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comparison subset_data.xml @ 2:caba07f41453 draft default tip

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"planemo upload for repository https://github.com/secimTools/SECIMTools/tree/main/galaxy commit 498abad641099412df56f04ff6e144e4193bbc34-dirty"
author malex
date Thu, 10 Jun 2021 15:41:17 +0000
parents 2e7d47c0b027
children
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1:2e7d47c0b027 2:caba07f41453
1 <tool id="secimtools_subset_data" name="Subset Wide Data and Design File" version="@WRAPPER_VERSION@"> 1 <tool id="secimtools_subset_data" name="Subset Wide Data and Design File" version="@WRAPPER_VERSION@">
2 <description>- Based on groups.</description> 2 <description>- Based on groups.</description>
3 <requirements> 3 <macros>
4 <requirement type="python-module">os</requirement> 4 <import>macros.xml</import>
5 <requirement type="python-module">pandas</requirement> 5 </macros>
6 <requirement type="python-module">interface</requirement> 6 <expand macro="requirements" />
7 </requirements>
8 <command detect_errors="exit_code"><![CDATA[ 7 <command detect_errors="exit_code"><![CDATA[
9 subset_data.py 8 subset_data.py
10 --input $input 9 --input $input
11 --design $design 10 --design $design
12 --uniqID $uniqID 11 --uniqID $uniqID
13 #if $group 12 #if $group
14 --group $group 13 --group $group
15 #end if 14 #end if
16 --drops $toDrop 15 --drops $toDrop
17 --out $out 16 --out $out
18 ]]></command> 17 ]]></command>
19 <inputs> 18 <inputs>
20 <param name="input" type="data" format="tabular" label="Wide Dataset" help="Input your tab-separated wide format dataset. If not tab separated see TIP below."/> 19 <param name="input" type="data" format="tabular" label="Wide Dataset" help="Input your tab-separated wide format dataset. If not tab separated see TIP below."/>
21 <param name="design" type="data" format="tabular" label="Design File" help="Input your design file (tab-separated). Note you need a 'sampleID' column. If not tab separated see TIP below."/> 20 <param name="design" type="data" format="tabular" label="Design File" help="Input your design file (tab-separated). Note you need a 'sampleID' column. If not tab separated see TIP below."/>
22 <param name="uniqID" type="text" size="30" value="" label="Unique Feature ID" help="Name of the column in your wide dataset that has unique identifiers."/> 21 <param name="uniqID" type="text" size="30" value="" label="Unique Feature ID" help="Name of the column in your wide dataset that has unique identifiers."/>
24 <param name="toDrop" type="text" size="30" optional="false" label="Group(s)/Sample(s) to drop" help="Name of the Group(s)/Sample(s), comma separated, that will be removed from your wide datset."/> 23 <param name="toDrop" type="text" size="30" optional="false" label="Group(s)/Sample(s) to drop" help="Name of the Group(s)/Sample(s), comma separated, that will be removed from your wide datset."/>
25 </inputs> 24 </inputs>
26 <outputs> 25 <outputs>
27 <data format="tabular" name="out" label="${tool.name} on ${on_string}: Value"/> 26 <data format="tabular" name="out" label="${tool.name} on ${on_string}: Value"/>
28 </outputs> 27 </outputs>
29 <macros>
30 <import>macros.xml</import>
31 </macros>
32 <tests> 28 <tests>
33 <test> 29 <test>
34 <param name="input" value="ST000006_data.tsv"/> 30 <param name="input" value="ST000006_data.tsv"/>
35 <param name="design" value="ST000006_design_names_underscore.tsv"/> 31 <param name="design" value="ST000006_design_names_underscore.tsv"/>
36 <param name="uniqID" value="Retention_Index" /> 32 <param name="uniqID" value="Retention_Index" />
37 <param name="group" value="White_wine_type_and_source" /> 33 <param name="group" value="White_wine_type_and_source" />
38 <param name="drops" value="Chardonnay_ Napa_ CA 2003,Riesling_ CA 2004" /> 34 <param name="drops" value="Chardonnay_ Napa_ CA 2003,Riesling_ CA 2004" />
39 <output name="out" file="ST000006_subset_data_output.tsv" /> 35 <output name="out" file="ST000006_subset_data_output.tsv" />
40 </test> 36 </test>
41 </tests> 37 </tests>
42 <help> 38 <help><![CDATA[
43 39
44 @TIP_AND_WARNING@ 40 @TIP_AND_WARNING@
45 41
46 **Tool Description** 42 **Tool Description**
47 43