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New tool addition: MerquryFK ASMPlot (#6786)
* Add ASMplot * Add associated test-data * Minor changes to description and added single quotes to parameters
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| <tool id="merquryfk_asmplot" name="MerquryFK ASMplot" version="@VERSION@+galaxy@VERSION_SUFFIX@" profile="24.2"> | ||
| <description>Analyzes k-mer spectra for unique, shared, and missing k-mers</description> | ||
| <macros> | ||
| <import>macros.xml</import> | ||
| </macros> | ||
| <expand macro="requirements"/> | ||
| <command detect_errors="exit_code"><![CDATA[ | ||
| #set ASSEMBLY1="assembly."+$assembly_1.ext | ||
| ln -s '$reads' assembly.ktab && | ||
| ln -s '$assembly_1' $ASSEMBLY1 && | ||
| #if $assembly_2: | ||
| #set ASSEMBLY2="assembly2."+$assembly_2.ext | ||
| ln -s '$assembly_2' $ASSEMBLY2 && | ||
| #end if | ||
| ln -s '$fastk_ktab_files' ktab_files.tar.gz && | ||
| tar -xf ktab_files.tar.gz -C '.' && | ||
| ASMplot | ||
| @PLOTS@ | ||
| @MEASURE@ | ||
| @GRAPHS@ | ||
| -T\${GALAXY_SLOTS:-1} | ||
| assembly.ktab | ||
| '$ASSEMBLY1' | ||
| #if $assembly_2: | ||
| $ASSEMBLY2 | ||
| #end if | ||
| asmplot | ||
| ]]></command> | ||
| <inputs> | ||
| <param name="reads" type="data" format="fastk_ktab" label="K-mer table (ktab) obtained from FastK tool"/> | ||
| <param name="fastk_ktab_files" type="data" format="fastk_ktab_tar" label="Select the TAR file consisting of all intermediate Ktab file from FastK"/> | ||
| <param name="assembly_1" type="data" format="fasta,fasta.gz" label="Assembly of genome" help="Must be same genome as the K-mer table was generated from"/> | ||
| <param name="assembly_2" type="data" format="fasta,fasta.gz" label="Additional assembly file" optional="true" help="Additional genome against which to compare"/> | ||
| <expand macro="plots"/> | ||
| <expand macro="sizes"/> | ||
| <expand macro="graphs"/> | ||
| <expand macro="pdf"/> | ||
| </inputs> | ||
| <outputs> | ||
| <collection name="outputs_png" type="list" label="${tool.name} on ${on_string}: PNG figures"> | ||
| <filter>pdf is not True</filter> | ||
| <discover_datasets pattern="(?P<designation>.*).png" format="png"/> | ||
| </collection> | ||
| <collection name="outputs_pdf" type="list" label="${tool.name} on ${on_string}: PDF figures"> | ||
| <filter>pdf is True</filter> | ||
| <discover_datasets pattern="(?P<designation>.*).pdf" format="pdf"/> | ||
| </collection> | ||
| </outputs> | ||
| <tests> | ||
| <test expect_num_outputs="1"> | ||
| <param name="reads" value="assembly.ktab"/> | ||
| <param name="fastk_ktab_files" ftype="fastk_ktab_tar" location="https://zenodo.org/records/14905247/files/asmplot_ktab.tar.gz"/> | ||
| <param name="assembly_1" value="assembly.fasta.gz"/> | ||
| <param name="width" value="6.0"/> | ||
| <param name="height" value="4.5"/> | ||
| <param name="graphs" value="-l,-f,-s"/> | ||
| <param name="pdf" value="False"/> | ||
| <conditional name="measure"> | ||
| <param name="measurement" value="absolute"/> | ||
| <param name="max_x" value="2"/> | ||
| <param name="max_y" value="1"/> | ||
| </conditional> | ||
| <output_collection name="outputs_png" type="list" count="3"/> | ||
| </test> | ||
| <test expect_num_outputs="1"> | ||
| <param name="reads" value="assembly.ktab"/> | ||
| <param name="fastk_ktab_files" ftype="fastk_ktab_tar" location="https://zenodo.org/records/14905247/files/asmplot_ktab.tar.gz"/> | ||
| <param name="assembly_1" value="assembly.fasta.gz"/> | ||
| <param name="assembly_2" value="assembly_2.fasta.gz"/> | ||
| <param name="width" value="6.0"/> | ||
| <param name="height" value="4.5"/> | ||
| <param name="graphs" value="-l,-f,-s"/> | ||
| <param name="pdf" value="False"/> | ||
| <conditional name="measure"> | ||
| <param name="measurement" value="absolute"/> | ||
| <param name="max_x" value="2"/> | ||
| <param name="max_y" value="1"/> | ||
| </conditional> | ||
| <output_collection name="outputs_png" type="list" count="3"/> | ||
| </test> | ||
| <test expect_num_outputs="1"> | ||
| <param name="reads" value="assembly.ktab"/> | ||
| <param name="fastk_ktab_files" ftype="tar" location="https://zenodo.org/records/14905247/files/asmplot_ktab.tar.gz"/> | ||
| <param name="assembly_1" value="assembly.fasta.gz"/> | ||
| <param name="assembly_2" value="assembly_2.fasta.gz"/> | ||
| <param name="width" value="6.0"/> | ||
| <param name="height" value="4.5"/> | ||
| <param name="graphs" value="-l,-f,-s"/> | ||
| <param name="pdf" value="True"/> | ||
| <conditional name="measure"> | ||
| <param name="measurement" value="absolute"/> | ||
| <param name="max_x" value="2"/> | ||
| <param name="max_y" value="1"/> | ||
| </conditional> | ||
| <output_collection name="outputs_pdf" type="list" count="3"/> | ||
| </test> | ||
| </tests> | ||
| <help><![CDATA[ | ||
| ASMplot looks at the spectra of the k-mers that: | ||
| (a) are in neither genome assembly file or the additional assembly file, | ||
| (b) in genome assembly file but not the additional assembly file, | ||
| (c) in the additional assembly file but not genome assembly file, and | ||
| (d) in both genome assembly file and the additional assembly file. | ||
| If the second assembly file is missing, then it looks at the spectra of the read k-mers that are and are not in the first assembly file. | ||
| ]]></help> | ||
| <expand macro="citation"/> | ||
| </tool> |
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