Mercurial > repos > galaxy-australia > smudgeplot
changeset 4:5e0825476fb7 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc commit 72ae2e05f35098c4cb6dd4f038bff07fd36917ed
| author | iuc |
|---|---|
| date | Tue, 04 Apr 2023 17:23:19 +0000 |
| parents | 24e471d13fe9 |
| children | 5a0ddb4dc3a4 |
| files | smudgeplot.xml test-data/my_genome_smudgeplot_02.png test-data/test_reads_4.fasta.gz test-data/test_reads_5.fasta.gz |
| diffstat | 4 files changed, 32 insertions(+), 15 deletions(-) [+] |
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--- a/smudgeplot.xml Thu Jun 30 22:45:21 2022 +0000 +++ b/smudgeplot.xml Tue Apr 04 17:23:19 2023 +0000 @@ -3,7 +3,7 @@ <macros> <token name="@TOOL_VERSION@">0.2.5</token> - <token name="@VERSION_SUFFIX@">1</token> + <token name="@VERSION_SUFFIX@">2</token> </macros> <xrefs> @@ -16,6 +16,7 @@ </requirements> <command detect_errors="exit_code"><![CDATA[ + set -o pipefail; #if $file.input.input_select == 'reads' @@ -24,21 +25,17 @@ ## Jellyfish kmer count ## --------------------------------------------------------------------- - #if $file.input.reads[0].is_of_type("fastqsanger.gz") or $file.input.reads[0].is_of_type("fasta.gz") - gunzip -c + mkdir -p './files/' && + #if $file.input.reads[0].ext.endswith(".gz") + zcat #for $f in $file.input.reads - #if $f - '$f' - #end if - | jellyfish count -m 21 -t 4 -s 1M -o 1_counts.jf -C /dev/stdin + '$f' #end for - + | jellyfish count -m $file.input.mer_len -t \${GALAXY_SLOTS:-8} -s 1M -o 1_counts.jf -C /dev/stdin #else - jellyfish count -m 21 -t 4 -s 1M -o 1_counts.jf -C + jellyfish count -m $file.input.mer_len -t \${GALAXY_SLOTS:-8} -s 1M -o 1_counts.jf -C #for $f in $file.input.reads - #if $f - '$f' - #end if + '$f' #end for #end if @@ -47,13 +44,13 @@ ## Calculate lower and upper kmer count cutoffs ## --------------------------------------------------------------------- - #if $file.input.lower_cutoff is not None: + #if $file.input.lower_cutoff: && L=$file.input.lower_cutoff #else && L=\$(smudgeplot.py cutoff 1_kmer_k21.hist L) #end if - #if $file.input.upper_cutoff is not None: + #if $file.input.upper_cutoff: && U=$file.input.upper_cutoff #else && U=\$(smudgeplot.py cutoff 1_kmer_k21.hist U) @@ -77,7 +74,7 @@ ## --------------------------------------------------------------------- ## Plot - && smudgeplot.py plot 2_kmer_pairs_coverages.tsv -o my_genome + && smudgeplot.py plot $homozygous 2_kmer_pairs_coverages.tsv -o my_genome ]]></command> @@ -101,9 +98,18 @@ Don't worry about read pairing as it is not used in Kmer-counting. If selecting multiple datasets, please do not mix datatypes!" /> + + <param argument="--mer-len" + type="integer" + min="1" + value="21" + label="K-mer size" + help="The size of k-mers should be large enough allowing the k-mer to map uniquely to the genome" /> + <param name="lower_cutoff" + min="1" label="Lower kmer cutoff" type="integer" optional="true" @@ -115,6 +121,7 @@ <param name="upper_cutoff" + min="1" label="Upper kmer cutoff" type="integer" optional="true" @@ -135,6 +142,7 @@ </when> </conditional> </section> + <param argument="--homozygous" type="boolean" truevalue="--homozygous" falsevalue="" checked="false" label="Homozygous" help="Assume no heterozygosity in the genome - plotting a paralog structure." /> <param name="table_output" type="boolean" label="Output summary table"></param> <param name="verbose_output" type="boolean" label="Output verbose summary"></param> @@ -224,6 +232,15 @@ <param name="dump" value="dump.jf" ftype="txt"/> <output name="smudgeplot" ftype="png" file="my_genome_smudgeplot.png" compare="sim_size"/> </test> + <!-- Standard run without specifying cutoffs and compressed file --> + <test expect_num_outputs="2"> + <param name="input_select" value="reads"/> + <param name="reads" value="test_reads_4.fasta.gz,test_reads_5.fasta.gz"/> + <output name="smudgeplot" ftype="png" file="my_genome_smudgeplot_02.png" compare="sim_size"/> + <assert_stdout> + <has_text text="Dump with cutoffs L=10, U=70" /> + </assert_stdout> + </test> </tests> <help><![CDATA[