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comparison modify_design_file.xml @ 1:2e7d47c0b027 draft

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"planemo upload for repository https://malex@toolshed.g2.bx.psu.edu/repos/malex/secimtools"
author malex
date Mon, 08 Mar 2021 22:04:06 +0000
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0:b54326490b4d 1:2e7d47c0b027
1 <tool id="secimtools_modify_design_file" name="Modify design file" version="@WRAPPER_VERSION@">
2 <description>to remove specified group types or sampleIDs</description>
3 <macros>
4 <import>macros.xml</import>
5 </macros>
6 <expand macro="requirements" />
7 <command><![CDATA[
8 modify_design_file.py
9 --input $input
10 --design $design
11 --uniqID $uniqID
12 #if $group
13 --group $group
14 #end if
15 --drops $toDrop
16 --out $out
17 ]]></command>
18 <inputs>
19 <param name="input" type="data" format="tabular" label="Wide Dataset" help="Input your tab-separated wide format dataset. If not tab separated see TIP below."/>
20 <param name="design" type="data" format="tabular" label="Design File" help="Input your design file (tab-separated). Note you need a 'sampleID' column. If not tab separated see TIP below."/>
21 <param name="uniqID" type="text" size="30" value="" label="Unique Feature ID" help="Name of the column in your wide dataset that has unique identifiers.."/>
22 <param name="group" type="text" size="30" value="" optional="false" label="Group/Treatment [Optional]" help="Name of the column in your design file that contains group classifications. If not provided, the drop will be performed by 'sampleID'."/>
23 <param name="toDrop" type="text" size="30" optional="false" label="Group(s)/Sample(s) to drop" help="Name of the Group(s) or Sample(s), comma separated, to remove from your design file."/>
24 </inputs>
25 <outputs>
26 <data format="tabular" name="out" label="${tool.name} on ${on_string}: Value"/>
27 </outputs>
28 <tests>
29 <test>
30 <param name="input" value="ST000006_data.tsv"/>
31 <param name="design" value="ST000006_design_group_name_underscore.tsv"/>
32 <param name="uniqID" value="Retention_Index" />
33 <param name="group" value="White_wine_type_and_source_no_space" />
34 <param name="toDrop" value="Chardonnay_Napa_CA2003,Riesling_CA2004,SauvignonBlanc_LakeCounty_CA2001" />
35 <output name="out" file="ST000006_modify_design_output.tsv" />
36 </test>
37 </tests>
38 <help><![CDATA[
39
40 @TIP_AND_WARNING@
41
42 **Tool Description**
43
44 The tool creates a new design file based on the existing wide dataset and design file where the specified group types or samples are removed from the existing design file.
45
46 --------------------------------------------------------------------------------
47
48 **Input**
49
50 - Two input datasets are required.
51
52 @WIDE@
53
54 **NOTE:** The sample IDs must match the sample IDs in the Design File
55 (below). Extra columns will automatically be ignored.
56
57 @METADATA@
58
59 @UNIQID@
60
61 **Group/Treatment [Optional]**
62
63 - Name of the column in your Design File that contains group classifications. If not provided, the drop will be performed by 'sampleID's.
64
65 **Group(s)/Sample(s) to drop**
66
67 - Name of the Group(s) or Sample(s), comma separated, to remove from the design file.
68
69 --------------------------------------------------------------------------------
70
71 **Output**
72
73 This tool will output a single design file that contains only the samples not selected for removal.
74
75 ]]></help>
76 <expand macro="citations"/>
77 </tool>