Mercurial > repos > galaxy-australia > smudgeplot
changeset 5:5a0ddb4dc3a4 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc commit 77e22c56f8da58853100ef1be59ba8d077ab1bf4
| author | iuc |
|---|---|
| date | Thu, 04 May 2023 16:33:09 +0000 |
| parents | 5e0825476fb7 |
| children | 015283de3004 |
| files | macros.xml smudgeplot.xml test-data/histogram.tabular test-data/kmerdb.meryldb test-data/my_genome_smudgeplot.png test-data/my_genome_smudgeplot_02.png test-data/my_genome_smudgeplot_03.png test-data/my_genome_smudgeplot_04.png |
| diffstat | 8 files changed, 194 insertions(+), 48 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros.xml Thu May 04 16:33:09 2023 +0000 @@ -0,0 +1,48 @@ +<macros> + <token name="@TOOL_VERSION@">0.2.5</token> + <token name="@VERSION_SUFFIX@">3</token> + <xml name="requirements"> + <requirements> + <requirement type="package" version="@TOOL_VERSION@">smudgeplot</requirement> + <requirement type="package" version="1.3">meryl</requirement> + <requirement type="package" version="2.3.0">kmer-jellyfish</requirement> + <requirement type="package" version="1.34">tar</requirement> + </requirements> + </xml> + <xml name="citations"> + <citations> + <citation type="doi">10.1038/s41467-020-14998-3</citation> + </citations> + </xml> + <xml name="xrefs"> + <xrefs> + <xref type="bio.tools">smudgeplots</xref> + </xrefs> + </xml> + + <xml name="cutoff_macro"> + <param + name="lower_cutoff" + min="1" + label="Lower kmer cutoff" + type="integer" + optional="true" + help="Optionally set a manual lower limit for filtering kmers with + smudgeplot hetkmers. If no value is set, a cutoff will be + estimated with smudgeplot cutoff. Use the GenomeScope tool to + visualize your kmer histogram when choosing cutoff values." + /> + + <param + name="upper_cutoff" + min="1" + label="Upper kmer cutoff" + type="integer" + optional="true" + help="Optionally set a manual upper limit for filtering kmers with + smudgeplot hetkmers. If no value is set, a cutoff will be + estimated with smudgeplot cutoff. Use the GenomeScope tool to + visualize your kmer histogram when choosing cutoff values." + /> + </xml> +</macros>
--- a/smudgeplot.xml Tue Apr 04 17:23:19 2023 +0000 +++ b/smudgeplot.xml Thu May 04 16:33:09 2023 +0000 @@ -1,19 +1,10 @@ -<tool id="smudgeplot" name="Smudgeplot" version="@TOOL_VERSION@+galaxy+@VERSION_SUFFIX@" profile="21.05"> +<tool id="smudgeplot" name="Smudgeplot" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05"> <description>inference of ploidy and heterozygosity structure using whole genome sequencing</description> - <macros> - <token name="@TOOL_VERSION@">0.2.5</token> - <token name="@VERSION_SUFFIX@">2</token> + <import>macros.xml</import> </macros> - - <xrefs> - <xref type="bio.tools">smudgeplots</xref> - </xrefs> - - <requirements> - <requirement type="package" version="@TOOL_VERSION@">smudgeplot</requirement> - <requirement type="package" version="2.3.0">kmer-jellyfish</requirement> - </requirements> + <expand macro="xrefs"/> + <expand macro="requirements"/> <command detect_errors="exit_code"><![CDATA[ set -o pipefail; @@ -63,11 +54,29 @@ && jellyfish dump -c -L \$L -U \$U 1_counts.jf > 2_dump.jf && smudgeplot.py hetkmers -o 2_kmer_pairs 2_dump.jf + #else + #if $file.input.input_mode.selector == 'meryl' + tar -zxf '${file.input.input_mode.meryl_database}' -C ./ && + #if $file.input.input_mode.lower_cutoff: + L=$file.input.input_mode.lower_cutoff && + #else + L=\$(smudgeplot.py cutoff '${file.input.input_mode.meryl_histogram}' L) && + #end if - ## ~~~~~~~~~~~~~~~~~~~ Use provided kmer dump ~~~~~~~~~~~~~~~~~~~~~~~~~~ + #if $file.input.input_mode.upper_cutoff: + U=$file.input.input_mode.upper_cutoff && + #else + U=\$(smudgeplot.py cutoff '${file.input.input_mode.meryl_histogram}' U) && + #end if - smudgeplot.py hetkmers -o 2_kmer_pairs '$file.input.dump' + meryl print less-than \$U greater-than \$L threads=\${GALAXY_SLOTS:-8} memory=\$((\${GALAXY_MEMORY_MB:-8192}/1024)) read-db.meryl | sort > meryl.dump && + smudgeplot.py hetkmers -o 2_kmer_pairs < meryl.dump + + #else + + smudgeplot.py hetkmers -o 2_kmer_pairs '$file.input.input_mode.dump' + #end if #end if @@ -106,39 +115,31 @@ label="K-mer size" help="The size of k-mers should be large enough allowing the k-mer to map uniquely to the genome" /> + <expand macro="cutoff_macro"/> - <param - name="lower_cutoff" - min="1" - label="Lower kmer cutoff" - type="integer" - optional="true" - help="Optionally set a manual lower limit for filtering kmers with - smudgeplot hetkmers. If no value is set, a cutoff will be - estimated with smudgeplot cutoff. Use the GenomeScope tool to - visualize your kmer histogram when choosing cutoff values." - /> - - <param - name="upper_cutoff" - min="1" - label="Upper kmer cutoff" - type="integer" - optional="true" - help="Optionally set a manual upper limit for filtering kmers with - smudgeplot hetkmers. If no value is set, a cutoff will be - estimated with smudgeplot cutoff. Use the GenomeScope tool to - visualize your kmer histogram when choosing cutoff values." - /> </when> <when value="dump"> - <param - name="dump" type="data" format="txt" - label="Kmer dump" - help="Upload your own Kmer dump file created with the Jellyfish or KMC tool. - This enables control over kmer-counting parameters." - /> + <conditional name="input_mode"> + <param name="selector" type="select" label="Input mode"> + <option value="default">Default k-mer dump dataset</option> + <option value="meryl">Meryl database</option> + </param> + <when value="default"> + <param + name="dump" type="data" format="txt" + label="Kmer dump" + help="Upload your own Kmer dump file created with the Jellyfish or KMC tool. + This enables control over kmer-counting parameters." + /> + </when> + <when value="meryl"> + <param argument="meryl_histogram" type="data" format="tabular" label="Meryl histogram"/> + <param argument="meryl_database" type="data" format="meryldb" label="Meryl database"/> + <expand macro="cutoff_macro"/> + </when> + </conditional> + </when> </conditional> </section> @@ -229,7 +230,10 @@ <!-- K-mer dump input --> <test expect_num_outputs="2"> <param name="input_select" value="dump"/> - <param name="dump" value="dump.jf" ftype="txt"/> + <conditional name="input_mode"> + <param name="selector" value="default"/> + <param name="dump" value="dump.jf" ftype="txt"/> + </conditional> <output name="smudgeplot" ftype="png" file="my_genome_smudgeplot.png" compare="sim_size"/> </test> <!-- Standard run without specifying cutoffs and compressed file --> @@ -241,6 +245,28 @@ <has_text text="Dump with cutoffs L=10, U=70" /> </assert_stdout> </test> + <!-- K-mer dump meryl input --> + <test expect_num_outputs="2"> + <param name="input_select" value="dump"/> + <conditional name="input_mode"> + <param name="selector" value="meryl"/> + <param name="meryl_histogram" value="histogram.tabular" ftype="tabular"/> + <param name="meryl_database" value="kmerdb.meryldb" ftype="meryldb"/> + </conditional> + <output name="smudgeplot" ftype="png" file="my_genome_smudgeplot_03.png" compare="sim_size"/> + </test> + <!-- K-mer dump meryl input with specific cutoff--> + <test expect_num_outputs="2"> + <param name="input_select" value="dump"/> + <conditional name="input_mode"> + <param name="selector" value="meryl"/> + <param name="meryl_histogram" value="histogram.tabular" ftype="tabular"/> + <param name="meryl_database" value="kmerdb.meryldb" ftype="meryldb"/> + <param name="lower_cutoff" value="2"/> + <param name="upper_cutoff" value="2500000"/> + </conditional> + <output name="smudgeplot" ftype="png" file="my_genome_smudgeplot_04.png" compare="sim_size"/> + </test> </tests> <help><![CDATA[ @@ -303,7 +329,5 @@ - ``smudgeplot.py plot kmer_pairs_coverages.tsv -o my_genome`` ]]></help> - <citations> - <citation type="doi">10.1038/s41467-020-14998-3</citation> - </citations> + <expand macro="citations"/> </tool>
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