comparison add_pval_flags.xml @ 1:ec9ee8edb84d draft

Initial upload of 21.6.10 release.
author malex
date Fri, 18 Jun 2021 20:23:19 +0000
parents
children 2c218a253d56
comparison
equal deleted inserted replaced
0:864fc6430432 1:ec9ee8edb84d
1 <tool id="secimtools_add_pval_flags" name="Add Binary (0/1) -value Flags" version="@WRAPPER_VERSION@">
2 <description>using custom thresholds</description>
3 <macros>
4 <import>macros.xml</import>
5 </macros>
6 <expand macro="requirements" />
7 <command detect_errors="exit_code"><![CDATA[
8 add_pval_flags.py
9 -de=$DE_Dataset
10 -id=$uniqID
11 -p=$pvalue
12 -t=$thresholds
13 -o=$output
14 -fl=$flags
15 ]]></command>
16 <inputs>
17 <param name="DE_Dataset" type="data" format="tabular" label="Select Dataset containing p-values from your history"/>
18 <param name="uniqID" type="text" size="30" value="" label="Unique FeatureID" help="Name of the column in your Dataset that contains unique FeatureIDs."/>
19 <param name="pvalue" type="text" size="30" value="" label="P-Value" help="Name of the column containing your p-values."/>
20 <param name="thresholds" type="text" size="30" value="0.1,0.05,0.01" label="P-Value Thresholds" help="Enter the threshold(s). P-values less than the given threshold(s) will be flagged with a 1. Separate more than 1 threshold value with a comma, no spaces allowed."/>
21 </inputs>
22 <outputs>
23 <data format="tabular" name="output" label="${tool.name} on ${on_string}: Output File"/>
24 <data format="tabular" name="flags" label="${tool.name} on ${on_string}: Flags File"/>
25 </outputs>
26 <tests>
27 <test>
28 <param name="DE_Dataset" value="limma_voom_gene_file_01fhl.tsv"/>
29 <param name="uniqID" value="UniqueID"/>
30 <param name="pvalue" value="P.Value"/>
31 <param name="thresholds" value="0.1,0.05,0.01"/>
32 <output name="output" file="add_flags_gene_output_file_01fhl.tsv"/>
33 <output name="flags" file="add_flags_gene_flags_file_01fhl.tsv"/>
34 </test>
35 <test>
36 <param name="DE_Dataset" value="limma_voom_metabolite_file_01fhl.tsv"/>
37 <param name="uniqID" value="UniqueID"/>
38 <param name="pvalue" value="P.Value"/>
39 <param name="thresholds" value="0.1,0.05,0.01"/>
40 <output name="output" file="add_flags_metabolite_output_file_01fhl.tsv"/>
41 <output name="flags" file="add_flags_metabolite_flags_file_01fhl.tsv"/>
42 </test>
43 </tests>
44 <help><![CDATA[
45
46
47 **Tool Description**
48
49 This tool generates an indicator variable (0 or 1) to identify p-values below a user-specified threshold. A “1” is used to indicate (flag)
50 p-values less than the indicated threshold p-value. The user can flag nominal p-values or p-values after correction for multiple testing.
51
52 --------------------------------------------------------------------------------
53
54 **INPUT**
55
56 **Example of a dataset containing p-values**
57
58 +-----------+---------+---------+-----+
59 | FeatureID | P-value | FDR | ... |
60 +===========+=========+=========+=====+
61 | one | 2.02e-6 | 1.83e-6 | ... |
62 +-----------+---------+---------+-----+
63 | two | 2.87e-5 | 0.0063 | ... |
64 +-----------+---------+---------+-----+
65 | three | 0.001 | 0.19 | ... |
66 +-----------+---------+---------+-----+
67 | four | 0.22 | 0.99 | ... |
68 +-----------+---------+---------+-----+
69 | ... | ... | ... | ... |
70 +-----------+---------+---------+-----+
71
72 **P-value**
73
74 Name of the column in your Dataset that contains p-values.
75
76 **P-value Threshold**
77
78 P-values less than the threshold will be flagged with a 1. P-values greater than the threshold will be flagged with a 0.
79
80 **NOTE:** More than one threshold value is allowed. Separate flags will be generated for each threshold value.
81
82 --------------------------------------------------------------------------------
83
84 **OUTPUT**
85
86 Two output files are generated from the Add Binary (0/1) P-value Flags tool:
87
88 **Output File.** A TSV file containing the same columns as the Input Dataset plus an additional column(s) containing 0/1 binary indicators for whether the P-value was less that the user-specified threshold. The indicator columns are named by appending the user-specified threshold to 'Flag_' prefix (e.g. Flag_user-specified threshold, Flag_0.10).
89
90 +-----------+---------+---------+--------+-------------+-----+
91 | FeatureID | p-value | FDR | Flag_0.2 | Flag_0.05 | ... |
92 +===========+=========+=========+==========+===========+=====+
93 | one | 2.02e-6 | 1.83e-6 | 1 | 1 | ... |
94 +-----------+---------+---------+----------+-----------+-----+
95 | two | 2.87e-5 | 0.0063 | 1 | 1 | ... |
96 +-----------+---------+---------+----------+-----------+-----+
97 | three | 0.001 | 0.19 | 1 | 0 | ... |
98 +-----------+---------+---------+----------+-----------+-----+
99 | four | 0.22 | 0.99 | 0 | 0 | ... |
100 +-----------+---------+---------+----------+-----------+-----+
101 | ... | ... | ... | ... | ... | ... |
102 +-----------+---------+---------+----------+-----------+-----+
103
104 **Flag Table.** A TSV file containing only the FeatureID column from the input dataset and the tool-generated binary indicator flags.
105
106 +-----------+----------+-----------+-----+
107 | FeatureID | Flag_0.2 | Flag_0.05 | ... |
108 +===========+==========+===========+=====+
109 | one | 1 | 1 | ... |
110 +-----------+----------+-----------+-----+
111 | two | 1 | 1 | ... |
112 +-----------+----------+-----------+-----+
113 | three | 1 | 0 | ... |
114 +-----------+----------+-----------+-----+
115 | four | 0 | 0 | ... |
116 +-----------+----------+-----------+-----+
117 | ... | ... | ... | ... |
118 +-----------+----------+-----------+-----+
119
120 ]]>
121 </help>
122 <citations>
123 <citation type="bibtex">@ARTICLE{Kirpich17secimtools,
124 author = {Alexander S. Kirpich, Miguel Ibarra, Oleksandr Moskalenko, Justin M. Fear, Joseph Gerken, Xinlei Mi, Ali Ashrafi, Alison M. Morse, Lauren M. McIntyre},
125 title = {SECIMTools: A suite of Metabolomics Data Analysis Tools},
126 journal = {BMC Bioinformatics},
127 year = {in press}
128 }</citation>
129 <citation type="bibtex">@article{garcia2010paintomics,
130 title={Paintomics: a web based tool for the joint visualization of transcriptomics and metabolomics data},
131 author={Garc{\'\i}a-Alcalde, Fernando and Garc{\'\i}a-L{\'o}pez, Federico and Dopazo, Joaqu{\'\i}n and Conesa, Ana},
132 journal={Bioinformatics},
133 volume={27},
134 number={1},
135 pages={137--139},
136 year={2010},
137 publisher={Oxford University Press}
138 }</citation>
139 </citations>
140 </tool>