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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastspar commit 0e305d21d0634a1788b9105ec4d0ab1c2da62359
author iuc
date Thu, 19 Jun 2025 21:51:44 +0000
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1 <tool id="fastspar_reduce" name="FastSpar: Reduce correlation table" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
2 <description>
3 Filter correlation and p-value table into sparse matrices
4 </description>
5 <macros>
6 <import>macros.xml</import>
7 </macros>
8 <expand macro="biotools"/>
9 <expand macro="requirements"/>
10 <command detect_errors="exit_code"><![CDATA[
11 fastspar_reduce
12 --correlation_table '$correlation_table'
13 --pvalue_table '$pvalue_table'
14 --correlation $correlation
15 --pvalue $pvalue
16 --output_prefix sparse
17 ]]></command>
18 <inputs>
19 <param argument="--correlation_table" type="data" format="tabular" label="Correlation table"/>
20 <param argument="--pvalue_table" type="data" format="tabular" label="P-value table"/>
21 <param argument="--correlation" type="float" min="0.0" max="1.0" value="0.10" label="Absolute correlation threshold"/>
22 <param argument="--pvalue" type="float" min="0.0" max="1.0" value="0.05" label="P-value threshold"/>
23 </inputs>
24 <outputs>
25 <data name="correlations" format="tabular" from_work_dir="sparse_filtered_correlation.tsv" label="${tool.name} on ${on_string}: filtered_correlations.tsv">
26 <actions>
27 <action type="metadata" name="column_names" default="column,row,value" />
28 </actions>
29 </data>
30 <data name="pvalues" format="tabular" from_work_dir="sparse_filtered_pvalue.tsv" label="${tool.name} on ${on_string}: filtered_pvalues.tsv">
31 <actions>
32 <action type="metadata" name="column_names" default="column,row,value" />
33 </actions>
34 </data>
35 </outputs>
36 <tests>
37 <test expect_num_outputs="2">
38 <param name="correlation_table" ftype="tabular" value="fake_data_cor.tsv"/>
39 <param name="pvalue_table" ftype="tabular" value="pvalues.tsv"/>
40 <output name="correlations" file="filtered_correlations.tsv" compare="diff"/>
41 <output name="pvalues" file="filtered_pvalues.tsv" compare="diff"/>
42 </test>
43 </tests>
44 <help><![CDATA[
45 What it does
46 ============
47
48 This tool filters pairwise correlations and p-values from FastSpar outputs to generate sparse matrices suitable for network construction or visualization. It is typically used as the final step in a FastSpar pipeline.
49
50 Filtering Criteria
51 ==================
52
53 - **Absolute correlation threshold**: Only retain OTU pairs whose absolute correlation exceeds this value.
54 - **P-value threshold**: Only retain OTU pairs whose empirical p-value is below this cutoff.
55
56 Both conditions must be satisfied (logical AND).
57
58 Required Inputs
59 ===============
60
61 - **Correlation table**: A symmetric matrix from FastSpar.
62 - **P-value table**: A matching symmetric matrix from FastSpar p-value estimation.
63
64 Generated Outputs
65 =================
66
67 - `filtered_correlations.tsv`: Correlation values that passed both thresholds.
68 - `filtered_pvalues.tsv`: Matching p-values for retained entries.
69
70 Notes
71 =====
72
73 - Both input matrices must have identical dimensions and OTU order.
74 - The output tables are still symmetric and retain all diagonal values (e.g., self-correlations).
75
76 Additional Resources
77 ====================
78
79 - FastSpar GitHub: https://github.com/scwatts/fastspar
80 ]]></help>
81 <expand macro="citations"/>
82 </tool>