Mercurial > repos > bgruening > hifiasm
changeset 6:b1e0be6fdc9a draft
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 6817ef65c64c0800e21815822c38beba52075f75"
| author | bgruening |
|---|---|
| date | Sat, 12 Feb 2022 17:15:02 +0000 |
| parents | 68539508aa51 |
| children | 6a3eeb09a252 |
| files | hifiasm.xml |
| diffstat | 1 files changed, 9 insertions(+), 6 deletions(-) [+] |
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--- a/hifiasm.xml Wed Oct 06 20:10:31 2021 +0000 +++ b/hifiasm.xml Sat Feb 12 17:15:02 2022 +0000 @@ -2,7 +2,7 @@ <description>haplotype-resolved de novo assembler for PacBio Hifi reads</description> <macros> <token name="@TOOL_VERSION@">0.16.1</token> - <token name="@VERSION_SUFFIX@">1</token> + <token name="@VERSION_SUFFIX@">2</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" /> @@ -220,7 +220,8 @@ <param name="correction_rounds" argument="-r" type="integer" value="3" label="Correction rounds" /> <param argument="--min-hist-cnt" type="integer" min="0" value="" optional="true" label="Minimum count threshold" help="When analyzing the k-mer spectrum, ignore counts below this value" /> <param argument="--max-kocc" type="integer" min="0" value="20000" label="Maximum k-mer ocurrence" help="Employ k-mers occurring less than INT times to rescue repetitive overlaps" /> - <param argument="--hg-size" type="text" value="" optional="true" label="Estimated haploid genome size" help="Estimated haploid genome size used for inferring read coverage. If not provided, this parameter will be infered by hifism. Common suffices are required, for example, 100m or 3g"> + <param argument="--hg-size" type="text" value="" optional="true" label="Estimated haploid genome size" + help="Estimated haploid genome size used for inferring read coverage. If not provided, this parameter will be infered by hifism. Common suffices are required, for example, 100m or 3g"> <sanitizer invalid_char=""> <valid initial="string.digits"> <add value="k" /> @@ -271,10 +272,10 @@ <data name="hic_acontig_graph" format="gfa1" from_work_dir="output.hic.a_ctg.gfa" label="${tool.name} ${on_string}: Hi-C alternate contig graph"> <filter>mode['mode_selector'] == 'standard' and hic_partition['hic_partition_selector'] == 'set'</filter> </data> - <data name="hic_balanced_contig_hap1_graph" format="gfa1" from_work_dir="output.bp.hap1.p_ctg.gfa" label="${tool.name} ${on_string}: Hi-C hap1 balanced contig graph hap1"> + <data name="hic_balanced_contig_hap1_graph" format="gfa1" from_work_dir="output.hic.hap1.p_ctg.gfa" label="${tool.name} ${on_string}: Hi-C hap1 balanced contig graph hap1"> <filter>mode['mode_selector'] == 'standard' and hic_partition['hic_partition_selector'] == 'set'</filter> </data> - <data name="hic_balanced_contig_hap2_graph" format="gfa1" from_work_dir="output.bp.hap2.p_ctg.gfa" label="${tool.name} ${on_string}: Hi-C hap2 balanced contig graph hap2"> + <data name="hic_balanced_contig_hap2_graph" format="gfa1" from_work_dir="output.hic.hap2.p_ctg.gfa" label="${tool.name} ${on_string}: Hi-C hap2 balanced contig graph hap2"> <filter>mode['mode_selector'] == 'standard' and hic_partition['hic_partition_selector'] == 'set'</filter> </data> <!--Trio outputs with Hi-c reads--> @@ -354,12 +355,14 @@ <output name="hic_acontig_graph" file="hifiasm-out-hifi-a.gfa" ftype="gfa1" /> <output name="hic_balanced_contig_hap1_graph" ftype="gfa1"> <assert_contents> - <has_size value="0"/> + <has_text_matching expression="^S" /> + <has_size value="59529" delta="500"/> </assert_contents> </output> <output name="hic_balanced_contig_hap1_graph" ftype="gfa1" > <assert_contents> - <has_size value="0"/> + <has_text_matching expression="^S" /> + <has_size value="59529" delta="500"/> </assert_contents> </output> </test>