Mercurial > repos > ecology > table_template

comparison table_template.xml @ 0:6b4808a4c75e draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/EMLassemblyline commit ea09df299078ff13beda210b36b7edaa6a79c099
author ecology
date Sat, 02 Dec 2023 01:50:44 +0000
parents
children
comparison
equal deleted inserted replaced
-1:000000000000 0:6b4808a4c75e
1 <tool id="table_template" name="Make templates for data tables" version="0.1.0+galaxy0" profile="22.05">
2 <description>attributes and categorical variables for EML metadata creation</description>
3 <requirements>
4 <requirement type="package" version="4.3.1">r-base</requirement>
5 <requirement type="package" version="3.5.5">r-emlassemblyline</requirement>
6 </requirements>
7 <command detect_errors="exit_code"><![CDATA[
8
9 #set $table = ""
10 mkdir data_files &&
11 #for $indata in $inputdata
12 ln -s '$indata' 'data_files/${indata.element_identifier}' &&
13 #set $table += $indata.element_identifier + " "
14 #end for
15
16 Rscript
17 '$__tool_directory__/table_templates.R'
18 '$table'
19
20 ]]></command>
21 <inputs>
22 <param name="inputdata" type="data_collection" collection_type="list" label="Upload all data files wich are data table" help= "Input a data collection."/>
23 </inputs>
24 <outputs>
25 <collection name="templates" type="list" label="Templates for data table">
26 <discover_datasets pattern="__designation_and_ext__"/>
27 </collection>
28 </outputs>
29 <tests>
30 <test>
31 <param name="inputdata">
32 <collection type="list">
33 <element name="datafile_1.tsv" value="datafile_1.tsv" />
34 </collection>
35 </param>
36 <output_collection name='templates' type = "list" count="2"/>
37 </test>
38 </tests>
39 <help><![CDATA[
40
41 To use this tool, you need to select, in your history a data collection with your data table (one or more).To do so, you can select the **Upload file** tool, select the *Collection* tab, upload all your templates, click on the *Start* button to integrate the files to Galaxy and then click on *Build*. You will need to choose a name and select *Create collection* to build a collection with your templates.
42 You also can upload your files to Galaxy, select them in the history by clicking the *Select items* button, click on the newly appeared box on the right and select *Build dataset list*.
43
44 ]]></help>
45 </tool>