Mercurial > repos > gga > chado_feature_load_fasta

comparison feature_load_fasta.xml @ 12:5a1a37db2784 draft

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planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 0b135f1ea2623ea68e41ac88e13d99e6b4ad8bea
author gga
date Mon, 08 Jul 2019 05:30:24 -0400
parents 9e309f028169
children 313a27d7d64a
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11:9e309f028169 12:5a1a37db2784
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 @START_PSQL@ &&
11 11
12 chakin feature load_fasta 12 chakin feature load_fasta
13 '$fasta' 13 '$fasta'
14 '$organism' 14 '$organism'
15 15
42 --re_parent '${relationships.rel_subject_re}' 42 --re_parent '${relationships.rel_subject_re}'
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
48 && @ZIP_PSQL@
47 ]]></command> 49 ]]></command>
48 <inputs> 50 <inputs>
51 <expand macro="psql_target"/>
49 <!-- arguments --> 52 <!-- arguments -->
50 <param name="fasta" label="Fasta" argument="fasta" type="data" format="fasta" help="Path to the Fasta file to load" /> 53 <param name="fasta" label="Fasta" argument="fasta" type="data" format="fasta" help="Path to the Fasta file to load" />
51 <param argument="--organism" type="select" dynamic_options="list_organisms()" label="Organism" /> 54 <param argument="--organism" type="select" dynamic_options="list_organisms()" label="Organism" />
52 55
53 <!-- options --> 56 <!-- options -->
88 </section> 91 </section>
89 <expand macro="wait_for"/> 92 <expand macro="wait_for"/>
90 </inputs> 93 </inputs>
91 <outputs> 94 <outputs>
92 <data format="json" name="results"/> 95 <data format="json" name="results"/>
96 <data format="postgresql" name="outfile" from_work_dir="postgresql_out.tar.bz2" label="${tool.name} on ${on_string}">
97 <filter>psql_target['method'] == "pgtools"</filter>
98 </data>
93 </outputs> 99 </outputs>
94 <help> 100 <help>
95 Load features from a fasta file 101 Load features from a fasta file
96 102
97 @HELP@ 103 @HELP@