# HG changeset patch
# User iuc
# Date 1765527612 0
# Node ID 9b1836ad6c2e3cc16b70cb02c7ff2282f88eb28d
# Parent  0a8f9bce9dd660325f29711eb545c44c7f23f87b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/nanocomp commit 69a2f2135f021f6e7bc35bce7b4954d2779efc07

diff -r 0a8f9bce9dd6 -r 9b1836ad6c2e nanocomp.xml
--- a/nanocomp.xml	Tue Dec 02 17:29:53 2025 +0000
+++ b/nanocomp.xml	Fri Dec 12 08:20:12 2025 +0000
@@ -1,26 +1,29 @@
 <tool id="nanocomp" name="NanoComp" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="23.2">
-	<description>Compare multiple runs of long read sequencing data and alignments</description>
-	<macros>
-		<token name="@TOOL_VERSION@">1.25.6</token>
-		<token name="@VERSION_SUFFIX@">0</token>
-	</macros>
-	<xrefs>
-		<xref type="bio.tools">nanocomp</xref>
-	</xrefs>
-		<requirements>
-			<requirement type="package" version="@TOOL_VERSION@">nanocomp</requirement>
-		</requirements>
-	<version_command>NanoComp -v</version_command>
-	<command detect_errors="exit_code"><![CDATA[
+  <description>Compare multiple runs of long read sequencing data and alignments</description>
+  <macros>
+    <token name="@TOOL_VERSION@">1.25.6</token>
+    <token name="@VERSION_SUFFIX@">1</token>
+  </macros>
+  <xrefs>
+    <xref type="bio.tools">nanocomp</xref>
+  </xrefs>
+    <requirements>
+      <requirement type="package" version="@TOOL_VERSION@">nanocomp</requirement>
+    </requirements>
+  <version_command>NanoComp -v</version_command>
+  <command detect_errors="exit_code"><![CDATA[
  #import re
- ##link input file with names
+
+ ##link input files with proper names (Nanocomp checks file-extensions)
+  #set $linked_files = []
   #for $file in $inputs.input_type.input_data
-   #if '.' in str($file.name)
-    #set $in_name = re.sub('[\-\:\s]', '_', str($file.name))
-   #else
-    #set $in_name = re.sub('[\-\:\s]', '_', str($file.name))  + "." + $file.ext
-   #end if
-   ln -sf $file $in_name &&
+    #if '.' in str($file.name)
+      #set $in_name = re.sub('[\-\:\s]', '_', str($file.name))
+    #else
+      #set $in_name = re.sub('[\-\:\s]', '_', str($file.name)) + "." + $file.ext
+    #end if
+    ln -sf '$file' '$in_name' &&
+    #silent $linked_files.append($in_name)
   #end for
 
  ##run nanocomp
@@ -29,7 +32,7 @@
   ##no need for the static images (becomes deprecated)
   --make_no_static
 
- ## Compute options
+ ##Compute options
   --threads \${GALAXY_SLOTS:-4}
 
  ##add input files
@@ -51,13 +54,9 @@
    --arrow
   #end if
 
-  #for $file in $inputs.input_type.input_data
-   #if '.' in str($file.name)
-    #set $in_name = re.sub('[\-\:\s]', '_', str($file.name))
-   #else
-    #set $in_name = re.sub('[\-\:\s]', '_', str($file.name))  + "." + $file.ext
-   #end if
-   $in_name
+  ## add the input files
+  #for $file in $linked_files
+    '$file'
   #end for
 
  ##Filter options
@@ -94,148 +93,151 @@
   >& $out_log
 
 ]]></command>
-	<inputs>
-		<section name="inputs" title="Input data" expanded="True"> 
-			<conditional name="input_type">
-				<param name="input_type_selector" type="select" label="Choose Input Format and Files">
-					<option value="fastq" selected="true">FASTQ files</option>
-					<option value="fastq_r">FASTQ-rich files</option>
-					<option value="fasta">FASTA files</option>
-					<option value="bam">BAM files</option>
-					<option value="ubam">uBAM files</option>
-					<option value="cram">CRAM files</option>
-					<option value="pickle">PICKLE files</option>
-					<option value="arrow">ARROW files</option>
-				</param>
-				<when value="fastq">
-					<param name="input_data" type="data" format="fastq,fastq.gz" multiple="true" label="FASTQ input files" help="Data is in (compressed) fastq format" />
-				</when>
-				<when value="fastq_r">
-					<param name="input_data" type="data" format="fastq,fastq.gz" multiple="true" label="FASTQ input files" help="Data is in one or more fastq file(s) generated by MinKNOW or guppy with additional information concerning channel and time" />
-				</when>
-				<when value="fasta">
-					<param name="input_data" type="data" format="fasta,fasta.gz" multiple="true" label="FASTA input files" help="Data is in (compressed) fasta format" />
-				</when>
-				<when value="bam">
-					<param name="input_data" type="data" format="bam" multiple="true" label="BAM input files" help="Data is in sorted bam files." />
-				</when>
-				<when value="ubam">
-					<param name="input_data" type="data" format="bam" multiple="true" label="Unmapped BAM input files" help="Data is in one or more unmapped bam files." />
-				</when>
-				<when value="cram">
-					<param name="input_data" type="data" format="cram" multiple="true" label="CRAM input files" help="Data is in sorted cram files." />
-				</when>
-				<when value="pickle">
-					<param name="input_data" type="data" format="binary" multiple="true" label="PICKLE input files" help="Data is in one or more pickle file(s) from using NanoComp/NanoPlot." />
-				</when>
-				<when value="arrow">
-					<param name="input_data" type="data" format="binary" multiple="true" label="ARROW input files" help="Data is in one or more feather/arrow file(s)." />
-				</when>
-			</conditional>
-		</section>	
+  <inputs>
+    <section name="inputs" title="Input data" expanded="True"> 
+      <conditional name="input_type">
+        <param name="input_type_selector" type="select" label="Choose Input Format and Files">
+          <option value="fastq" selected="true">FASTQ files</option>
+          <option value="fastq_r">FASTQ-rich files</option>
+          <option value="fasta">FASTA files</option>
+          <option value="bam">BAM files</option>
+          <option value="ubam">uBAM files</option>
+          <option value="cram">CRAM files</option>
+          <option value="pickle">PICKLE files</option>
+          <option value="arrow">ARROW files</option>
+        </param>
+        <when value="fastq">
+          <param name="input_data" type="data" format="fastqsanger,fastqsanger.gz" multiple="true" label="FASTQ input files" help="Data is in (compressed) fastq format" />
+        </when>
+        <when value="fastq_r">
+          <param name="input_data" type="data" format="fastqsanger,fastqsanger.gz" multiple="true" label="FASTQ input files" help="Data is in one or more fastq file(s) generated by MinKNOW or guppy with additional information concerning channel and time" />
+        </when>
+        <when value="fasta">
+          <param name="input_data" type="data" format="fasta,fasta.gz" multiple="true" label="FASTA input files" help="Data is in (compressed) fasta format" />
+        </when>
+        <when value="bam">
+          <param name="input_data" type="data" format="bam" multiple="true" label="BAM input files" help="Data is in sorted bam files." />
+        </when>
+        <when value="ubam">
+          <param name="input_data" type="data" format="bam" multiple="true" label="Unmapped BAM input files" help="Data is in one or more unmapped bam files." />
+        </when>
+        <when value="cram">
+          <param name="input_data" type="data" format="cram" multiple="true" label="CRAM input files" help="Data is in sorted cram files." />
+        </when>
+        <when value="pickle">
+          <param name="input_data" type="data" format="binary" multiple="true" label="PICKLE input files" help="Data is in one or more pickle file(s) from using NanoComp/NanoPlot." />
+        </when>
+        <when value="arrow">
+          <param name="input_data" type="data" format="binary" multiple="true" label="ARROW input files" help="Data is in one or more feather/arrow file(s)." />
+        </when>
+      </conditional>
+    </section>  
 
-		<section name="filters" title="Filtering Input Prior To Plotting" expanded="false">
-			<param argument="--maxlength" type="integer" optional="true" label="Max read length filtering" help="Drop reads longer than length specified." />
-			<param argument="--minlength" type="integer" optional="true" label="Min read length filtering" help="Drop reads shorter than length specified." />
-		</section>
+    <section name="filters" title="Filtering Input Prior To Plotting" expanded="false">
+      <param argument="--maxlength" type="integer" optional="true" label="Max read length filtering" help="Drop reads longer than length specified." />
+      <param argument="--minlength" type="integer" optional="true" label="Min read length filtering" help="Drop reads shorter than length specified." />
+    </section>
 
-		<section name="plot_options" title="Plot Customization Options" expanded="false">
-			<param argument="--plot" type="select" label="Plot Type" help="Specify the type of plot to be used.">
-				<option value="box">Box plot</option>
-				<option value="violin" selected="true">Violin plot</option>
-				<option value="ridge">Ridge (joyplot) plot</option>
-				<option value="not">No plot</option>
-			</param>
-			<param argument="--title" type="text" label="Custom plot titles" help="Add a title to all plots." />
-			<param argument="--names" type="text" label="Custom names" help="Specify the names (space seperated, respective to input) to be used for the datasets." />
-			<param argument="--colors" type="text" label="Custom colors" help="Specify the colors (space seperated, respective to input) to be used for each the datasets. Can be any valid Matplotlib color: Named, HEX-string, RGB, ... " />
-		</section>	
+    <section name="plot_options" title="Plot Customization Options" expanded="false">
+      <param argument="--plot" type="select" label="Plot Type" help="Specify the type of plot to be used.">
+        <option value="box">Box plot</option>
+        <option value="violin" selected="true">Violin plot</option>
+        <option value="ridge">Ridge (joyplot) plot</option>
+        <option value="not">No plot</option>
+      </param>
+      <param argument="--title" type="text" label="Custom plot titles" help="Add a title to all plots." />
+      <param argument="--names" type="text" label="Custom names" help="Specify the names (space seperated, respective to input) to be used for the datasets." />
+      <param argument="--colors" type="text" label="Custom colors" help="Specify the colors (space seperated, respective to input) to be used for each the datasets. Can be any valid Matplotlib color: Named, HEX-string, RGB, ... " />
+    </section>  
 
-		<section name="output_options" title="Output Options" expanded="false">
-			<param argument="--tsv_stats" type="boolean" truevalue="--tsv_stats" falsevalue="" optional="true" checked="false" label="TSV Output Format" help="Output the statistics file as properly formatted TSV."/>
-		</section>
+    <section name="output_options" title="Output Options" expanded="false">
+      <param argument="--tsv_stats" type="boolean" truevalue="--tsv_stats" falsevalue="" optional="true" checked="false" label="TSV Output Format" help="Output the statistics file as properly formatted TSV."/>
+    </section>
 
-	</inputs>
-
+  </inputs>
 
-	<outputs>
-		<data name="out_log" format="txt" label="${tool.name} on ${on_string}: Log file"/>
-		<data name="stats_file" format="txt" from_work_dir="NanoStats.txt" label="${tool.name} on ${on_string}: Statistics file"/>	
-		<data name="html_report" format="html" from_work_dir="NanoComp-report.html" label="${tool.name} on ${on_string}: Html Report"/>	
-	</outputs>
-	<tests>
-		<test expect_num_outputs="3">
-			<section name="inputs">
-				<conditional name="input_type">	
-					<param name="input_type_selector" value="fastq" />
-					<param name="input_data" value="in1.fastq.gz,in2.fastq.gz,in3.fastq.gz" />
-				</conditional>
-			</section>
-			<output name="stats_file" > 
-				<assert_contents>
-					<has_text text="General summary" />
-				</assert_contents>
-			</output>
-			<output name="html_report"> 
-				<assert_contents>
-					<has_text text="html"/>
-					<has_text text="Summary statistics"/>
-				</assert_contents>
-			</output>
-		</test>
-		<test expect_num_outputs="3">
-			<section name="inputs">
-				<conditional name="input_type">
-					<param name="input_type_selector" value="bam" />
-					<param name="input_data" value="in4.bam,in5.bam" />
-				</conditional>
-			</section>
-			<section name="filters" >
-				<param name="maxlength" value="15000"/>
-				<param name="minlength" value="500"/>
-			</section>
-			<output name="html_report">
-				<assert_contents>
-					<has_text text="html"/>
-					<has_text text="Summary statistics"/>
-				</assert_contents>
-			</output>
-		</test>
-		<test expect_num_outputs="3">
-			<section name="inputs">
-				<conditional name="input_type">	
-					<param name="input_type_selector" value="fastq" />
-					<param name="input_data" value="in1.fastq.gz,in3.fastq.gz" />
-				</conditional>
-			</section>
-			<section name="output_options">
-				<param name="tsv_stats" value="true"/>
-			</section>
-			<output name="stats_file" > 
-			<assert_contents>
-				<has_text text="Metrics" />
-			</assert_contents>
-			</output>
-		</test>
-		<test expect_num_outputs="3">
-			<section name="inputs">
-				<conditional name="input_type">
-					<param name="input_type_selector" value="bam" />
-					<param name="input_data" value="in4.bam,in5.bam" />
-				</conditional>
-			</section>
-			<section name="plot_options" >
-		<param name="plot" value="box"/>
-			</section>
-			<output name="html_report">
-				<assert_contents>
-					<has_text text="html"/>
-					<has_text text="Plots"/>
-				</assert_contents>
-			</output>
-		</test>
-	</tests>
-	<help><![CDATA[
+  <outputs>
+    <data name="out_log" format="txt" label="${tool.name} on ${on_string}: Log file"/>
+    <data name="stats_file" format="txt" from_work_dir="NanoStats.txt" label="${tool.name} on ${on_string}: Statistics file"/>  
+    <data name="html_report" format="html" from_work_dir="NanoComp-report.html" label="${tool.name} on ${on_string}: Html Report"/>  
+  </outputs>
+  <tests>
+    <!-- 1) fastq.gz input -->
+    <test expect_num_outputs="3">
+      <section name="inputs">
+        <conditional name="input_type">  
+          <param name="input_type_selector" value="fastq" />
+          <param name="input_data" ftype="fastqsanger.gz" value="in1.fastq.gz,in2.fastq.gz,in3.fastq.gz" />
+        </conditional>
+      </section>
+      <output name="stats_file" ftype="txt"> 
+        <assert_contents>
+          <has_text text="General summary" />
+        </assert_contents>
+      </output>
+      <output name="html_report" ftype="html"> 
+        <assert_contents>
+          <has_text text="html"/>
+          <has_text text="Summary statistics"/>
+        </assert_contents>
+      </output>
+    </test>
+    <!-- 2) bam input -->
+    <test expect_num_outputs="3">
+      <section name="inputs">
+        <conditional name="input_type">
+          <param name="input_type_selector" value="bam" />
+          <param name="input_data" ftype="bam" value="in4.bam,in5.bam" />
+        </conditional>
+      </section>
+      <section name="filters" >
+        <param name="maxlength" value="15000"/>
+        <param name="minlength" value="500"/>
+      </section>
+      <output name="html_report" ftype="html">
+        <assert_contents>
+          <has_text text="html"/>
+          <has_text text="Summary statistics"/>
+        </assert_contents>
+      </output>
+    </test>
+    <!-- 3) fastq.gz input, tsv output -->
+    <test expect_num_outputs="3">
+      <section name="inputs">
+        <conditional name="input_type">  
+          <param name="input_type_selector" value="fastq" />
+          <param name="input_data" ftype="fastqsanger.gz" value="in1.fastq.gz,in3.fastq.gz" />
+        </conditional>
+      </section>
+      <section name="output_options">
+        <param name="tsv_stats" value="true"/>
+      </section>
+      <output name="stats_file" ftype="txt"> 
+      <assert_contents>
+        <has_text text="Metrics" />
+      </assert_contents>
+      </output>
+    </test>
+    <!-- 4) bam input, box plot output -->
+    <test expect_num_outputs="3">
+      <section name="inputs">
+        <conditional name="input_type">
+          <param name="input_type_selector" value="bam" />
+          <param name="input_data" ftype="bam" value="in4.bam,in5.bam" />
+        </conditional>
+      </section>
+      <section name="plot_options" >
+    <param name="plot" value="box"/>
+      </section>
+      <output name="html_report" ftype="html">
+        <assert_contents>
+          <has_text text="html"/>
+          <has_text text="Plots"/>
+        </assert_contents>
+      </output>
+    </test>
+  </tests>
+  <help><![CDATA[
 **NanoComp** 
 
 Compare multiple runs of long read sequencing data and alignments. Creates violin plots or box plots of length, quality and percent identity and creates dynamic, overlaying read length histograms and a cumulative yield plot.
@@ -252,7 +254,7 @@
 
 - **Official Repository**: [GitHub - wdecoster/nanocomp](https://github.com/wdecoster/nanocomp)  
 ]]></help>
-	<citations>
-		<citation type="doi">10.1093/bioinformatics/btad311</citation>
-	</citations>
+  <citations>
+    <citation type="doi">10.1093/bioinformatics/btad311</citation>
+  </citations>
 </tool>