changeset 4:7bf95986aaa4 draft

planemo upload for repository https://github.com/vgl-hub/rdeval commit 0d51c740073961b52774f611929f062b06de80da

--- a/macros.xml	Tue Feb 18 17:24:35 2025 +0000
+++ b/macros.xml	Wed Apr 23 19:31:12 2025 +0000
@@ -4,23 +4,14 @@
             <requirement type="package" version="@TOOL_VERSION@">rdeval</requirement>
         </requirements>
     </xml>
+    <!-- should be: 0.0.5=r44h35c04b2_2 -->
     <token name="@TOOL_VERSION@">0.0.5</token>
-    <token name="@VERSION_SUFFIX@">3</token>
+    <token name="@VERSION_SUFFIX@">4</token>
     <token name="@PROFILE@">23.02</token>
     <xml name="citations">
         <citations>
-            <citation type="bibtex">
-                @article{formenti2022gfastats,
-                    title={Gfastats: conversion, evaluation and manipulation of genome sequences using assembly graphs},
-                    author={Formenti, Giulio and Abueg, Linelle and Brajuka, Angelo and Brajuka, Nadolina and Gallardo-Alba, Crist{\'o}bal and Giani, Alice and Fedrigo, Olivier and Jarvis, Erich D},
-                    journal={Bioinformatics},
-                    volume={38},
-                    number={17},
-                    pages={4214--4216},
-                    year={2022},
-                    publisher={Oxford University Press}
-                    }
-            </citation>
+            <citation type="doi">10.1101/2025.02.01.636073</citation>
+            <citation type="doi">10.1093/bioinformatics/btac460</citation>
         </citations>
     </xml>
 </macros>

--- a/rdeval.xml	Tue Feb 18 17:24:35 2025 +0000
+++ b/rdeval.xml	Wed Apr 23 19:31:12 2025 +0000
@@ -60,7 +60,7 @@
 		> '$stats_outfile'
 	]]></command>
     <inputs>
-        <param argument="--input-reads" type="data" format="bam,cram,fasta,fasta.gz,fastq,fastq.gz" multiple="true" label="Input dataset" help="FASTA/FASTQ, BAM, or CRAM files."/>
+        <param argument="--input-reads" type="data" format="bam,cram,fasta,fasta.gz,fastq,fastq.gz" multiple="true" label="Input dataset" help="BAM, CRAM, FASTA, FASTQ, or RD files"/>
         <param name="expected_gsize" type="integer" label="Expected Genome Size" optional="true" help="Integer (e.g., 3000000000 for human)."/>
         <section name="input_filter" title="Filter input reads" expanded="false">
             <conditional name="file_filter">
@@ -183,9 +183,13 @@
         </test>
         <test expect_num_outputs="2">
             <param name="input_reads" value="test2.bam" ftype="bam"/>
-            <param name="type_selector" value="combined_reads"/>
+            <section name="output_options">
+                <conditional name="output_type">
+                    <param name="type_selector" value="combined_reads"/>
+                    <param name="format_selector" value="fastq.gz"/>
+                </conditional>
+            </section>
             <output name="stats_outfile" file="output2.tabular" ftype="tabular"/>
-            <param name="format_selector" value="fastq.gz"/>
             <output name="reads_outfile" file="output2.fastq.gz" ftype="fastq.gz"/>
         </test>
     </tests>

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/rdeval_report.xml	Wed Apr 23 19:31:12 2025 +0000
@@ -0,0 +1,40 @@
+<tool id="rdeval_report" name="rdeval report" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
+    <description>Read summary and figures.</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements"/>
+    <command detect_errors="exit_code"><![CDATA[
+    mkdir render &&
+    cd render &&
+    export RDEVAL_SHARE_DIR="\$(dirname \$(dirname \$(type -P rdeval)))/share/rdeval" &&
+    ln -s "\$RDEVAL_SHARE_DIR/figures.Rmd" &&
+    ln -s "\$RDEVAL_SHARE_DIR/rdeval_interface.R" &&
+    #set $num_files = 0
+    #for $input_file in $input_files
+        ln -s '$input_file' '${num_files}.rd' &&
+        #set $num_files += 1
+    #end for
+    R -e "rmarkdown::render('figures.Rmd', output_file='$html_outfile')" --args #for $idx in range($num_files)# '${idx}.rd' #end for
+	]]></command>
+    <inputs>
+        <param name="input_files" type="data" format="data" multiple="true" label="Input dataset" help="RD files"/>
+    </inputs>
+    <outputs>
+        <data name="html_outfile" format="html" label="Rdeval report"/>
+    </outputs>
+    <tests>
+        <test expect_num_outputs="1">
+            <param name="input_files" value="test.rd"/>
+            <output name="html_outfile" ftype="html">
+                <assert_contents>
+                    <has_size size="833000" delta="8330"/>
+                </assert_contents>
+            </output>
+        </test>
+    </tests>
+    <help><![CDATA[
+This tool creates a report containing a read summary and figures from input RD files.
+    ]]></help>
+    <expand macro="citations"/>
+</tool>

Binary file test-data/test.rd has changed