Mercurial > repos > bgruening > hifiasm
diff hifiasm.xml @ 1:6505bd37670d draft
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 1122ef1b9a407a781d1416d07b272016d16a6a85"
| author | bgruening |
|---|---|
| date | Wed, 03 Mar 2021 16:16:42 +0000 |
| parents | bf0a4667e3ce |
| children | f3c89da3af16 |
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--- a/hifiasm.xml Tue Mar 02 20:23:49 2021 +0000 +++ b/hifiasm.xml Wed Mar 03 16:16:42 2021 +0000 @@ -1,10 +1,10 @@ -<tool id="hifiasm" name="Hifiasm" version="@VERSION@"> +<tool id="hifiasm" name="Hifiasm" version="@VERSION@+galaxy0"> <description>de novo assembler</description> <macros> <token name="@VERSION@">0.14</token> <token name="@FORMATS@">fasta,fasta.gz,fastq,fastq.gz</token> <xml name="reads"> - <param name="reads" type="data" format="@FORMATS@" label="Input reads" /> + <param name="reads" type="data" format="@FORMATS@" multiple="true" label="Input reads" /> </xml> </macros> <requirements> @@ -14,15 +14,35 @@ <version_command>hifiasm --version</version_command> <command detect_errors="exit_code"> <![CDATA[ - #if str($mode.mode_selector) == 'standard': - ln -s '$mode.reads' input.${mode.reads.extension} && - #else: - ln -s '$mode.hap1_reads' hap1_reads.${mode.hap1_reads.extension} && - ln -s '$mode.hap2_reads' hap2_reads.${mode.hap2_reads.extension} && - yak count -k31 -b37 -t\${GALAXY_SLOTS:-1} -o hap1.yak hap1_reads.${mode.hap1_reads.extension} && - yak count -k31 -b37 -t\${GALAXY_SLOTS:-1} -o hap2.yak hap2_reads.${mode.hap2_reads.extension} && + #set $input_files = list() + #set $hap1_inputs = list() + #set $hap2_inputs = list() + #for idx, read in enumerate($mode.reads): + #set $inputfile = 'input_%d.%s' % ($idx, $read.dataset.extension) + ln -s '$read' $inputfile && + $input_files.append($inputfile) + #end for + #set $input_filenames = ' '.join($input_files) + #if str($mode.mode_selector) == 'trio': + #for idx, read in enumerate($mode.hap1_reads): + #set $inputfile = 'hap1_input_%d.%s' % ($idx, $read.dataset.extension) + ln -s '$read' $inputfile && + $hap1_inputs.append($inputfile) + #end for + #for idx, read in enumerate($mode.hap2_reads): + #set $inputfile = 'hap2_input_%d.%s' % ($idx, $read.dataset.extension) + ln -s '$read' $inputfile && + $hap2_inputs.append($inputfile) + #end for + #set $hap1_filenames = ' '.join($hap1_inputs) + #set $hap2_filenames = ' '.join($hap2_inputs) + yak count -k31 -b37 -t\${GALAXY_SLOTS:-1} -o hap1.yak $hap1_filenames && + yak count -k31 -b37 -t\${GALAXY_SLOTS:-1} -o hap2.yak $hap2_filenames && #end if - hifiasm -i input.${mode.reads.extension} -t \${GALAXY_SLOTS:-1} -o output -f $filter_bits + hifiasm -i $input_filenames -t \${GALAXY_SLOTS:-1} -o output -f $filter_bits + #if str($mode.mode_selector) == 'trio': + -1 hap1.yak -2 hap2.yak + #end if #if str($advanced_options.advanced_selector) == 'set': -z $advanced_options.adapter_length -k $advanced_options.kmer_length @@ -39,7 +59,6 @@ -x $assembly_options.max_overlap -y $assembly_options.min_overlap $assembly_options.disable_post_join - --pb-range $assembly_options.pb_range #end if #if str($mode.mode_selector) == 'trio': -1 hap1.yak @@ -69,8 +88,8 @@ </when> <when value="trio"> <expand macro="reads" /> - <param name="hap1_reads" type="data" format="fastq,fastq.gz" label="Haplotype 1 reads" /> - <param name="hap2_reads" type="data" format="fastq,fastq.gz" label="Haplotype 2 reads" /> + <param name="hap1_reads" type="data" format="fastq,fastq.gz" multiple="true" label="Haplotype 1 reads" /> + <param name="hap2_reads" type="data" format="fastq,fastq.gz" multiple="true" label="Haplotype 2 reads" /> <param name="max_kmers" argument="-c" type="integer" value="2" label="Lower bound of the binned k-mer's frequency" /> <param name="min_kmers" argument="-d" type="integer" value="5" label="Upper bound of the binned k-mer's frequency" /> </when> @@ -105,7 +124,6 @@ <param name="max_overlap" argument="-x" type="float" min="0" max="1" value="0.8" label="Maximum overlap drop ratio" /> <param name="min_overlap" argument="-y" type="float" min="0" max="1" value="0.2" label="Minimum overlap drop ratio" /> <param name="disable_post_join" argument="-u" type="boolean" truevalue="-u" falsevalue="" label="Skip post join contigs step" help="May improve N50" /> - <param argument="--pb-range" type="integer" min="0" max="100" value="0" label="Inconsistent contigs" help="If this option is set to a value greater than zero the tool generates an additional BED dataset containing regions that are >= x% inconsistent." /> </when> </conditional> <conditional name="purge_options"> @@ -128,25 +146,25 @@ </conditional> </inputs> <outputs> - <data name="raw_unitigs" format="gfa1" from_work_dir="output.r_utg.gfa" label="${tool.name} on ${on_string} Haplotype-resolved raw unitig graph"> + <data name="raw_unitigs" format="gfa1" from_work_dir="output.r_utg.gfa" label="${tool.name} on ${on_string}, haplotype-resolved raw unitig graph"> <filter>mode['mode_selector'] == 'standard'</filter> </data> - <data name="raw_unitigs" format="gfa1" from_work_dir="output.dip.r_utg.gfa" label="${tool.name} on ${on_string} Haplotype-resolved raw unitig graph"> + <data name="raw_unitigs" format="gfa1" from_work_dir="output.dip.r_utg.gfa" label="${tool.name} on ${on_string}, haplotype-resolved raw unitig graph"> <filter>mode['mode_selector'] == 'trio'</filter> </data> - <data name="processed_unitigs" format="gfa1" from_work_dir="output.p_utg.gfa" label="${tool.name} on ${on_string} Processed unitig graph"> + <data name="processed_unitigs" format="gfa1" from_work_dir="output.p_utg.gfa" label="${tool.name} on ${on_string}, processed unitig graph"> <filter>mode['mode_selector'] == 'standard'</filter> </data> - <data name="primary_contig_graph" format="gfa1" from_work_dir="output.p_ctg.gfa" label="${tool.name} on ${on_string} Primary assembly contig graph"> + <data name="primary_contig_graph" format="gfa1" from_work_dir="output.p_ctg.gfa" label="${tool.name} on ${on_string}, primary assembly contig graph"> <filter>mode['mode_selector'] == 'standard'</filter> </data> - <data name="alternate_contig_graph" format="gfa1" from_work_dir="output.a_ctg.gfa" label="${tool.name} on ${on_string} Alternate assembly contig graph"> + <data name="alternate_contig_graph" format="gfa1" from_work_dir="output.a_ctg.gfa" label="${tool.name} on ${on_string}, alternate assembly contig graph"> <filter>mode['mode_selector'] == 'standard'</filter> </data> - <data name="hap1_contigs" format="gfa1" from_work_dir="output.hap1.p_ctg.gfa" label="${tool.name} ${mode.hap1_reads.name} contig graph"> + <data name="hap1_contigs" format="gfa1" from_work_dir="output.hap1.p_ctg.gfa" label="${tool.name} ${mode.hap1_reads.name}, contig graph"> <filter>mode['mode_selector'] == 'trio'</filter> </data> - <data name="hap2_contigs" format="gfa1" from_work_dir="output.hap2.p_ctg.gfa" label="${tool.name} ${mode.hap2_reads.name} contig graph"> + <data name="hap2_contigs" format="gfa1" from_work_dir="output.hap2.p_ctg.gfa" label="${tool.name} ${mode.hap2_reads.name}, contig graph"> <filter>mode['mode_selector'] == 'trio'</filter> </data> </outputs> @@ -160,6 +178,15 @@ <output name="primary_contig_graph" file="hifiasm-out1-primary.gfa" ftype="gfa1" /> <output name="alternate_contig_graph" file="hifiasm-out1-alternate.gfa" ftype="gfa1" /> </test> + <test> + <param name="reads" value="hifiasm-in2-0.fa.gz,hifiasm-in2-1.fa.gz,hifiasm-in2-2.fa.gz,hifiasm-in2-3.fa.gz,hifiasm-in2-4.fa.gz" ftype="fasta.gz" /> + <param name="filter_bits" value="0" /> + <param name="mode_selector" value="standard" /> + <output name="raw_unitigs" file="hifiasm-out2-raw.gfa" ftype="gfa1" /> + <output name="processed_unitigs" file="hifiasm-out2-processed.gfa" ftype="gfa1" /> + <output name="primary_contig_graph" file="hifiasm-out2-primary.gfa" ftype="gfa1" /> + <output name="alternate_contig_graph" file="hifiasm-out2-alternate.gfa" ftype="gfa1" /> + </test> </tests> <help><![CDATA[ *********************************** @@ -196,7 +223,6 @@ - *Maximum overlap drop ratio* - *Minimum overlap drop ratio* - *Skip post join contigs step* disable post join contigs step which may improve N50 -- *Inconsistent contigs* If this option is set to a value greater than zero the tool generates an additional BED dataset containing regions that are >= x% inconsistent. #### Options for purging duplicates - *Purge level* 0: no purging; 1: light; 2: aggressive [0 for trio; 2 for unzip]