annotate expression_add_biomaterial.xml @ 8:8904dc99a492 draft

"planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit bfca9a8c38694bbf04d92a6668e4ea31cf658eb8"
author gga
date Thu, 14 Nov 2019 09:56:24 -0500
parents 04bdb1e66a27
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
676c49ac9cb5 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 3c4fb887c809face4fbe4602617d6dc094b15864
gga
parents:
diff changeset
1 <?xml version="1.0"?>
7
04bdb1e66a27 "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
gga
parents: 6
diff changeset
2 <tool id="expression_add_biomaterial" name="Chado biomaterial add" version="@WRAPPER_VERSION@">
2
ecf81582c5cc planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit f5c5d81fc9781371e12b91c0d609b9201587cda5
gga
parents: 0
diff changeset
3 <description></description>
0
676c49ac9cb5 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 3c4fb887c809face4fbe4602617d6dc094b15864
gga
parents:
diff changeset
4 <macros>
676c49ac9cb5 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 3c4fb887c809face4fbe4602617d6dc094b15864
gga
parents:
diff changeset
5 <import>macros.xml</import>
676c49ac9cb5 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 3c4fb887c809face4fbe4602617d6dc094b15864
gga
parents:
diff changeset
6 </macros>
676c49ac9cb5 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 3c4fb887c809face4fbe4602617d6dc094b15864
gga
parents:
diff changeset
7 <expand macro="requirements"/>
676c49ac9cb5 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 3c4fb887c809face4fbe4602617d6dc094b15864
gga
parents:
diff changeset
8 <code file="chado.py"/>
676c49ac9cb5 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 3c4fb887c809face4fbe4602617d6dc094b15864
gga
parents:
diff changeset
9 <command detect_errors="aggressive"><![CDATA[
5
9692e46b267a planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 0b135f1ea2623ea68e41ac88e13d99e6b4ad8bea
gga
parents: 4
diff changeset
10 @START_PSQL@ &&
0
676c49ac9cb5 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 3c4fb887c809face4fbe4602617d6dc094b15864
gga
parents:
diff changeset
11
676c49ac9cb5 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 3c4fb887c809face4fbe4602617d6dc094b15864
gga
parents:
diff changeset
12 chakin expression add_biomaterial
676c49ac9cb5 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 3c4fb887c809face4fbe4602617d6dc094b15864
gga
parents:
diff changeset
13
676c49ac9cb5 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 3c4fb887c809face4fbe4602617d6dc094b15864
gga
parents:
diff changeset
14 #if $description:
676c49ac9cb5 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 3c4fb887c809face4fbe4602617d6dc094b15864
gga
parents:
diff changeset
15 --description '$description'
676c49ac9cb5 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 3c4fb887c809face4fbe4602617d6dc094b15864
gga
parents:
diff changeset
16 #end if
676c49ac9cb5 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 3c4fb887c809face4fbe4602617d6dc094b15864
gga
parents:
diff changeset
17 #if $biomaterial_provider:
676c49ac9cb5 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 3c4fb887c809face4fbe4602617d6dc094b15864
gga
parents:
diff changeset
18 --biomaterial_provider '$biomaterial_provider'
676c49ac9cb5 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 3c4fb887c809face4fbe4602617d6dc094b15864
gga
parents:
diff changeset
19 #end if
676c49ac9cb5 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 3c4fb887c809face4fbe4602617d6dc094b15864
gga
parents:
diff changeset
20 #if $biosample_accession:
676c49ac9cb5 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 3c4fb887c809face4fbe4602617d6dc094b15864
gga
parents:
diff changeset
21 --biosample_accession '$biosample_accession'
676c49ac9cb5 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 3c4fb887c809face4fbe4602617d6dc094b15864
gga
parents:
diff changeset
22 #end if
676c49ac9cb5 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 3c4fb887c809face4fbe4602617d6dc094b15864
gga
parents:
diff changeset
23 #if $sra_accession:
676c49ac9cb5 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 3c4fb887c809face4fbe4602617d6dc094b15864
gga
parents:
diff changeset
24 --sra_accession '$sra_accession'
676c49ac9cb5 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 3c4fb887c809face4fbe4602617d6dc094b15864
gga
parents:
diff changeset
25 #end if
676c49ac9cb5 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 3c4fb887c809face4fbe4602617d6dc094b15864
gga
parents:
diff changeset
26 #if $bioproject_accession:
676c49ac9cb5 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 3c4fb887c809face4fbe4602617d6dc094b15864
gga
parents:
diff changeset
27 --bioproject_accession '$bioproject_accession'
676c49ac9cb5 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 3c4fb887c809face4fbe4602617d6dc094b15864
gga
parents:
diff changeset
28 #end if
676c49ac9cb5 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 3c4fb887c809face4fbe4602617d6dc094b15864
gga
parents:
diff changeset
29 #if $attributes:
676c49ac9cb5 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 3c4fb887c809face4fbe4602617d6dc094b15864
gga
parents:
diff changeset
30 --attributes '$attributes'
676c49ac9cb5 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 3c4fb887c809face4fbe4602617d6dc094b15864
gga
parents:
diff changeset
31 #end if
676c49ac9cb5 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 3c4fb887c809face4fbe4602617d6dc094b15864
gga
parents:
diff changeset
32
676c49ac9cb5 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 3c4fb887c809face4fbe4602617d6dc094b15864
gga
parents:
diff changeset
33 '$biomaterial_name'
676c49ac9cb5 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 3c4fb887c809face4fbe4602617d6dc094b15864
gga
parents:
diff changeset
34 '$organism_id'
676c49ac9cb5 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 3c4fb887c809face4fbe4602617d6dc094b15864
gga
parents:
diff changeset
35
4
b0684eb7d975 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 35c5eff77b573a66f3611b4906417df9a440c857
gga
parents: 2
diff changeset
36 | jq -S . > '$results'
5
9692e46b267a planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 0b135f1ea2623ea68e41ac88e13d99e6b4ad8bea
gga
parents: 4
diff changeset
37
6
8c7e2b5c228f planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit bc69ce09372c8c2701b726c326e671af279adb4d
gga
parents: 5
diff changeset
38 @ZIP_PSQL@
0
676c49ac9cb5 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 3c4fb887c809face4fbe4602617d6dc094b15864
gga
parents:
diff changeset
39 ]]></command>
676c49ac9cb5 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 3c4fb887c809face4fbe4602617d6dc094b15864
gga
parents:
diff changeset
40 <inputs>
5
9692e46b267a planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 0b135f1ea2623ea68e41ac88e13d99e6b4ad8bea
gga
parents: 4
diff changeset
41 <expand macro="psql_target"/>
0
676c49ac9cb5 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 3c4fb887c809face4fbe4602617d6dc094b15864
gga
parents:
diff changeset
42 <!-- arguments -->
676c49ac9cb5 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 3c4fb887c809face4fbe4602617d6dc094b15864
gga
parents:
diff changeset
43 <param name="biomaterial_name" label="Biomaterial Name" argument="biomaterial_name" type="text" help="Biomaterial name" />
676c49ac9cb5 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 3c4fb887c809face4fbe4602617d6dc094b15864
gga
parents:
diff changeset
44 <param argument="organism_id" type="select" dynamic_options="list_organisms()" label="Organism" />
676c49ac9cb5 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 3c4fb887c809face4fbe4602617d6dc094b15864
gga
parents:
diff changeset
45
676c49ac9cb5 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 3c4fb887c809face4fbe4602617d6dc094b15864
gga
parents:
diff changeset
46 <!-- options -->
2
ecf81582c5cc planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit f5c5d81fc9781371e12b91c0d609b9201587cda5
gga
parents: 0
diff changeset
47 <param name="description" label="Description" argument="--description" type="text" help="Description of the biomaterial" optional="true" />
ecf81582c5cc planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit f5c5d81fc9781371e12b91c0d609b9201587cda5
gga
parents: 0
diff changeset
48 <param name="biomaterial_provider" label="Biomaterial Provider" argument="--biomaterial_provider" type="text" help="Biomaterial provider name" optional="true" />
ecf81582c5cc planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit f5c5d81fc9781371e12b91c0d609b9201587cda5
gga
parents: 0
diff changeset
49 <param name="biosample_accession" label="Biosample Accession" argument="--biosample_accession" type="text" help="Biosample accession number" optional="true" />
ecf81582c5cc planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit f5c5d81fc9781371e12b91c0d609b9201587cda5
gga
parents: 0
diff changeset
50 <param name="sra_accession" label="Sra Accession" argument="--sra_accession" type="text" help="SRA accession number" optional="true" />
ecf81582c5cc planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit f5c5d81fc9781371e12b91c0d609b9201587cda5
gga
parents: 0
diff changeset
51 <param name="bioproject_accession" label="Bioproject Accession" argument="--bioproject_accession" type="text" help="Bioproject accession number" optional="true" />
ecf81582c5cc planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit f5c5d81fc9781371e12b91c0d609b9201587cda5
gga
parents: 0
diff changeset
52 <param name="attributes" label="Attributes" argument="--attributes" type="data" format="json" help="Custom attributes (In JSON dict form)" optional="true" />
0
676c49ac9cb5 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 3c4fb887c809face4fbe4602617d6dc094b15864
gga
parents:
diff changeset
53
676c49ac9cb5 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 3c4fb887c809face4fbe4602617d6dc094b15864
gga
parents:
diff changeset
54 <expand macro="wait_for"/>
676c49ac9cb5 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 3c4fb887c809face4fbe4602617d6dc094b15864
gga
parents:
diff changeset
55
676c49ac9cb5 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 3c4fb887c809face4fbe4602617d6dc094b15864
gga
parents:
diff changeset
56 </inputs>
676c49ac9cb5 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 3c4fb887c809face4fbe4602617d6dc094b15864
gga
parents:
diff changeset
57 <outputs>
676c49ac9cb5 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 3c4fb887c809face4fbe4602617d6dc094b15864
gga
parents:
diff changeset
58 <data format="json" name="results"/>
5
9692e46b267a planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 0b135f1ea2623ea68e41ac88e13d99e6b4ad8bea
gga
parents: 4
diff changeset
59 <data format="postgresql" name="outfile" from_work_dir="postgresql_out.tar.bz2" label="${tool.name} '${biomaterial_name}' on ${on_string}">
9692e46b267a planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 0b135f1ea2623ea68e41ac88e13d99e6b4ad8bea
gga
parents: 4
diff changeset
60 <filter>psql_target['method'] == "pgtools"</filter>
9692e46b267a planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 0b135f1ea2623ea68e41ac88e13d99e6b4ad8bea
gga
parents: 4
diff changeset
61 </data>
0
676c49ac9cb5 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 3c4fb887c809face4fbe4602617d6dc094b15864
gga
parents:
diff changeset
62 </outputs>
676c49ac9cb5 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 3c4fb887c809face4fbe4602617d6dc094b15864
gga
parents:
diff changeset
63 <help>
676c49ac9cb5 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 3c4fb887c809face4fbe4602617d6dc094b15864
gga
parents:
diff changeset
64 Add a new biomaterial to the database
676c49ac9cb5 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 3c4fb887c809face4fbe4602617d6dc094b15864
gga
parents:
diff changeset
65
676c49ac9cb5 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 3c4fb887c809face4fbe4602617d6dc094b15864
gga
parents:
diff changeset
66 @HELP@
676c49ac9cb5 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 3c4fb887c809face4fbe4602617d6dc094b15864
gga
parents:
diff changeset
67 </help>
676c49ac9cb5 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 3c4fb887c809face4fbe4602617d6dc094b15864
gga
parents:
diff changeset
68 </tool>