Mercurial > repos > malex > gait_gm

comparison add_pval_flags.xml @ 1:ec9ee8edb84d draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
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>