diff cdhit_analysis.xml @ 1:ff68835adb2b draft

planemo upload for repository https://github.com/Onnodg/Naturalis_NLOOR/tree/main/NLOOR_scripts/process_clusters_tool commit d771f9fbfd42bcdeda1623d954550882a0863847-dirty

--- a/cdhit_analysis.xml	Tue Oct 14 09:09:46 2025 +0000
+++ b/cdhit_analysis.xml	Mon Oct 20 12:27:31 2025 +0000
@@ -1,4 +1,4 @@
-<tool id="cdhit_cluster_analysis" name="CD-HIT Cluster Analysis" version="1.0.0">
+<tool id="cdhit_cluster_analysis" name="CD-HIT Cluster Analysis" version="1.0.1">
     <description>Analyze CD-HIT clustering results with taxonomic annotation</description>
 
     <requirements>
@@ -14,19 +14,19 @@
         --input_annotation '$input_annotation'
 
         #if $output_options.similarity_output:
-            --output_similarity_txt '$output_similarity_txt'
-            --output_similarity_plot '$output_similarity_plot'
+            --output_similarity_txt '$similarity_txt'
+            --output_similarity_plot '$similarity_plot'
         #end if
         #if $output_options.evalue_output:
-            --output_evalue_txt '$output_evalue_txt'
-            --output_evalue_plot '$output_evalue_plot'
+            --output_evalue_txt '$evalue_txt'
+            --output_evalue_plot '$evalue_plot'
         #end if
         #if $output_options.count_output:
-            --output_count '$output_count'
+            --output_count '$cluster_count'
         #end if
         #if $output_options.taxa_output:
-            --output_taxa_clusters '$output_taxa_clusters'
-            --output_taxa_processed '$output_taxa_processed'
+            --output_taxa_clusters '$cluster_taxa'
+            --output_taxa_processed '$processed_taxa'
         #end if
 
         --simi_plot_y_min '$plot_params.simi_plot_y_min'
@@ -48,24 +48,24 @@
     ]]></command>
 
     <inputs>
-        <param name="input_cluster" type="data" format="txt" label="CD-HIT cluster file (.clstr/.txt)"
+        <param name="input_cluster" type="data" format="txt" label="CD-HIT cluster file"
                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)" />
+               label="Excel Annotations file"
+               help="Excel workfile with annotations per header" />
 
         <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"
+                   checked="true" label="Create cluster 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"
+                   checked="true" label="Create cluster 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"
+                   checked="true" label="Create cluster count output"
                    help="Generate read count summaries" />
             <param name="taxa_output" type="boolean" truevalue="true" falsevalue="false"
-                   checked="true" label="Create taxa output"
+                   checked="true" label="Create taxa annotations output"
                    help="Generate taxonomic analysis" />
         </section>
 
@@ -104,31 +104,31 @@
     </inputs>
 
     <outputs>
-        <data name="output_similarity_txt" format="txt" label="Similarity data" >
+        <data name="similarity_txt" format="txt" label="Similarity data" >
             <filter>output_options['similarity_output']</filter>
         </data>
 
-        <data name="output_similarity_plot" format="png" label="Similarity plot" >
+        <data name="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" >
+        <data name="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" >
+        <data name="evalue_plot" format="png" label="E-value plot" >
             <filter>output_options['evalue_output']</filter>
         </data>
 
-        <data name="output_count" format="txt" label="Count summary" >
+        <data name="cluster_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" >
+        <data name="cluster_taxa" format="xlsx" label="Raw taxa per cluster" >
             <filter>output_options['taxa_output']</filter>
         </data>
 
-        <data name="output_taxa_processed" format="xlsx" label="Processed taxa" >
+        <data name="processed_taxa" format="xlsx" label="Processed taxa" >
             <filter>output_options['taxa_output']</filter>
         </data>
     </outputs>
@@ -143,13 +143,13 @@
                 <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"/>
+            <output name="similarity_txt" file="sim_out.txt" />
+            <output name="similarity_plot" file="sim_out.png" compare="sim_size"/>
+            <output name="evalue_txt" file="evalue_out.txt" />
+            <output name="evalue_plot" file="evalue_out.png" compare="sim_size"/>
+            <output name="cluster_count" file="count_out.txt" />
+            <output name="cluster_taxa" file="taxa_out.xlsx" decompress="true"/>
+            <output name="processed_taxa" file="processed.xlsx" decompress="true"/>
         </test>
         <test expect_num_outputs="7">
             <param name="input_cluster" value="input2_test.clstr.txt" />
@@ -160,13 +160,13 @@
                 <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"/>
+            <output name="similarity_txt" file="test2_sim_out.txt" />
+            <output name="similarity_plot" file="test2_sim_out.png" compare="sim_size"/>
+            <output name="evalue_txt" file="test2_evalue_out.txt" />
+            <output name="evalue_plot" file="test2_evalue_out.png" compare="sim_size"/>
+            <output name="cluster_count" file="test_2count_out.txt" />
+            <output name="cluster_taxa" file="test_2taxa_out.xlsx" decompress="true"/>
+            <output name="processed_taxa" file="test_2processed.xlsx" decompress="true"/>
         </test>
         <test expect_num_outputs="5">
             <param name="input_cluster" value="input2_test.clstr.txt" />
@@ -178,7 +178,7 @@
                 <param name="evalue_output" value="false" />
             </section>
             <section name="processing_options">
-                <param name="show_unnanotated_clusters" value="true"/>
+                <param name="show_unannotated_clusters" value="true"/>
                 <param name="make_taxa_in_cluster_split" value="true"/>
                 <param name="print_empty_files" value="true"/>
             </section>
@@ -187,15 +187,15 @@
                 <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">
+            <section name="plot_params">
                 <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"/>
+            <output name="similarity_txt" file="test2_sim_extra_out.txt" />
+            <output name="similarity_plot" file="test2_sim_extra_out.png" compare="sim_size"/>
+            <output name="cluster_count" file="test_2count_extra_out.txt" />
+            <output name="cluster_taxa" file="test_2taxa_extra_out.xlsx" decompress="true"/>
+            <output name="processed_taxa" file="test_2processed_extra.xlsx" decompress="true"/>
         </test>
     </tests>
 
@@ -212,10 +212,10 @@
 
 **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
+- **Cluster similarity output**: Creates similarity analysis with plots and text files showing intra-cluster similarity distributions
+- **Cluster e-value output**: Creates E-value analysis with plots and text files showing E-value distributions
+- **Cluster count output**: Creates summary tables with annotated/unannotated read counts per cluster
+- **Taxa annotations output**: Creates taxonomic analysis determining the most likely taxa for each cluster
 
 **Parameters:**
 
@@ -235,9 +235,23 @@
 
 **Note**: The tool expects that sequence counts are included in the cluster file headers in the format "header(count)".
 
+-------------
+
+.. class:: infomark
+
 **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
+Developed for the New light on old remedies project, a PhD research by Anja Fischer.
+
+Link to the project website:
+
+* https://ahm.uva.nl/funded-research-projects/new-lights-on-old-remedies/new-lights-on-old-remedies.html
+
     ]]></help>
+    <creator>
+        <organization name="Naturalis Biodiversity Center" url="https://www.naturalis.nl/en/science" />
+        <person givenName="Onno" familyName="de Gorter" url="https://github.com/Onnodg"/>
+        <person givenName="Nick" familyName="Kortleven" url="https://github.com/tombkingsts" />
+    </creator>
 </tool>
\ No newline at end of file