diff cdhit_analysis.xml @ 0:00d56396b32a draft

planemo upload for repository https://github.com/Onnodg/Naturalis_NLOOR/tree/main/NLOOR_scripts/process_clusters_tool commit c944fd5685f295acba06679e85b67973c173b137

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/cdhit_analysis.xml	Tue Oct 14 09:09:46 2025 +0000
@@ -0,0 +1,243 @@
+<tool id="cdhit_cluster_analysis" name="CD-HIT Cluster Analysis" version="1.0.0">
+    <description>Analyze CD-HIT clustering results with taxonomic annotation</description>
+
+    <requirements>
+        <requirement type="package" version="3.12.3">python</requirement>
+        <requirement type="package" version="3.10.6">matplotlib</requirement>
+        <requirement type="package" version="2.3.2">pandas</requirement>
+        <requirement type="package" version="3.1.5">openpyxl</requirement>
+    </requirements>
+
+    <command detect_errors="exit_code"><![CDATA[
+        python '$__tool_directory__/cdhit_analysis.py'
+        --input_cluster '$input_cluster'
+        --input_annotation '$input_annotation'
+
+        #if $output_options.similarity_output:
+            --output_similarity_txt '$output_similarity_txt'
+            --output_similarity_plot '$output_similarity_plot'
+        #end if
+        #if $output_options.evalue_output:
+            --output_evalue_txt '$output_evalue_txt'
+            --output_evalue_plot '$output_evalue_plot'
+        #end if
+        #if $output_options.count_output:
+            --output_count '$output_count'
+        #end if
+        #if $output_options.taxa_output:
+            --output_taxa_clusters '$output_taxa_clusters'
+            --output_taxa_processed '$output_taxa_processed'
+        #end if
+
+        --simi_plot_y_min '$plot_params.simi_plot_y_min'
+        --simi_plot_y_max '$plot_params.simi_plot_y_max'
+
+        --uncertain_taxa_use_ratio '$taxa_params.uncertain_taxa_use_ratio'
+        --min_to_split '$taxa_params.min_to_split'
+        --min_count_to_split '$taxa_params.min_count_to_split'
+
+        #if $processing_options.show_unannotated_clusters:
+            --show_unannotated_clusters
+        #end if
+        #if $processing_options.make_taxa_in_cluster_split:
+            --make_taxa_in_cluster_split
+        #end if
+        #if $processing_options.print_empty_files:
+            --print_empty_files
+        #end if
+    ]]></command>
+
+    <inputs>
+        <param name="input_cluster" type="data" format="txt" label="CD-HIT cluster file (.clstr/.txt)"
+               help="Output cluster file from cd-hit-est" />
+        <param name="input_annotation" type="data" format="xlsx"
+               label="Annotation file"
+               help="Excel workfile with sequence annotations (header, evalue, taxa)" />
+
+        <section name="output_options" title="Output Options" expanded="true">
+            <param name="similarity_output" type="boolean" truevalue="true" falsevalue="false"
+                   checked="true" label="Create similarity output"
+                   help="Generate similarity analysis and plots" />
+            <param name="evalue_output" type="boolean" truevalue="true" falsevalue="false"
+                   checked="true" label="Create E-value output"
+                   help="Generate E-value analysis and plots" />
+            <param name="count_output" type="boolean" truevalue="true" falsevalue="false"
+                   checked="true" label="Create count output"
+                   help="Generate read count summaries" />
+            <param name="taxa_output" type="boolean" truevalue="true" falsevalue="false"
+                   checked="true" label="Create taxa output"
+                   help="Generate taxonomic analysis" />
+        </section>
+
+        <section name="plot_params" title="Plot Parameters" expanded="false">
+            <param name="simi_plot_y_min" type="float" value="95.0" min="0" max="100"
+                   label="Similarity plot Y-axis minimum"
+                   help="Minimum value for similarity plot Y-axis" />
+            <param name="simi_plot_y_max" type="float" value="100.0" min="0" max="100"
+                   label="Similarity plot Y-axis maximum"
+                   help="Maximum value for similarity plot Y-axis" />
+        </section>
+
+        <section name="taxa_params" title="Taxonomic Analysis Parameters" expanded="false">
+            <param name="uncertain_taxa_use_ratio" type="float" value="0.5" min="0" max="1"
+                   label="Uncertain taxa ratio"
+                   help="Ratio at which uncertain taxa count toward the correct taxa" />
+            <param name="min_to_split" type="float" value="0.45" min="0" max="1"
+                   label="Minimum percentage to split"
+                   help="Minimum percentage for taxonomic split" />
+            <param name="min_count_to_split" type="integer" value="10" min="1"
+                   label="Minimum count to split"
+                   help="Minimum count for taxonomic split" />
+        </section>
+
+        <section name="processing_options" title="Processing Options" expanded="false">
+            <param name="show_unannotated_clusters" type="boolean" truevalue="true" falsevalue="false"
+                   checked="false" label="Show unannotated clusters"
+                   help="Include unannotated clusters in output" />
+            <param name="make_taxa_in_cluster_split" type="boolean" truevalue="true" falsevalue="false"
+                   checked="false" label="Split clusters with multiple taxa"
+                   help="Split clusters containing multiple taxa instead of marking as uncertain" />
+            <param name="print_empty_files" type="boolean" truevalue="true" falsevalue="false"
+                   checked="false" label="Print empty file messages"
+                   help="Print messages about empty annotation files" />
+        </section>
+    </inputs>
+
+    <outputs>
+        <data name="output_similarity_txt" format="txt" label="Similarity data" >
+            <filter>output_options['similarity_output']</filter>
+        </data>
+
+        <data name="output_similarity_plot" format="png" label="Similarity plot" >
+            <filter>output_options['similarity_output']</filter>
+        </data>
+
+        <data name="output_evalue_txt" format="txt" label="E-value data" >
+            <filter>output_options['evalue_output']</filter>
+        </data>
+
+        <data name="output_evalue_plot" format="png" label="E-value plot" >
+            <filter>output_options['evalue_output']</filter>
+        </data>
+
+        <data name="output_count" format="txt" label="Count summary" >
+            <filter>output_options['count_output']</filter>
+        </data>
+
+        <data name="output_taxa_clusters" format="xlsx" label="Raw taxa per cluster" >
+            <filter>output_options['taxa_output']</filter>
+        </data>
+
+        <data name="output_taxa_processed" format="xlsx" label="Processed taxa" >
+            <filter>output_options['taxa_output']</filter>
+        </data>
+    </outputs>
+
+    <tests>
+        <test expect_num_outputs="7">
+            <param name="input_cluster" value="29-test.clstr.txt" />
+            <param name="input_annotation" value="header_anno_29_test.xlsx" />
+            <section name="output_options">
+                <param name="similarity_output" value="true" />
+                <param name="evalue_output" value="true" />
+                <param name="count_output" value="true" />
+                <param name="taxa_output" value="true" />
+            </section>
+            <output name="output_similarity_txt" file="sim_out.txt" />
+            <output name="output_similarity_plot" file="sim_out.png" compare="sim_size"/>
+            <output name="output_evalue_txt" file="evalue_out.txt" />
+            <output name="output_evalue_plot" file="evalue_out.png" compare="sim_size"/>
+            <output name="output_count" file="count_out.txt" />
+            <output name="output_taxa_clusters" file="taxa_out.xlsx" decompress="true"/>
+            <output name="output_taxa_processed" file="processed.xlsx" decompress="true"/>
+        </test>
+        <test expect_num_outputs="7">
+            <param name="input_cluster" value="input2_test.clstr.txt" />
+            <param name="input_annotation" value="header_anno_excel.xlsx" />
+            <section name="output_options">
+                <param name="similarity_output" value="true" />
+                <param name="evalue_output" value="true" />
+                <param name="count_output" value="true" />
+                <param name="taxa_output" value="true" />
+            </section>
+            <output name="output_similarity_txt" file="test2_sim_out.txt" />
+            <output name="output_similarity_plot" file="test2_sim_out.png" compare="sim_size"/>
+            <output name="output_evalue_txt" file="test2_evalue_out.txt" />
+            <output name="output_evalue_plot" file="test2_evalue_out.png" compare="sim_size"/>
+            <output name="output_count" file="test_2count_out.txt" />
+            <output name="output_taxa_clusters" file="test_2taxa_out.xlsx" decompress="true"/>
+            <output name="output_taxa_processed" file="test_2processed.xlsx" decompress="true"/>
+        </test>
+        <test expect_num_outputs="5">
+            <param name="input_cluster" value="input2_test.clstr.txt" />
+            <param name="input_annotation" value="header_anno_excel.xlsx" />
+            <section name="output_options">
+                <param name="similarity_output" value="true" />
+                <param name="count_output" value="true" />
+                <param name="taxa_output" value="true" />
+                <param name="evalue_output" value="false" />
+            </section>
+            <section name="processing_options">
+                <param name="show_unnanotated_clusters" value="true"/>
+                <param name="make_taxa_in_cluster_split" value="true"/>
+                <param name="print_empty_files" value="true"/>
+            </section>
+            <section name="taxa_params">
+                <param name="uncertain_taxa_use_ratio" value="0.6"/>
+                <param name="min_to_split" value="0.6"/>
+                <param name="min_count_to_split" value="6"/>
+            </section>
+            <section name="plot_params" title="Plot Parameters" expanded="false">
+                <param name="simi_plot_y_min" value="0.4" />
+                <param name="simi_plot_y_max"  value="0.4"  />
+            </section>
+            <output name="output_similarity_txt" file="test2_sim_extra_out.txt" />
+            <output name="output_similarity_plot" file="test2_sim_extra_out.png" compare="sim_size"/>
+            <output name="output_count" file="test_2count_extra_out.txt" />
+            <output name="output_taxa_clusters" file="test_2taxa_extra_out.xlsx" decompress="true"/>
+            <output name="output_taxa_processed" file="test_2processed_extra.xlsx" decompress="true"/>
+        </test>
+    </tests>
+
+    <help><![CDATA[
+**CD-HIT Cluster Analysis**
+
+This tool analyzes CD-HIT clustering results and provides various outputs including taxonomic analysis, similarity analysis, E-value analysis, and read count summaries.
+
+**Input Files:**
+
+1. **CD-HIT cluster file (.txt/.clstr)**: Required. The cluster file output from cd-hit-est containing clustered sequences.
+
+2. **Annotation file (.xlsx)**: Tab-separated file containing sequence annotations with columns:
+
+**Output Options:**
+
+- **Similarity output**: Creates similarity analysis with plots and text files showing intra-cluster similarity distributions
+- **E-value output**: Creates E-value analysis with plots and text files showing E-value distributions
+- **Count output**: Creates summary tables with annotated/unannotated read counts per cluster
+- **Taxa output**: Creates taxonomic analysis determining the most likely taxa for each cluster
+
+**Parameters:**
+
+- **Plot Parameters**: Control the size of similarity plots (X and Y-axis limits)
+- **Taxonomic Analysis Parameters**: Control how uncertain taxa are handled and when clusters are split
+- **Processing Options**: Control display of unannotated clusters and verbose output
+
+**Output Files:**
+
+- **Similarity data**: Tab-separated file with similarity statistics
+- **Similarity plot**: PNG image showing similarity distribution across clusters
+- **E-value data**: Tab-separated file with E-value statistics
+- **E-value plot**: PNG image showing E-value distribution
+- **Count summary**: Tab-separated file with read counts per cluster
+- **Raw taxa per cluster**: Excel file showing all taxa found in each cluster
+- **Processed taxa**: Excel file with clusters where a taxon was assigned
+
+**Note**: The tool expects that sequence counts are included in the cluster file headers in the format "header(count)".
+
+**Credits**
+Authors = Onno de Gorter, 2025.
+Based on a script by Nick Kortleven, translated, modified and wrapped by Onno de Gorter,
+Developed for the New light on old remedies project, a PhD research by Anja Fischer
+    ]]></help>
+</tool>
\ No newline at end of file