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comparison geo_cov_template.xml @ 4:d53b708cb348 draft

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planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/EMLassemblyline commit 2d36dc964f548b5acbc43ffd78e51e6fc7dc80bb
author ecology
date Tue, 10 Sep 2024 12:51:06 +0000
parents 0fe3b8bd9d8b
children
comparison
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3:a5f887cfcf94 4:d53b708cb348
1 <tool id="geo_cov_template" name="Make geographic coverage template" version="0.1.0+galaxy0" profile="22.05"> 1 <tool id="geo_cov_template" name="Make geographic coverage template" version="0.1.0+galaxy0" profile="22.05">
2 <description>for EML metadata creation</description> 2 <description>for EML metadata creation</description>
3 <requirements> 3 <requirements>
4 <requirement type="package" version="4.3.1">r-base</requirement> 4 <requirement type="package" version="4.3.1">r-base</requirement>
5 <requirement type="package" version="3.5.5">r-emlassemblyline</requirement> 5 <container type="docker">outils-patrinat.mnhn.fr/metashark:latest</container>
6 </requirements> 6 </requirements>
7 <command detect_errors="exit_code"><![CDATA[ 7 <command detect_errors="exit_code"><![CDATA[
8 8
9 mkdir data_files && 9 mkdir data_files &&
10 ln -s '$inputdata' 'data_files/${inputdata.element_identifier}' && 10 ln -s '$inputdata' 'data_files/${inputdata.element_identifier}' &&
20 '$empty' 20 '$empty'
21 21
22 ]]></command> 22 ]]></command>
23 <inputs> 23 <inputs>
24 <param name="inputdata" type="data" format="tabular" label="Upload table containing geographic coordinates" /> 24 <param name="inputdata" type="data" format="tabular" label="Upload table containing geographic coordinates" />
25 <param name="lat_col" type="data_column" label="What column of your table contains latitude coordinates in decimal degrees?" data_ref="inputdata" /> 25 <param name="lat_col" type="data_column" label="What column of your table contains latitude coordinates in decimal degrees?" data_ref="inputdata" use_header_names="true"/>
26 <param name="long_col" type="data_column" label="What column of your table contains longitude coordinates in decimal degrees ?" data_ref="inputdata"/> 26 <param name="long_col" type="data_column" label="What column of your table contains longitude coordinates in decimal degrees ?" data_ref="inputdata" use_header_names="true"/>
27 <param name="site_col" type="data_column" label="What column of your table contains site names ?" data_ref="inputdata"/> 27 <param name="site_col" type="data_column" label="What column of your table contains site names ?" data_ref="inputdata" use_header_names="true"/>
28 <param name="empty" type="boolean" label="Write an empty template file ?" /> 28 <param name="empty" type="boolean" label="Write an empty template file ?" />
29 </inputs> 29 </inputs>
30 <outputs> 30 <outputs>
31 <data name="output" from_work_dir="geographic_coverage.txt" format="txt" label="geographic_coverage.txt"/> 31 <data name="output" from_work_dir="geographic_coverage.txt" format="txt" label="geographic_coverage.txt"/>
32 </outputs> 32 </outputs>
33 <tests> 33 <tests>
34 <test> 34 <test>
35 <param name="inputdata" value="test-geocov.tabular"/> 35 <param name="inputdata" value="test_geocov.tsv"/>
36 <param name="lat_col" value="2"/> 36 <param name="lat_col" value="2"/>
37 <param name="long_col" value="3"/> 37 <param name="long_col" value="3"/>
38 <param name="site_col" value="1"/> 38 <param name="site_col" value="1"/>
39 <param name="empty" value="false"/> 39 <param name="empty" value="false"/>
40 <output name="output" value="geographic_coverage.txt"/> 40 <output name="output" value="geographic_coverage.txt"/>
64 |139.22|-65.57| name of site 2 | 64 |139.22|-65.57| name of site 2 |
65 +------+------+----------------------+ 65 +------+------+----------------------+
66 | ... | ... | ... | 66 | ... | ... | ... |
67 +------+------+----------------------+ 67 +------+------+----------------------+
68 ]]></help> 68 ]]></help>
69 <citations>
70 <citation type="bibtex">@Manual{,
71 title = {EMLassemblyline: A tool kit for building EML metadata workflows},
72 author = {Colin Smith},
73 year = {2022},
74 note = {https://github.com/EDIorg/EMLassemblyline,
75 https://ediorg.github.io/EMLassemblyline/},
76 }</citation>
77 </citations>
69 </tool> 78 </tool>