Mercurial > repos > tduigou > save_to_db

annotate save_to_db.xml @ 0:034686b5bc15 draft

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planemo upload for repository https://github.com/brsynth commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
author tduigou
date Thu, 24 Apr 2025 09:56:36 +0000
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034686b5bc15 planemo upload for repository https://github.com/brsynth commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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1 <tool id="save_to_db" name="Save Data To DB" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.09">
034686b5bc15 planemo upload for repository https://github.com/brsynth commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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2 <description>Save data to SQL DB</description>
034686b5bc15 planemo upload for repository https://github.com/brsynth commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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3 <macros>
034686b5bc15 planemo upload for repository https://github.com/brsynth commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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4 <token name="@VERSION_SUFFIX@">0</token>
034686b5bc15 planemo upload for repository https://github.com/brsynth commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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5 <token name="@TOOL_VERSION@">0.1.0</token>
034686b5bc15 planemo upload for repository https://github.com/brsynth commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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6 </macros>
034686b5bc15 planemo upload for repository https://github.com/brsynth commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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7 <requirements>
034686b5bc15 planemo upload for repository https://github.com/brsynth commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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8 <requirement type="package" version="2.2.3">pandas</requirement>
034686b5bc15 planemo upload for repository https://github.com/brsynth commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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9 <requirement type="package" version="2.0.40">sqlalchemy</requirement>
034686b5bc15 planemo upload for repository https://github.com/brsynth commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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10 <requirement type="package" version="2.9.9">psycopg2</requirement>
034686b5bc15 planemo upload for repository https://github.com/brsynth commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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11 </requirements>
034686b5bc15 planemo upload for repository https://github.com/brsynth commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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12 <command detect_errors="exit_code"><![CDATA[
034686b5bc15 planemo upload for repository https://github.com/brsynth commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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13 #set $file_name_mapping = ",".join(["%s:%s" % (file.file_name, file.name) for file in $genbank_files])
034686b5bc15 planemo upload for repository https://github.com/brsynth commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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14 python '$__tool_directory__/save_to_db.py'
034686b5bc15 planemo upload for repository https://github.com/brsynth commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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15 --input '$genbank_files'
034686b5bc15 planemo upload for repository https://github.com/brsynth commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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16 --sequence_column '$sequence_column'
034686b5bc15 planemo upload for repository https://github.com/brsynth commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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17 --annotation_column '$annotation_column'
034686b5bc15 planemo upload for repository https://github.com/brsynth commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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18 --db_uri '$db_uri'
034686b5bc15 planemo upload for repository https://github.com/brsynth commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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19 --table '$table'
034686b5bc15 planemo upload for repository https://github.com/brsynth commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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20 --fragment_column '$fragment_column'
034686b5bc15 planemo upload for repository https://github.com/brsynth commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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21 --output '$output'
034686b5bc15 planemo upload for repository https://github.com/brsynth commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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22 --file_name_mapping '$file_name_mapping'
034686b5bc15 planemo upload for repository https://github.com/brsynth commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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23 ]]></command>
034686b5bc15 planemo upload for repository https://github.com/brsynth commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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24 <inputs>
034686b5bc15 planemo upload for repository https://github.com/brsynth commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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25 <param name="genbank_files" type="data" format="genbank" multiple="true" label="GenBank File(s)"/>
034686b5bc15 planemo upload for repository https://github.com/brsynth commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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26 <param name="table" type="text" label="Database Table Name" optional="false" />
034686b5bc15 planemo upload for repository https://github.com/brsynth commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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27 <param name="sequence_column" type="text" label="DB column contains sequence for ganbank file" optional="false" />
034686b5bc15 planemo upload for repository https://github.com/brsynth commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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28 <param name="annotation_column" type="text" label="DB column contains annotation for ganbank file" optional="false" />
034686b5bc15 planemo upload for repository https://github.com/brsynth commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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29 <param name="fragment_column" type="text" label="Database Fragments Column Name" optional="false" />
034686b5bc15 planemo upload for repository https://github.com/brsynth commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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30 <param name="db_uri" type="text" label="Database Connection URI" help="postgresql+psycopg2://username:password@db_container_name:port/database" optional="false" />
034686b5bc15 planemo upload for repository https://github.com/brsynth commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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31 </inputs>
034686b5bc15 planemo upload for repository https://github.com/brsynth commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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32 <outputs>
034686b5bc15 planemo upload for repository https://github.com/brsynth commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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33 <data name="output" format="txt" label="text raport" />
034686b5bc15 planemo upload for repository https://github.com/brsynth commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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34 </outputs>
034686b5bc15 planemo upload for repository https://github.com/brsynth commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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35 <tests>
034686b5bc15 planemo upload for repository https://github.com/brsynth commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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36 <!--python save_to_db.py -input 'test-data/p7_L7Ae-Weiss.gb,test-data/p6_Nt-IgKLsequence.gb,test-data/p6_Kozak-ATG.gb,test-data/p4_Kt-L7Ae-Weiss.gb,test-data/HC_Amp_ccdB.gb' -sequence_column 'sequence' -annotation_column 'annotation' -db_uri 'postgresql://postgres:RK17@localhost:5432/test_fragments_db' -table 'sample' -fragment_column 'fragment' -output 'test-data/test_raport.txt'
034686b5bc15 planemo upload for repository https://github.com/brsynth commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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37 but it will not work as there is an extra param '-file_name_mapping' that are generated by galaxy and contain the dict for 'file.dat:fragment name' to stock the fragment name from file name thus use planemo with debug to test -->
034686b5bc15 planemo upload for repository https://github.com/brsynth commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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38 <test>
034686b5bc15 planemo upload for repository https://github.com/brsynth commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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39 <param name="genbank_files" value="p7_L7Ae-Weiss.gb,p6_Nt-IgKLsequence.gb,p6_Kozak-ATG.gb,p4_Kt-L7Ae-Weiss.gb,HC_Amp_ccdB.gb" />
034686b5bc15 planemo upload for repository https://github.com/brsynth commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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40 <param name="table" value="sample" />
034686b5bc15 planemo upload for repository https://github.com/brsynth commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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41 <param name="sequence_column" value="sequence" />
034686b5bc15 planemo upload for repository https://github.com/brsynth commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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42 <param name="annotation_column" value="annotation" />
034686b5bc15 planemo upload for repository https://github.com/brsynth commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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43 <param name="fragment_column" value="fragment" />
034686b5bc15 planemo upload for repository https://github.com/brsynth commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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44 <param name="db_uri" value="postgresql://postgres:RK17@localhost:5432/test_fragments_db" />
034686b5bc15 planemo upload for repository https://github.com/brsynth commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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45 <output name="output" file="test_raport.txt" ftype="txt" >
034686b5bc15 planemo upload for repository https://github.com/brsynth commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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46 <assert_contents>
034686b5bc15 planemo upload for repository https://github.com/brsynth commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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47 <has_n_lines n="5" />
034686b5bc15 planemo upload for repository https://github.com/brsynth commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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48 <has_line_matching expression="p7_L7Ae-Weiss" />
034686b5bc15 planemo upload for repository https://github.com/brsynth commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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49 <has_line_matching expression="p6_Nt-IgKLsequence" />
034686b5bc15 planemo upload for repository https://github.com/brsynth commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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50 <has_line_matching expression="p6_Kozak-ATG" />
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51 <has_line_matching expression="p4_Kt-L7Ae-Weiss" />
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52 <has_line_matching expression="HC_Amp_ccdB" />
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53 </assert_contents>
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54 </output>
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55 </test>
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56 </tests>
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57
034686b5bc15 planemo upload for repository https://github.com/brsynth commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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58 <help><![CDATA[
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59 Save Data To DB
034686b5bc15 planemo upload for repository https://github.com/brsynth commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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60 ===================
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61
034686b5bc15 planemo upload for repository https://github.com/brsynth commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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62 Save GanDank data in SQL DB.
034686b5bc15 planemo upload for repository https://github.com/brsynth commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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63 ]]></help>
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64 <citations>
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65 <citation type="bibtex">
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66 @unpublished{save_to_db
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67 author = {Ramiz Khaled},
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68 title = {{save_to_db}},
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69 url = {https://github.com/brsynth/},
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70 }
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71 </citation>
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72 </citations>
034686b5bc15 planemo upload for repository https://github.com/brsynth commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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73 </tool>