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comparison secimtools/remove_selected_features_samples.xml @ 0:b54326490b4d draft

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Upload 21.3.4.2 release
author malex
date Mon, 08 Mar 2021 20:55:03 +0000
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1 <tool id="secimtools_remove_selected_features" name="Remove Selected Features or Samples" version="@WRAPPER_VERSION@">
2 <description>from the data using a flag file.</description>
3 <macros>
4 <import>macros.xml</import>
5 </macros>
6 <expand macro="requirements" />
7 <command><![CDATA[
8 remove_selected_features_samples.py
9 --input $input
10 --design $design
11 --ID $uniqID
12 --flags $flags
13 --outWide $outWide
14 --outFlags $outFlags
15 --flagDrop $flagToDrop
16 --value $reference
17 --flagfiletype $typeofdrop
18
19 #if $flagUniqID
20 --flagUniqID $flagUniqID
21 #end if
22 #if str( $conditional ) == '0'
23 --condition '0'
24 #end if
25 #if str( $conditional ) == '1'
26 --condition '1'
27 #end if
28 #if str( $conditional ) == '2'
29 --condition '2'
30 #end if
31 ]]></command>
32 <inputs>
33 <param name="input" type="data" format="tabular" label="Wide Dataset"
34 help="Input your tab-separated wide format dataset. If file is not tab separated see TIP below."/>
35 <param name="design" type="data" format="tabular" label="Design File"
36 help="Input your design file (tab-separated). Note you need a 'sampleID' column. If not tab separated see TIP below."/>
37 <param name="flags" type="data" format="tabular" label="Flag File"
38 help="Input dataset containing binary indicator flag value for each feature or sample."/>
39 <param name="uniqID" type="text" size="30" value="" label="Unique Feature ID"
40 help="Name of the column in your wide dataset that has unique identifiers."/>
41 <param name="flagUniqID" type="text" size="30" value="" label="Unique ID for Flag file (feature ID or sample ID)"
42 help="Name of the column in your flag file that has unique identifiers.."/>
43 <param name="flagToDrop" type="text" size="30" value="" label="Flag to Drop"
44 help="Name of the column/row in your flag file to use for dropping."/>
45 <param name="conditional" size="30" type="select" value="" label="Condition of drop." help="Select type of conditional to use.">
46 <option value="0" selected="true">Equals to</option>
47 <option value="1" selected="false">Greater than</option>
48 <option value="2" selected="false">Less than</option>
49 </param>
50 <param name="reference" type="text" size="30" value="1" label="Cutoff Value"
51 help="Any rows or columns with a flag value equal to, greater than or less than (as set above) this Cutoff Value will be dropped."/>
52 <param name="typeofdrop" type="select" size="30" display="radio" value="row" label="Type of drop to be carried out." help="Select whether you want to drop by rows or by columns, default = rows.">
53 <option value="row">Drop Rows</option>
54 <option value="column">Drop Columns</option>
55 </param>
56 </inputs>
57 <outputs>
58 <data format="tabular" name="outWide" label="${tool.name} on ${on_string}: Dropped wide"/>
59 <data format="tabular" name="outFlags" label="${tool.name} on ${on_string}: Dropped flags"/>
60 </outputs>
61 <tests>
62 <test>
63 <param name="input" value="ST000006_data.tsv"/>
64 <param name="design" value="ST000006_design.tsv"/>
65 <param name="uniqID" value="Retention_Index" />
66 <param name="flags" value="ST000006_kruskal_wallis_with_group_flags.tsv"/>
67 <param name="typeofdrop" value="row"/>
68 <param name="flagUniqID" value="Retention_Index" />
69 <param name="flagToDrop" value="flag_significant_0p10_on_all_groups" />
70 <param name="reference" value="0" />
71 <param name="conditional" value="0" />
72 <output name="outWide" file="ST000006_remove_selected_features_samples_wide.tsv" />
73 <output name="outFlags" file="ST000006_remove_selected_features_samples_flags.tsv" />
74 </test>
75 </tests>
76 <help><![CDATA[
77
78 @TIP_AND_WARNING@
79
80 **Tool Description**
81
82 The tool removes features (rows) or samples (columns) from a wide format dataset based on the flags in a separate flag file.
83 The user specifies a flag file and column to indicate removal.
84 Features or samples with a flag value equal to, greater than, or less than a user specified Cutoff Value (Default = 1) will be dropped from the wide dataset.
85
86 The flag file should be either a wide format flag file (used for dropping features) or design format flag file (used for dropping samples).
87 The difference between the flag file formats is described in the beginning of the user manual (Kirpich et al. 2017).
88
89 **NOTE:** Flag files generated outside of SECIM Tools can be used.
90
91 --------------------------------------------------------------------------------
92
93 **Input**
94
95 - Two input datasets are required.
96
97 @WIDE@
98
99 **NOTE:** The sample IDs must match the sample IDs in the Design File
100 (below). Extra columns will automatically be ignored.
101
102 @METADATA@
103
104 @FLAGS@
105
106 @UNIQID@
107
108 **Unique ID for Flag file (feature ID or sample ID).**
109
110 - Name of the column in your Flag file that contains unique Feature IDs.
111
112 **Flag to use for Drop.**
113
114 - Name of the column/row in your Flag File to use drop.
115
116 **Condition of drop.**
117
118 -Select type of conditional.
119
120 **Cutoff Value**
121
122 - Any row (or column) with a flag value equals to, greater than or less than this Cutoff Value (Default = 1) will be dropped.
123
124 **Type of drop.**
125
126 - Select whether you want to drop rows or columns, default = rows.
127
128 --------------------------------------------------------------------------------
129
130 **Output**
131
132 This tool outputs two TSV files:
133
134 (1) The first TSV file is a wide format dataset generated from the input wide format dataset where features (or samples) flagged in the flag file have been removed.
135
136 (2) The second TSV file is the flag file generated from the input flag file where the flagged features (or samples) have been dropped. The resulting flag file contains only features (or samples) that have not been dropped from the wide format dataset.
137
138 ]]></help>
139 <expand macro="citations"/>
140 </tool>