Mercurial > repos > gga > chado_feature_load_fasta

annotate macros.xml @ 8:e2076be814d9 draft

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planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit c5b949de324bf86c88c680767e56ac77685cd14c
author gga
date Mon, 05 Nov 2018 12:09:29 -0500
parents c768f590d1d8
children 11b65a23c85d
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1 <?xml version="1.0"?>
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2 <macros>
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3 <xml name="requirements">
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4 <requirements>
7
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5 <requirement type="package" version="2.2.2">python-chado</requirement>
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6 <requirement type="package" version="1.5">jq</requirement>
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7 <yield/>
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8 </requirements>
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9 </xml>
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11 <xml name="stdio">
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12 <stdio>
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13 <regex level="fatal" match="Exception:" source="stderr" />
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14 <regex level="fatal" match="error" source="stderr" />
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15 <exit_code range="1:" />
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16 </stdio>
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17 </xml>
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18
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19 <token name="@WRAPPER_VERSION@">2.2.2</token>
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21 <xml name="citation">
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22 <citations>
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23 </citations>
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24 </xml>
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26 <token name="@HELP_OVERVIEW@"><![CDATA[
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27 **Python-chado Overview**
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29 Python-cado provides several tools allowing to load data into a remote Chado database.
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30 ]]></token>
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32 <token name="@HELP@"><![CDATA[
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33 ]]></token>
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35 <token name="@AUTH@"><![CDATA[
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36 echo "__default: local" > '.auth.yml' &&
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37 echo "local:" >> '.auth.yml' &&
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38 echo " dbhost: \"\$GALAXY_CHADO_DBHOST\"" >> '.auth.yml' &&
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39 echo " dbname: \"\$GALAXY_CHADO_DBNAME\"" >> '.auth.yml' &&
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40 echo " dbpass: \"\$GALAXY_CHADO_DBPASS\"" >> '.auth.yml' &&
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41 echo " dbuser: \"\$GALAXY_CHADO_DBUSER\"" >> '.auth.yml' &&
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42 echo " dbschema: \"\$GALAXY_CHADO_DBSCHEMA\"" >> '.auth.yml' &&
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43 echo " dbport: \"\$GALAXY_CHADO_DBPORT\"" >> '.auth.yml' &&
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44
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45 CHAKIN_GLOBAL_CONFIG_PATH='.auth.yml'
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46 ]]></token>
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47
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48 <xml name="sanitized">
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49 <sanitizer>
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50 <valid initial="string.printable">
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51 <remove value="&apos;"/>
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52 </valid>
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53 <mapping initial="none">
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54 <add source="&apos;" target="&apos;&quot;&apos;&quot;&apos;"/>
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55 <add source="(" target="\("/>
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56 <add source=")" target="\)"/>
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57 </mapping>
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58 </sanitizer>
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59 </xml>
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60
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61 <!-- I'm not proud of it, but it is needed for workflows -->
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62 <xml name="wait_for">
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63 <param name="wait_for"
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64 type="data"
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65 format="data"
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66 optional="true"
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67 label="Run this only after the following dataset is ready"
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68 help="Use this if you want to delay the job execution until some data is already loaded. The selected dataset will not be used for anything else."/>
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69 </xml>
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70
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71 <xml name="feature_rel">
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72 <param name="rel_subject_re"
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73 argument="--rel-subject-re"
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74 type="text"
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75 label="Regular expression to extract the unique name of the parent feature"
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76 help="this regex will be applied on the fasta definition line to generate the unique name of the parent feature">
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77 <expand macro="sanitized"/>
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78 </param>
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79
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80 <param name="rel_subject_type"
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81 argument="--rel-subject-type"
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82 type="text"
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83 label="Sequence type of the parent"
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84 help="this should be a Sequence Ontology term" />
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85 </xml>
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86 </macros>