687f776 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0c9e55ffdc126b76e52d083d24c8f18ac1a901de
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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"
58ee3687f776 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0c9e55ffdc126b76e52d083d24c8f18ac1a901de
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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"
58ee3687f776 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0c9e55ffdc126b76e52d083d24c8f18ac1a901de
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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" />
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40 <param type="text" name="galaxy_url" label="Galaxy URL"
58ee3687f776 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0c9e55ffdc126b76e52d083d24c8f18ac1a901de
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41 help="URL of the Galaxy site (not required, but useful for a reference)" />
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45 </inputs>
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46 <outputs>
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47 <data name="curl_out" format="json" label="${tool.name} on ${on_string}: submit to MOGI (json if successful)"
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48 from_work_dir="curl_out.txt" />
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50 </outputs>
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51 <tests>
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52 <test>
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54 <param name="mogi_data" value="alldata.sqlite"/>
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55 <param name="mogi_url" value="https://www.djangoproject.com/"/>
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57 <output name="curl_out" >
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58 <assert_contents>
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59 <has_text_matching expression=".*django.*" />
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60 </assert_contents>
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61 </output>
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62 </test>
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63 </tests>
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65 <help><![CDATA[
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66 =============================================================
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67 Submit SQLite Database to MOGI
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68 =============================================================
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69
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71 -----------
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72 Output
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73 -----------
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74 * out.json: The JSON request sent to MOGI
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75
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76 ]]></help>
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77 <expand macro="citations" />
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78 </tool>