Mercurial > repos > gga > chado_feature_load_fasta

annotate feature_load_fasta.xml @ 13:313a27d7d64a draft

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planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit bc69ce09372c8c2701b726c326e671af279adb4d
author gga
date Thu, 11 Jul 2019 08:33:47 -0400
parents 5a1a37db2784
children 86589f36dfad
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1 <?xml version="1.0"?>
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2 <tool id="feature_load_fasta" name="Chado load fasta" version="@WRAPPER_VERSION@.1">
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3 <description></description>
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4 <macros>
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5 <import>macros.xml</import>
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6 </macros>
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7 <expand macro="requirements"/>
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8 <code file="chado.py"/>
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9 <command detect_errors="aggressive"><![CDATA[
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10 @START_PSQL@ &&
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12 chakin feature load_fasta
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13 '$fasta'
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14 '$organism'
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16 #if $sequence_type:
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17 --sequence_type '$sequence_type'
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18 #end if
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19 #if $analysis_id:
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20 --analysis_id '$analysis_id'
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21 #end if
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22 #if $re_name:
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23 --re_name '$re_name'
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24 #end if
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25 #if $re_uniquename:
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26 --re_uniquename '$re_uniquename'
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27 #end if
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29 $match_on_name
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31 $do_update
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33 #if $ext_db.db:
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34 --db '${ext_db.db}'
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35 #end if
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36 #if $ext_db.re_db_accession:
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37 --re_db_accession '${ext_db.re_db_accession}'
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38 #end if
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40 #if str($relationships.rel_type) != "none":
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41 --rel_type '${relationships.rel_type}'
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42 --re_parent '${relationships.rel_subject_re}'
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43 --parent_type '${relationships.rel_subject_type}'
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44 #end if
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45
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46 | jq -S . > '$results'
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47
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48 @ZIP_PSQL@
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49 ]]></command>
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50 <inputs>
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51 <expand macro="psql_target"/>
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52 <!-- arguments -->
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53 <param name="fasta" label="Fasta" argument="fasta" type="data" format="fasta" help="Path to the Fasta file to load" />
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54 <param argument="--organism" type="select" dynamic_options="list_organisms()" label="Organism" />
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55
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56 <!-- options -->
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57 <param argument="--analysis_id" type="select" dynamic_options="list_analyses()" label="Analysis" />
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58 <param name="sequence_type" label="Sequence Type" type="text" value="contig" help="this should be a Sequence Ontology term"/>
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59
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60 <param name="re_name" label="Name regular expression" argument="--re_name" type="text" help="Regular expression to extract the feature name from the fasta sequence id (first capturing group will be used)." optional="true">
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61 <expand macro="sanitized"/>
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62 </param>
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63 <param name="re_uniquename" label="Uniquename regular expression" argument="--re_uniquename" type="text" help="Regular expression to extract the feature name from the fasta sequence id (first capturing group will be used)." optional="true">
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64 <expand macro="sanitized"/>
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65 </param>
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66 <param name="match_on_name" label="Match on name" argument="--match_on_name" type="boolean" truevalue="--match_on_name" falsevalue="" help="Match existing features using their name instead of their uniquename" />
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67 <param name="do_update" label="Update" argument="--update" type="boolean" truevalue="--update" falsevalue="" help="Update existing feature with new sequence instead of throwing an error" />
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68 <conditional name="relationships">
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69 <param name="rel_type"
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70 argument="--rel_type"
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71 type="select"
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72 label="Relationship type"
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73 help="Use this when inserting features that should be associated to other already existing features">
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74 <option value="none" selected="true">No relationship</option>
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75 <option value="part_of">Part of (for CDS sequences)</option>
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76 <option value="derives_from">Derives from (for peptide sequences)</option>
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77 </param>
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78 <when value="none"/>
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79 <when value="part_of">
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80 <expand macro="feature_rel" />
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81 </when>
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82 <when value="derives_from">
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83 <expand macro="feature_rel" />
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84 </when>
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85 </conditional>
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86 <section name="ext_db" title="Cross references to external database">
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87 <param name="db" label="Db" argument="--db" type="integer" help="External database to cross reference to." optional="true" /><!-- FIXME get this from db -->
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88 <param name="re_db_accession" label="Regex external db accession" argument="--re_db_accession" type="text" help="Regular expression to extract an external database accession from the fasta sequence id (first capturing group will be used)." optional="true">
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89 <expand macro="sanitized"/>
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90 </param>
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91 </section>
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92 <expand macro="wait_for"/>
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93 </inputs>
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94 <outputs>
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95 <data format="json" name="results"/>
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96 <data format="postgresql" name="outfile" from_work_dir="postgresql_out.tar.bz2" label="${tool.name} on ${on_string}">
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97 <filter>psql_target['method'] == "pgtools"</filter>
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98 </data>
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99 </outputs>
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100 <help>
0
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101 Load features from a fasta file
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102
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103 @HELP@
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104 </help>
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105 </tool>