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Commit message:
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 7132f1d3fddf9c07282e69b3c0d5c71f61d24947" |
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modified:
hifiasm.xml |
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| diff -r f3c89da3af16 -r 9ef6920c3089 hifiasm.xml --- a/hifiasm.xml Sun Jun 20 21:18:55 2021 +0000 +++ b/hifiasm.xml Thu Jun 24 19:42:15 2021 +0000 |
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| @@ -1,7 +1,7 @@ <tool id="hifiasm" name="Hifiasm" version="@VERSION@+galaxy0"> <description>haplotype-resolved de novo assembler for PacBio Hifi reads</description> <macros> - <token name="@VERSION@">0.15.3</token> + <token name="@VERSION@">0.15.4</token> <token name="@FORMATS@">fasta,fasta.gz,fastq,fastq.gz</token> <xml name="reads"> <param name="reads" type="data" format="@FORMATS@" multiple="true" label="Input reads" /> @@ -98,12 +98,15 @@ #if $hic_partition.f_perturb: --f-perturb $hic_partition.f_perturb #end if + --l-msjoin $hic_partition.l_msjoin #end if ## Changed the default outputs of hifiasm. Hifiasm outputs a primary assembly and two balanced haplotypes in default. Incorporated the option '--primary' to output primary assembly and alternate assembly. --primary $input_filenames - + #if $log_out: + 2> output.log + #end if ]]> </command> <inputs> @@ -125,7 +128,6 @@ </when> </conditional> <param name="filter_bits" argument="-f" type="integer" min="0" value="37" label="Bits for bloom filter" help="A value of 0 disables the bloom filter" /> - <conditional name="advanced_options"> <param name="advanced_selector" type="select" label="Advanced options"> <option value="blank">Leave default</option> @@ -194,9 +196,10 @@ <param argument="--n-weight" type="integer" min="1" value="" optional="true" label="Rounds of reweighting Hi-C links" /> <param argument="--n-perturb" type="integer" min="1" value="" optional="true" label="Rounds of perturbation" /> <param argument="--f-perturb" type="float" min="0" max="1" value="" optional="true" label="Fraction to flip for perturbation" /> - </when> + <param argument="--l-msjoin" type="integer" min="0" value="500000" label="Detect misjoined unitigs of greater than or equal to specified size" help="A value of 0 disables this filter"/> + </when> </conditional> - + <param name="log_out" type="boolean" label="Output log file?" truevalue="yes" falsevalue="no"/> </inputs> <outputs> <data name="raw_unitigs" format="gfa1" from_work_dir="output.r_utg.gfa" label="${tool.name} on ${on_string}, haplotype-resolved raw unitig graph"> @@ -230,6 +233,9 @@ <data name="hic_balanced_contig_hap2_graph" format="gfa1" from_work_dir="output.bp.hap2.p_ctg.gfa" label="${tool.name} ${on_string}, HI-C hap2 balanced contig graph hap2"> <filter>hic_partition['hic_partition_selector'] == 'set'</filter> </data> + <data name="log_file" format="txt" from_work_dir="output.log" label="${tool.name} ${on_string}, log file"> + <filter>log_out</filter> + </data> </outputs> <tests> <test> @@ -258,9 +264,29 @@ </assert_contents> </output> </test> + <!-- Test logfile out--> + <test> + <param name="reads" value="hifiasm-in1.fa.gz" ftype="fasta.gz" /> + <param name="filter_bits" value="0" /> + <param name="mode_selector" value="standard" /> + <param name="log_out" value="yes"/> + <output name="raw_unitigs" file="hifiasm-out1-raw.gfa" ftype="gfa1" /> + <output name="processed_unitigs" file="hifiasm-out1-processed.gfa" ftype="gfa1" /> + <output name="primary_contig_graph" file="hifiasm-out1-primary.gfa" ftype="gfa1" /> + <output name="alternate_contig_graph" ftype="gfa1"> + <assert_contents> + <has_size value="0"/> + </assert_contents> + </output> + <output name="log_file" ftype="txt"> + <assert_contents> + <has_line line="[M::main] CMD: hifiasm -t 1 -o output -f 0 --primary input_0.fasta.gz"/> + </assert_contents> + </output> + </test> <!-- Test Hi-C - <test> + <test> <param name="reads" value="hifiasm-in1.fa.gz" ftype="fasta.gz" /> <param name="filter_bits" value="0" /> <param name="mode_selector" value="standard" /> |