Mercurial > repos > gga > chado_feature_load_fasta

comparison feature_load_fasta.xml @ 9:11b65a23c85d draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit f5c5d81fc9781371e12b91c0d609b9201587cda5
author gga
date Fri, 23 Nov 2018 10:58:00 -0500
parents 0e2c2d7d080f
children 9e309f028169
comparison
equal deleted inserted replaced
8:e2076be814d9 9:11b65a23c85d
1 <?xml version="1.0"?> 1 <?xml version="1.0"?>
2 <tool id="feature_load_fasta" name="Chado load fasta" version="@WRAPPER_VERSION@.0"> 2 <tool id="feature_load_fasta" name="Chado load fasta" version="@WRAPPER_VERSION@.0">
3 <description></description> 3 <description></description>
4 <macros> 4 <macros>
5 <import>macros.xml</import> 5 <import>macros.xml</import>
6 </macros> 6 </macros>
7 <expand macro="requirements"/> 7 <expand macro="requirements"/>
8 <code file="chado.py"/> 8 <code file="chado.py"/>
9 <command detect_errors="aggressive"><![CDATA[ 9 <command detect_errors="aggressive"><![CDATA[
10 @AUTH@ 10 @AUTH@
11 11
12 chakin feature load_fasta 12 chakin feature load_fasta
13 '$fasta' 13 '$fasta'
14 '$organism' 14 '$organism'
43 --parent_type '${relationships.rel_subject_type}' 43 --parent_type '${relationships.rel_subject_type}'
44 #end if 44 #end if
45 45
46 | jq -S . > $results 46 | jq -S . > $results
47 ]]></command> 47 ]]></command>
48 <inputs> 48 <inputs>
49 <!-- arguments --> 49 <!-- arguments -->
50 <param name="fasta" label="Fasta" argument="fasta" type="data" format="fasta" help="Path to the Fasta file to load" /> 50 <param name="fasta" label="Fasta" argument="fasta" type="data" format="fasta" help="Path to the Fasta file to load" />
51 <param argument="--organism" 51 <param argument="--organism" type="select" dynamic_options="list_organisms()" label="Organism" />
52 type="select"
53 dynamic_options="list_organisms()"
54 label="Organism" />
55 52
56 <!-- options --> 53 <!-- options -->
57 <param argument="--analysis_id" 54 <param argument="--analysis_id" type="select" dynamic_options="list_analyses()" label="Analysis" />
58 type="select" 55 <param name="sequence_type" label="Sequence Type" type="text" value="contig" help="this should be a Sequence Ontology term"/>
59 dynamic_options="list_analyses()"
60 label="Analysis" />
61 <param name="sequence_type" label="Sequence Type" type="text" value="contig" help="this should be a Sequence Ontology term"/>
62 56
63 <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" /> 57 <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">
64 <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" /> 58 <expand macro="sanitized"/>
65 <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" /> 59 </param>
66 <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" /> 60 <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">
67 <conditional name="relationships"> 61 <expand macro="sanitized"/>
68 <param name="rel_type" 62 </param>
69 argument="--rel_type" 63 <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" />
70 type="select" 64 <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" />
71 label="Relationship type" 65 <conditional name="relationships">
72 help="Use this when inserting features that should be associated to other already existing features"> 66 <param name="rel_type"
73 <option value="none" selected="true">No relationship</option> 67 argument="--rel_type"
74 <option value="part_of">Part of (for CDS sequences)</option> 68 type="select"
75 <option value="derives_from">Derives from (for peptide sequences)</option> 69 label="Relationship type"
76 </param> 70 help="Use this when inserting features that should be associated to other already existing features">
77 <when value="none"/> 71 <option value="none" selected="true">No relationship</option>
78 <when value="part_of"> 72 <option value="part_of">Part of (for CDS sequences)</option>
79 <expand macro="feature_rel" /> 73 <option value="derives_from">Derives from (for peptide sequences)</option>
80 </when> 74 </param>
81 <when value="derives_from"> 75 <when value="none"/>
82 <expand macro="feature_rel" /> 76 <when value="part_of">
83 </when> 77 <expand macro="feature_rel" />
84 </conditional> 78 </when>
85 <section name="ext_db" title="Cross references to external database"> 79 <when value="derives_from">
86 <param name="db" label="Db" argument="db" type="integer" help="External database to cross reference to." optional="true" /><!-- FIXME get this from db --> 80 <expand macro="feature_rel" />
87 <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"> 81 </when>
82 </conditional>
83 <section name="ext_db" title="Cross references to external database">
84 <param name="db" label="Db" argument="--db" type="integer" help="External database to cross reference to." optional="true" /><!-- FIXME get this from db -->
85 <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">
88 <expand macro="sanitized"/> 86 <expand macro="sanitized"/>
89 </param> 87 </param>
90 </section> 88 </section>
91 <expand macro="wait_for"/> 89 <expand macro="wait_for"/>
92 </inputs> 90 </inputs>
93 <outputs> 91 <outputs>
94 <data format="json" name="results"/> 92 <data format="json" name="results"/>
95 </outputs> 93 </outputs>
96 <help> 94 <help>
97 Load features from a fasta file 95 Load features from a fasta file
98 96
99 @HELP@ 97 @HELP@
100 </help> 98 </help>
101 </tool> 99 </tool>