Mercurial > repos > malex > gait_gm
comparison add_pval_flags.xml @ 1:ec9ee8edb84d draft
Initial upload of 21.6.10 release.
author | malex |
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date | Fri, 18 Jun 2021 20:23:19 +0000 |
parents | |
children | 2c218a253d56 |
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0:864fc6430432 | 1:ec9ee8edb84d |
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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> |