Mercurial > repos > iuc > winnowmap
changeset 2:35ea4a8b1ea6 draft default tip
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f12e139eb362fea66360aefbbc678197e2440139"
author | iuc |
---|---|
date | Tue, 13 Jul 2021 12:16:19 +0000 |
parents | 44231ef8167a |
children | |
files | test-data/all_fasta.loc test-data/winnowmap-self-homology.bam test-data/winnowmap-test1-fasta.bam test-data/winnowmap-test1-fasta.cram test-data/winnowmap-test1.bam test-data/winnowmap-test2-fasta.bam test-data/winnowmap-test2.bam winnowmap.xml |
diffstat | 8 files changed, 50 insertions(+), 11 deletions(-) [+] |
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--- a/test-data/all_fasta.loc Mon May 10 19:28:32 2021 +0000 +++ b/test-data/all_fasta.loc Tue Jul 13 12:16:19 2021 +0000 @@ -1,1 +1,1 @@ -bwa-mem-mt-genome bwa-mem-mt-genome bwa-mem-mt-genome ${__HERE__}/bwa-mem-mt-genome.fa \ No newline at end of file +bwa-mem-mt-genome bwa-mem-mt-genome-dbkey bwa-mem-mt-genome-display ${__HERE__}/bwa-mem-mt-genome.fa \ No newline at end of file
--- a/winnowmap.xml Mon May 10 19:28:32 2021 +0000 +++ b/winnowmap.xml Tue Jul 13 12:16:19 2021 +0000 @@ -1,4 +1,4 @@ -<tool id="winnowmap" name="Winnowmap" version="@TOOL_VERSION@+galaxy0" profile="20.01"> +<tool id="winnowmap" name="Winnowmap" version="@TOOL_VERSION@+galaxy1" profile="20.05"> <description>a mapping tool optimized for repetitive sequences</description> <macros> <import>macros.xml</import> @@ -145,6 +145,7 @@ #if $io_options.output_format == 'BAM': -a | samtools sort + --no-PG -@\${GALAXY_SLOTS:-2} -T "\${TMPDIR:-.}" -O $io_options.output_format @@ -152,6 +153,7 @@ #else if $io_options.output_format == 'CRAM': -a | samtools sort + --no-PG -T "\${TMPDIR:-.}" -@\${GALAXY_SLOTS:-2} -O $io_options.output_format @@ -229,7 +231,7 @@ <param argument="-I" type="integer" min="1" optional="true" label="Split index for every N input gigabases" help=""/> </section> <section name="mapping_options" title="Mapping options" help="Sets -f, -g, -F, -r, -n, -m, -X, -p, --sv-off and --min-occ-floor options." expanded="False"> - <param name="sv_off" argument="--sv-off" type="boolean" truevalue="--sv-off" falsevalue="" checked="False" label="Turn off SV-aware mode" help="SV aware k-mer search allows to find approximate mapping locations for a read"/> + <param argument="--sv-off" type="boolean" truevalue="--sv-off" falsevalue="" checked="False" label="Turn off SV-aware mode" help="SV aware k-mer search allows to find approximate mapping locations for a read"/> <param argument="-F" type="integer" min="0" value="" optional="true" label="Max fragment length for PE alignment" help="The maximum apparent fragment length up to which paired-end reads are aligned together; at higher fragment lengths the mates will be aligned independent of each other; effective only for paired-end data and when spliced alignment mode is turned off; default=800" /> @@ -361,7 +363,7 @@ </conditional> </actions> <change_format> - <when input="io_options.output_format" value="paf" format="tabular" /> + <when input="io_options.output_format" value="paf" format="paf" /> <when input="io_options.output_format" value="CRAM" format="cram" /> </change_format> </data> @@ -375,18 +377,34 @@ <param name="fastq_input1" ftype="fastqsanger" value="bwa-mem-fasta1.fa"/> <param name="highfreq_kmers" ftype="tabular" value="repetitive_k15.txt"/> <param name="analysis_type_selector" value="map-ont"/> - <output name="alignment_output" ftype="bam" file="winnowmap-test1-fasta.bam" lines_diff="2" /> + <param name="min_occ_floor" value="1000"/> + <section name="alignment_options"> + <param name="min_occ_floor" value="1000"/> + <param name="A" value="2"/> + <param name="B" value="8"/> + <param name="O" value="12"/> + <param name="O2" value="32"/> + <param name="E" value="2"/> + <param name="E2" value="1"/> + <param name="z" value="400"/> + <param name="s" value="40"/> + </section> + <output name="alignment_output" ftype="bam" file="winnowmap-test1-fasta.bam" lines_diff="2" > + <metadata name="dbkey" value="?" /> + </output> </test> <test> <!-- test cram output --> <param name="reference_source_selector" value="history" /> - <param name="ref_file" ftype="fasta" value="bwa-mem-mt-genome.fa"/> + <param name="ref_file" ftype="fasta" value="bwa-mem-mt-genome.fa" dbkey="hg19"/> <param name="fastq_input_selector" value="single"/> <param name="fastq_input1" ftype="fastqsanger" value="bwa-mem-fasta1.fa"/> <param name="highfreq_kmers" ftype="tabular" value="repetitive_k15.txt"/> <param name="analysis_type_selector" value="map-ont"/> <param name="output_format" value="CRAM"/> - <output name="alignment_output" ftype="cram" file="winnowmap-test1-fasta.cram" compare="sim_size" /> + <output name="alignment_output" ftype="cram" file="winnowmap-test1-fasta.cram" lines_diff="2"> + <metadata name="dbkey" value="hg19" /> + </output> </test> <test> <!-- test paired input --> @@ -422,17 +440,30 @@ </collection> </param> <param name="highfreq_kmers" ftype="tabular" value="repetitive_k15.txt"/> - <output name="alignment_output" ftype="bam" file="winnowmap-test2.bam" lines_diff="2" /> + <output name="alignment_output" ftype="bam" file="winnowmap-test2.bam" lines_diff="2"/> </test> <test> <!-- test data table reference --> <param name="reference_source_selector" value="cached" /> - <param name="ref_file" value="bwa-mem-mt-genome"/> + <param name="ref_file" value="bwa-mem-mt-genome" dbkey="hg19"/> <param name="fastq_input_selector" value="single"/> <param name="fastq_input1" ftype="fastqsanger" value="bwa-mem-fasta1.fa"/> <param name="highfreq_kmers" ftype="tabular" value="repetitive_k15.txt"/> <param name="analysis_type_selector" value="map-ont"/> - <output name="alignment_output" ftype="bam" file="winnowmap-test1-fasta.bam" lines_diff="2" /> + <section name="alignment_options"> + <param name="min_occ_floor" value="1000"/> + <param name="A" value="2"/> + <param name="B" value="8"/> + <param name="O" value="12"/> + <param name="O2" value="32"/> + <param name="E" value="2"/> + <param name="E2" value="1"/> + <param name="z" value="400"/> + <param name="s" value="40"/> + </section> + <output name="alignment_output" ftype="bam" file="winnowmap-test1-fasta.bam" lines_diff="2" > + <metadata name="dbkey" value="bwa-mem-mt-genome-dbkey" /> + </output> </test> <test> <!-- test alignment options --> @@ -457,6 +488,14 @@ <param name="s" value="40" /> </section> <output name="alignment_output" ftype="bam" file="winnowmap-test1-fasta.bam" lines_diff="2" /> + <assert_command> + <has_text text="-A 2"/> + <has_text text="-B 8"/> + <has_text text="-O 12,32"/> + <has_text text="-E 2,1"/> + <has_text text="-z 400"/> + <has_text text="-s 40"/> + </assert_command> </test> <test> <!-- test paf output --> @@ -467,7 +506,7 @@ <param name="highfreq_kmers" ftype="tabular" value="repetitive_k15.txt"/> <param name="analysis_type_selector" value="map-ont"/> <param name="output_format" value="paf"/> - <output name="alignment_output" ftype="tabular" file="mini_reads.paf" /> + <output name="alignment_output" ftype="paf" file="mini_reads.paf" /> </test> <test> <!-- test self-homology mode -->