Merge pull request galaxyproject#5664 from rlibouba/compleasm

Add compleasm v.0.2.5

tools/compleasm/.shed.yml

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+categories: [Sequence Analysis]
+description: "Compleasm: a faster and more accurate reimplementation of BUSCO"
+long_description: "A tool for evaluating genome completeness form miniprot alignment but also form genome assembly"
+homepage_url: https://github.com/huangnengCSU/compleasm
+name: compleasm
+owner: iuc
+remote_repository_url: https://github.com/galaxyproject/tools-iuc/tree/master/tools/compleasm/

tools/compleasm/compleasm.xml

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+<tool id="compleasm" name="compleasm" version="@TOOL_VERSION@+galaxy0" profile="20.01">
+    <description>completeness of genome assemblies</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <requirements>
+        <requirement type="package" version="@TOOL_VERSION@">compleasm</requirement>
+    </requirements>
+    <command><![CDATA[
+    compleasm run
+    -a '$input'
+    -o galaxy
+    --mode $mode
+    -l '$busco_database'
+
+    #if str($specified_contigs) != '':
+        --specified_contigs '$specified_contigs'
+    #end if
+
+    ]]></command>
+    <inputs>
+        <param argument="-a" name="input" type="data" format="fasta" label="Input genome file"/>
+        <param name="mode" type="select" label="The mode of evaluation" help="If you want to use hmmsearch, select BUSCO mode. Otherwise, select lite mode">
+            <option value="busco" selected="true">BUSCO</option>
+            <option value="lite">Lite</option>
+        </param>
+
+        <param argument="--specified_contigs" type="text" label="Specify the contigs to be evaluated" optional="true" help="e.g. chr1 chr2 chr3. If not specified, all contigs will be evaluated">
+            <sanitizer invalid_char="">
+                <valid initial="string.letters,string.digits">
+                    <add value="_" />
+                </valid>
+            </sanitizer>
+            <validator type="regex">[0-9a-zA-Z_ ]+</validator>
+        </param>
+
+        <param name="outputs" type="select" multiple="true" label="Which outputs should be generated">
+            <option value="full_table_busco" selected="true">full busco table</option>
+            <option value="full_table">full table</option>
+            <option value="miniprot">miniprot</option>
+            <option value="translated_protein">translated proteins</option>
+        </param>
+
+        <param name="busco_database" label="Choose the BUSCO database to be used" type="select" multiple="false">
+            <options from_data_table="busco_database"/>
+        </param>
+    </inputs>
+
+    <outputs>
+        <data name='full_table_busco' format='tsv' label="${tool.name} on ${on_string}: full table BUSCO" from_work_dir="galaxy/*_odb10/full_table_busco_format.tsv">
+            <filter>outputs and 'full_table_busco' in outputs</filter>
+        </data>
+        <data name='full_table' format='tsv' label="${tool.name} on ${on_string}: full table" from_work_dir="galaxy/*_odb10/full_table.tsv">
+            <filter>outputs and 'full_table' in outputs</filter>
+        </data>
+        <data name='miniprot' format='gff3' label="${tool.name} on ${on_string}: Miniprot" from_work_dir="galaxy/*_odb10/miniprot_output.gff">
+            <filter>outputs and 'miniprot' in outputs</filter>
+        </data>
+        <data name='translated_protein' format='fasta' label="${tool.name} on ${on_string}: Translated protein" from_work_dir="galaxy/*_odb10/translated_protein.fasta">
+            <filter>outputs and 'translated_protein' in outputs</filter>
+        </data>              
+    </outputs>
+
+    <tests>
+        <test expect_num_outputs="4">
+            <param name="input" value="small_genome.fasta"/>
+            <param name="mode" value="busco"/>
+            <param name="outputs" value="full_table_busco,full_table,miniprot,translated_protein"/>
+            <param name="busco_database" value="eukaryota"/>
+            <output name="full_table_busco">
+                <assert_contents>
+                    <has_text text="Busco id"/>
+                    <has_text text="Missing"/>
+                </assert_contents>
+            </output>
+            <output name="full_table">
+                <assert_contents>
+                    <has_text text="Gene"/>
+                    <has_text text="Missing"/>
+                </assert_contents>
+            </output>
+            <output name="miniprot">
+                <assert_contents>
+                    <has_text text="##gff-version 3"/>
+                </assert_contents>
+            </output>
+            <output name="translated_protein">
+                <assert_contents>
+                    <has_text text="GGWLIGNGGAGGSGAAGVNGGAGGNGGAGGNGGAGG"/>
+                    <has_text text="AAVFADRGAHVVLAVRNLEKGNAARARIMAARPGAHVTLQQLDLCSLDSVRAAADALRTAYPRIDVLINNAGVMW"/>
+                </assert_contents>
+            </output>
+        </test>
+    </tests>
+    <help><![CDATA[
+
+    compleasm_ assesses genome completeness based on genome assembly. 
+
+    .. _compleasm: https://github.com/huangnengCSU/compleasm
+
+    ]]>    
+    </help>
+    <expand macro="citation"/>
+</tool>

tools/compleasm/macros.xml

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+<macros>
+    <token name="@TOOL_VERSION@">0.2.5</token>
+    <token name="@VERSION_SUFFIX@">0</token>
+
+    <xml name="citation">
+        <citations>
+            <citation type="doi">10.1101/2023.06.03.543588</citation> 
+        </citations>
+    </xml>
+
+</macros>