diff read2tree.xml @ 0:0e30cfea5f30 draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/read2tree commit b1e26e7371f5ea33d579cedf205c42201a81d9b3

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/read2tree.xml	Sun Nov 23 11:59:30 2025 +0000
@@ -0,0 +1,98 @@
+<tool id="read2tree" name="Read2Tree" version="@TOOL_VERSION@" profile="24.0">
+    <description>Infer a species tree from sequencing reads</description>
+    <macros>
+        <token name="@TOOL_VERSION@">2.0.1</token>
+    </macros>
+
+    <xrefs>
+       <xref type="bio.tools">read2tree</xref>
+    </xrefs>
+    
+    <requirements>
+        <requirement type="package" version="@TOOL_VERSION@">read2tree</requirement>
+    </requirements>
+
+    <command detect_errors="exit_code"><![CDATA[ 
+        #import re
+        mkdir -p ./genes_dir;
+
+        #for $i, $f in enumerate($marker_genes)
+            ln -s '$f' "./genes_dir/$i".fa;
+        #end for
+
+        #for $f in $reads
+            #set readln = re.sub(r'[^\w\-\\.]', '_', str($f.element_identifier)) 
+            ln -s '$f' './$readln';
+        #end for
+
+        read2tree --tree --standalone_path genes_dir --reads 
+        #for $read in $reads
+            #set readln = re.sub(r'[^\w\-\\.]', '_', str($f.element_identifier)) 
+            "$readln"
+        #end for
+        --output_path ./output --dna_reference $dna_ref
+    ]]></command>
+
+    <inputs>
+        <param argument="reads" type="data" multiple="true" format="fasta,fasta.gz,fastqsanger,fastqsanger.gz,fastqillumina,fastqillumina.gz" 
+            label="Input reads in FASTA or FASTQ" help="Set of input reads for the species of interest."/>
+
+        <param argument="marker_genes" type="data_collection" collection_type="list" format="fasta,fasta.gz"
+            label="Marker gene files" help="A set of reference orthologous groups, i.e. protein sequences of the marker genes for the reference species. See https://github.com/DessimozLab/read2tree for an example and information on how to obtain a list of marker genes."/>
+
+        <param argument="dna_ref" type="data" format="fasta,fasta.gz" label="DNA reference" 
+            help="Reference file containing nucleotide sequences for the set of marker genes presented. See https://github.com/DessimozLab/read2tree for detail."/>
+    </inputs>
+    
+    <outputs>
+        <data name="output_tree" format="newick" from_work_dir="output/tree_*.nwk"/>
+    </outputs>
+    
+
+    <tests>
+        <test>
+            <param name="reads" value="sample_1.fastq.gz,sample_2.fastq.gz" ftype="fastqsanger.gz"/>
+            <param name="marker_genes">
+                <collection type="list">
+                    <element name="gene1" value="marker_genes/OMAGroup_649157.fa" ftype="fasta"/>
+                    <element name="gene2" value="marker_genes/OMAGroup_649216.fa" ftype="fasta"/>
+                    <element name="gene3" value="marker_genes/OMAGroup_671579.fa" ftype="fasta"/>
+                    <element name="gene4" value="marker_genes/OMAGroup_681083.fa" ftype="fasta"/>
+                    <element name="gene5" value="marker_genes/OMAGroup_681195.fa" ftype="fasta"/>
+                    <element name="gene6" value="marker_genes/OMAGroup_671579.fa" ftype="fasta"/>
+                    <element name="gene7" value="marker_genes/OMAGroup_683078.fa" ftype="fasta"/>
+                    <element name="gene8" value="marker_genes/OMAGroup_894224.fa" ftype="fasta"/>
+                    <element name="gene9" value="marker_genes/OMAGroup_898327.fa" ftype="fasta"/>
+                    <element name="gene10" value="marker_genes/OMAGroup_944789.fa" ftype="fasta"/>
+                    <element name="gene11" value="marker_genes/OMAGroup_974829.fa" ftype="fasta"/>
+                    <element name="gene12" value="marker_genes/OMAGroup_1001241.fa" ftype="fasta"/>
+                    <element name="gene13" value="marker_genes/OMAGroup_1008242.fa" ftype="fasta"/>
+                    <element name="gene14" value="marker_genes/OMAGroup_1065415.fa" ftype="fasta"/>
+                    <element name="gene15" value="marker_genes/OMAGroup_1121053.fa" ftype="fasta"/>
+                    <element name="gene16" value="marker_genes/OMAGroup_1125645.fa" ftype="fasta"/>
+                    <element name="gene17" value="marker_genes/OMAGroup_1133018.fa" ftype="fasta"/>
+                    <element name="gene18" value="marker_genes/OMAGroup_1151179.fa" ftype="fasta"/>
+                    <element name="gene19" value="marker_genes/OMAGroup_1163384.fa" ftype="fasta"/>
+                    <element name="gene20" value="marker_genes/OMAGroup_1171372.fa" ftype="fasta"/>
+                    <element name="gene21" value="marker_genes/OMAGroup_1188079.fa" ftype="fasta"/>
+                </collection>
+                </param>
+            <param name="dna_ref" value="dna_ref.fa" ftype="fasta"/>
+            <output name="output_tree" ftype="newick">
+                <assert_contents>
+                    <has_text_matching expression="sample_\d+" />
+                </assert_contents>
+            </output>
+        </test>
+    </tests>
+
+    <help><![CDATA[
+        read2tree is a software tool for generating alignment matrices and performing tree inference directly from sequencing reads. It leverages the OMA database and a set of input reads, bypassing many of the standard steps typically required in phylogenomic analysis. In particular, it avoids for read filtering, assembly, gene prediction, gene annotation, all-vs-all comparison, orthology prediction, alignment, and concatenation.
+    ]]></help>
+
+    <citations>
+        <citation type="doi">10.1038/s41587-023-01753-4</citation>
+    </citations>
+
+
+</tool>