Mercurial > repos > galaxy-australia > metawrapmg_binning
changeset 3:6f7211f93b06 draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metawrapmg commit 0f381ce2cdb0683f1bc8e1da321a5a75440bf619
| author | iuc |
|---|---|
| date | Tue, 11 Mar 2025 12:23:05 +0000 |
| parents | 2a8bc1d26d06 |
| children | |
| files | macros.xml metawrapmg_binning.xml |
| diffstat | 2 files changed, 15 insertions(+), 13 deletions(-) [+] |
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--- a/macros.xml Thu Apr 11 21:56:14 2024 +0000 +++ b/macros.xml Tue Mar 11 12:23:05 2025 +0000 @@ -1,6 +1,6 @@ <macros> <token name="@TOOL_VERSION@">1.3.0</token> - <token name="@VERSION_SUFFIX@">1</token> + <token name="@VERSION_SUFFIX@">2</token> <token name="@PROFILE@">22.05</token> <xml name="requirements"> <requirements>
--- a/metawrapmg_binning.xml Thu Apr 11 21:56:14 2024 +0000 +++ b/metawrapmg_binning.xml Tue Mar 11 12:23:05 2025 +0000 @@ -16,13 +16,10 @@ ################## ## only plain FASTA and FASTQ - ln -s '$metagenome' metagenome.fasta - && + ln -s '$metagenome' metagenome.fasta && ## Metawrap checks for files named _1.fastq and _2.fastq. - ln -s '$input_1' reads_1.fastq - && - ln -s '$input_2' reads_2.fastq - && + ln -s '$input.forward' reads_1.fastq && + ln -s '$input.reverse' reads_2.fastq && ##################### ## INITIAL BINNING ## @@ -71,8 +68,7 @@ ]]></command> <inputs> <param name="metagenome" format="fasta" type="data" label="Metagenome" help="Metagenome co-assembly for binning"/> - <param name="input_1" format="fastqsanger" type="data" label="Read 1" help="Original reads that were used for the assembly: read 1."/> - <param name="input_2" format="fastqsanger" type="data" label="Read 2" help="Original reads that were used for the assembly: read 2."/> + <param name="input" type="data_collection" collection_type="paired" label="Reads" help="Original reads that were used for the assembly"/> <section name="binning" title="Binning parameters" expanded="false"> <param argument="-c" type="integer" value="70" min="50" max="100" label="Percent completion" help="Minimum % completion of bins"/> <param argument="-x" type="integer" value="10" min="0" max="100" label="Percent contamination" help="Maximum % contamination of bins that is acceptable"/> @@ -103,10 +99,16 @@ <!-- 01: basic function --> <test> <param name="metagenome" value="subset.fasta.gz"/> - <param name="input_1" value="mapped_reads.r1.fastq.gz"/> - <param name="input_2" value="mapped_reads.r2.fastq.gz"/> - <param name="c" value="60"/> - <param name="x" value="15"/> + <param name="input"> + <collection type="paired"> + <element name="forward" value="mapped_reads.r1.fastq.gz"/> + <element name="reverse" value="mapped_reads.r2.fastq.gz"/> + </collection> + </param> + <section name="binning"> + <param name="c" value="60"/> + <param name="x" value="15"/> + </section> <param name="hidden_quick" value="--quick"/> <output_collection name="metawrap_bins" type="list"> <element name="bin.1" ftype="fasta">