Mercurial > repos > bgruening > hifiasm
changeset 16:41cea2aa2dce draft
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 7dca92baf6a91f10bced28b883f14d3f4d7630c5
| author | bgruening |
|---|---|
| date | Fri, 20 Oct 2023 22:03:32 +0000 |
| parents | 60024a528cbd |
| children | 0ee0c3089254 |
| files | hifiasm.xml test-data/maternal.headers.txt test-data/paternal.headers.txt |
| diffstat | 3 files changed, 272 insertions(+), 22 deletions(-) [+] |
line wrap: on
line diff
--- a/hifiasm.xml Fri Oct 13 07:26:01 2023 +0000 +++ b/hifiasm.xml Fri Oct 20 22:03:32 2023 +0000 @@ -2,7 +2,7 @@ <description>haplotype-resolved de novo assembler for PacBio Hifi reads</description> <macros> <token name="@TOOL_VERSION@">0.19.7</token> - <token name="@VERSION_SUFFIX@">0</token> + <token name="@VERSION_SUFFIX@">1</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" /> @@ -50,20 +50,26 @@ #end for #end if #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 -k$mode.yak_kmer_length -b$filter_bits -t\${GALAXY_SLOTS:-1} -o hap1.yak $hap1_filenames && - yak count -k$mode.yak_kmer_length -b$filter_bits -t\${GALAXY_SLOTS:-1} -o hap2.yak $hap2_filenames && + #if str($mode.trioinput.trio_input_selector) == 'reads': + #for idx, read in enumerate($mode.trioinput.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.trioinput.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 -k$mode.yak_kmer_length -b$filter_bits -t\${GALAXY_SLOTS:-1} -o hap1.yak $hap1_filenames && + yak count -k$mode.yak_kmer_length -b$filter_bits -t\${GALAXY_SLOTS:-1} -o hap2.yak $hap2_filenames && + #end if + #if str($mode.trioinput.trio_input_selector) == 'lists': + #set $hap1_filenames = $mode.trioinput.hap1_list + #set $hap2_filenames = $mode.trioinput.hap2_list + #end if #end if hifiasm -t \${GALAXY_SLOTS:-1} @@ -99,10 +105,17 @@ #end if #end if #if str($mode.mode_selector) == 'trio': - -1 hap1.yak - -2 hap2.yak + #if str($mode.trioinput.trio_input_selector) == 'reads': + -1 hap1.yak + -2 hap2.yak + #end if + #if str($mode.trioinput.trio_input_selector) == 'lists': + -3 $hap1_filenames + -4 $hap2_filenames + #end if -c $mode.max_kmers -d $mode.min_kmers + $mode.trio_dual #end if #if str($purge_options.purge_selector) == 'set': -l $purge_options.purge_level @@ -175,11 +188,24 @@ </when> <when value="trio"> <expand macro="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" /> + <conditional name="trioinput"> + <param name="trio_input_selector" type="select" label="What parental information are you using?"> + <option value="reads">Parental reads (FASTQ files, gzipped or otherwise)</option> + <option value="lists">Lists of reads assigned by parent (text files)</option> + </param> + <when value="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" /> + </when> + <when value="lists"> + <param name="hap1_list" type="data" format="txt,tabular" label="Haplotype 1 read list" /> + <param name="hap2_list" type="data" format="txt,tabular" label="Haplotype 2 read list" /> + </when> + </conditional> <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" /> <param name="yak_kmer_length" type="integer" min="0" max="64" value="31" label="Yak counter k-mer length" /> + <param name="trio_dual" argument="--trio-dual" type="boolean" truevalue="--trio-dual" falsevalue="" label="Utilize homology information to correct trio-phasing errors" /> </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" /> @@ -428,9 +454,12 @@ <param name="filter_bits" value="0"/> <conditional name="mode"> <param name="mode_selector" value="trio"/> - <param name="reads" value="child.fasta.gz"/> - <param name="hap1_reads" value="paternal.fasta.gz"/> - <param name="hap2_reads" value="maternal.fasta.gz"/> + <param name="trio_input_selector" value="reads"/> + <conditional name="trioinput"> + <param name="reads" value="child.fasta.gz"/> + <param name="hap1_reads" value="paternal.fasta.gz"/> + <param name="hap2_reads" value="maternal.fasta.gz"/> + </conditional> <param name="max_kmers" value="2"/> <param name="min_kmers" value="5"/> </conditional> @@ -556,6 +585,27 @@ <param name="bins_out" value="yes" /> <output_collection name="bin_files" type="list" count="3" /> </test> + <!-- TEST 15: Test trio LIST mode --> + <test expect_num_outputs="6"> + <param name="filter_bits" value="0"/> + <param name="log_out" value="yes"/> + <conditional name="mode"> + <param name="mode_selector" value="trio"/> + <param name="reads" value="child.fasta.gz"/> + <conditional name="trioinput"> + <param name="trio_input_selector" value="lists"/> + <param name="hap1_list" value="maternal.headers.txt"/> + <param name="hap2_list" value="paternal.headers.txt"/> + </conditional> + <param name="max_kmers" value="2"/> + <param name="min_kmers" value="5"/> + </conditional> + <output name="log_file" ftype="txt"> + <assert_contents> + <has_text text="flagged 100 reads, out of 100 lines in file"/> + </assert_contents> + </output> + </test> </tests> <help><![CDATA[ .. class:: infomark
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/maternal.headers.txt Fri Oct 20 22:03:32 2023 +0000 @@ -0,0 +1,100 @@ +K12_1 +K12_3 +K12_5 +K12_7 +K12_9 +K12_11 +K12_13 +K12_15 +K12_17 +K12_19 +K12_21 +K12_23 +K12_25 +K12_27 +K12_29 +K12_31 +K12_33 +K12_35 +K12_37 +K12_39 +K12_41 +K12_43 +K12_45 +K12_47 +K12_49 +K12_51 +K12_53 +K12_55 +K12_57 +K12_59 +K12_61 +K12_63 +K12_65 +K12_67 +K12_69 +K12_71 +K12_73 +K12_75 +K12_77 +K12_79 +K12_81 +K12_83 +K12_85 +K12_87 +K12_89 +K12_91 +K12_93 +K12_95 +K12_97 +K12_99 +K12_101 +K12_103 +K12_105 +K12_107 +K12_109 +K12_111 +K12_113 +K12_115 +K12_117 +K12_119 +K12_121 +K12_123 +K12_125 +K12_127 +K12_129 +K12_131 +K12_133 +K12_135 +K12_137 +K12_139 +K12_141 +K12_143 +K12_145 +K12_147 +K12_149 +K12_151 +K12_153 +K12_155 +K12_157 +K12_159 +K12_161 +K12_163 +K12_165 +K12_167 +K12_169 +K12_171 +K12_173 +K12_175 +K12_177 +K12_179 +K12_181 +K12_183 +K12_185 +K12_187 +K12_189 +K12_191 +K12_193 +K12_195 +K12_197 +K12_199
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/paternal.headers.txt Fri Oct 20 22:03:32 2023 +0000 @@ -0,0 +1,100 @@ +K12_699 +K12_701 +K12_703 +K12_705 +K12_707 +K12_709 +K12_711 +K12_713 +K12_715 +K12_717 +K12_719 +K12_721 +K12_723 +K12_725 +K12_727 +K12_729 +K12_731 +K12_733 +K12_735 +K12_737 +K12_739 +K12_741 +K12_743 +K12_745 +K12_747 +K12_749 +K12_751 +K12_753 +K12_755 +K12_757 +K12_759 +K12_761 +K12_763 +K12_765 +K12_767 +K12_769 +K12_771 +K12_773 +K12_775 +K12_777 +K12_779 +K12_781 +K12_783 +K12_785 +K12_787 +K12_789 +K12_791 +K12_793 +K12_795 +K12_797 +K12_799 +K12_801 +K12_803 +K12_805 +K12_807 +K12_809 +K12_811 +K12_813 +K12_815 +K12_817 +K12_819 +K12_821 +K12_823 +K12_825 +K12_827 +K12_829 +K12_831 +K12_833 +K12_835 +K12_837 +K12_839 +K12_841 +K12_843 +K12_845 +K12_847 +K12_849 +K12_851 +K12_853 +K12_855 +K12_857 +K12_859 +K12_861 +K12_863 +K12_865 +K12_867 +K12_869 +K12_871 +K12_873 +K12_875 +K12_877 +K12_879 +K12_881 +K12_883 +K12_885 +K12_887 +K12_889 +K12_891 +K12_893 +K12_895 +K12_897