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