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comparison add_pval_flags.xml @ 2:2c218a253d56 draft default tip

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"planemo upload for repository https://github.com/secimTools/gait-gm/tree/main/galaxy commit 758394addb95b09e794132a23a1f7e95ba39df0b"
author malex
date Thu, 29 Jul 2021 20:48:10 +0000
parents ec9ee8edb84d
children
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1:ec9ee8edb84d 2:2c218a253d56
1 <tool id="secimtools_add_pval_flags" name="Add Binary (0/1) -value Flags" version="@WRAPPER_VERSION@"> 1 <tool id="secimtools_add_pval_flags" name="Add Binary (0/1) P-value Flags" version="@WRAPPER_VERSION@">
2 <description>using custom thresholds</description> 2 <description>using custom thresholds</description>
3 <macros> 3 <macros>
4 <import>macros.xml</import> 4 <import>macros.xml</import>
5 </macros> 5 </macros>
6 <expand macro="requirements" /> 6 <expand macro="requirements" />
15 ]]></command> 15 ]]></command>
16 <inputs> 16 <inputs>
17 <param name="DE_Dataset" type="data" format="tabular" label="Select Dataset containing p-values from your history"/> 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."/> 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."/> 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."/> 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. Default values are 0.1,0.05,0.01"/>
21 </inputs> 21 </inputs>
22 <outputs> 22 <outputs>
23 <data format="tabular" name="output" label="${tool.name} on ${on_string}: Output File"/> 23 <data format="tabular" name="output" label="${tool.name} on ${on_string}: Output File"/>
24 <data format="tabular" name="flags" label="${tool.name} on ${on_string}: Flags File"/> 24 <data format="tabular" name="flags" label="${tool.name} on ${on_string}: Flags File"/>
25 </outputs> 25 </outputs>
26 <tests> 26 <tests>
27 <test> 27 <test>
28 <param name="DE_Dataset" value="limma_voom_gene_file_01fhl.tsv"/> 28 <param name="DE_Dataset" value="limma_voom_gene.tsv"/>
29 <param name="uniqID" value="UniqueID"/> 29 <param name="uniqID" value="UniqueID"/>
30 <param name="pvalue" value="P.Value"/> 30 <param name="pvalue" value="P.Value"/>
31 <param name="thresholds" value="0.1,0.05,0.01"/> 31 <param name="thresholds" value="0.1,0.05,0.01"/>
32 <output name="output" file="add_flags_gene_output_file_01fhl.tsv"/> 32 <output name="output" file="add_flags_gene_output.tsv"/>
33 <output name="flags" file="add_flags_gene_flags_file_01fhl.tsv"/> 33 <output name="flags" file="add_flags_gene_flags.tsv"/>
34 </test> 34 </test>
35 <test> 35 <test>
36 <param name="DE_Dataset" value="limma_voom_metabolite_file_01fhl.tsv"/> 36 <param name="DE_Dataset" value="limma_voom_metabolite.tsv"/>
37 <param name="uniqID" value="UniqueID"/> 37 <param name="uniqID" value="UniqueID"/>
38 <param name="pvalue" value="P.Value"/> 38 <param name="pvalue" value="P.Value"/>
39 <param name="thresholds" value="0.1,0.05,0.01"/> 39 <param name="thresholds" value="0.1,0.05,0.01"/>
40 <output name="output" file="add_flags_metabolite_output_file_01fhl.tsv"/> 40 <output name="output" file="add_flags_metabolite_output.tsv"/>
41 <output name="flags" file="add_flags_metabolite_flags_file_01fhl.tsv"/> 41 <output name="flags" file="add_flags_metabolite_flags.tsv"/>
42 </test> 42 </test>
43 </tests> 43 </tests>
44 <help><![CDATA[ 44 <help><![CDATA[
45
46
47 **Tool Description** 45 **Tool Description**
48 46
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) 47 This tool generates 0/1 indicator variables to identify (‘flag’) p-values less than a user-specified threshold or less than the
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. 48 default values of 0.1, 0.05 and 0.01. The flag_threshold variable is equal to 1 if the p-value is less than or equal to the
49 threshold and equal to 0 if greater than the threshold. You can flag nominal p-values or p-values after correction for multiple testing.
51 50
52 -------------------------------------------------------------------------------- 51 --------------------------------------------------------------------------------
53 52
54 **INPUT** 53 **INPUT**
55 54
83 82
84 **OUTPUT** 83 **OUTPUT**
85 84
86 Two output files are generated from the Add Binary (0/1) P-value Flags tool: 85 Two output files are generated from the Add Binary (0/1) P-value Flags tool:
87 86
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). 87 **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 88
90 +-----------+---------+---------+--------+-------------+-----+ 89 +-----------+---------+---------+--------+-------------+-----+
91 | FeatureID | p-value | FDR | Flag_0.2 | Flag_0.05 | ... | 90 | FeatureID | p-value | FDR | Flag_0.2 | Flag_0.05 | ... |
92 +===========+=========+=========+==========+===========+=====+ 91 +===========+=========+=========+==========+===========+=====+
93 | one | 2.02e-6 | 1.83e-6 | 1 | 1 | ... | 92 | one | 2.02e-6 | 1.83e-6 | 1 | 1 | ... |
115 | four | 0 | 0 | ... | 114 | four | 0 | 0 | ... |
116 +-----------+----------+-----------+-----+ 115 +-----------+----------+-----------+-----+
117 | ... | ... | ... | ... | 116 | ... | ... | ... | ... |
118 +-----------+----------+-----------+-----+ 117 +-----------+----------+-----------+-----+
119 118
120 ]]> 119 ]]></help>
121 </help>
122 <citations> 120 <citations>
123 <citation type="bibtex">@ARTICLE{Kirpich17secimtools, 121 <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}, 122 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}, 123 title = {SECIMTools: A suite of Metabolomics Data Analysis Tools},
126 journal = {BMC Bioinformatics}, 124 journal = {BMC Bioinformatics},
127 year = {in press} 125 year = {2018}
128 }</citation> 126 }</citation>
129 <citation type="bibtex">@article{garcia2010paintomics, 127 <citation type="bibtex">@article{Mor2021GaitGM,
130 title={Paintomics: a web based tool for the joint visualization of transcriptomics and metabolomics data}, 128 title={GAIT-GM integrative cross-omics analyses reveal cholinergic defects in a C. elegans model of Parkinson's disease},
131 author={Garc{\'\i}a-Alcalde, Fernando and Garc{\'\i}a-L{\'o}pez, Federico and Dopazo, Joaqu{\'\i}n and Conesa, Ana}, 129 author={Mor, DE and Huertas, F and Morse, AM and Kaletsky, R and Murphy, CT and Kalia, V and Miller, GW and Moskalenko, O and Conesa, A and McIntyre, LM},
132 journal={Bioinformatics}, 130 journal={BMC Genomics},
133 volume={27}, 131 year={submitted},
134 number={1},
135 pages={137--139},
136 year={2010},
137 publisher={Oxford University Press}
138 }</citation> 132 }</citation>
139 </citations> 133 </citations>
140 </tool> 134 </tool>