Mercurial > repos > nml > metaspades
changeset 16:dada2881d772 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 099f08cce5c93f4ed22bc8b02296fd4b5d357390
| author | iuc |
|---|---|
| date | Mon, 03 Mar 2025 11:06:18 +0000 |
| parents | 2463908405d3 |
| children | c9ade0f3365c |
| files | macros.xml metaspades.xml |
| diffstat | 2 files changed, 9 insertions(+), 12 deletions(-) [+] |
line wrap: on
line diff
--- a/macros.xml Tue Aug 23 07:55:55 2022 +0000 +++ b/macros.xml Mon Mar 03 11:06:18 2025 +0000 @@ -1,6 +1,6 @@ <macros> - <token name="@TOOL_VERSION@">3.15.4</token> - <token name="@VERSION_SUFFIX@">2</token> + <token name="@TOOL_VERSION@">3.15.5</token> + <token name="@VERSION_SUFFIX@">3</token> <xml name="requirements"> <requirements> <requirement type="package" version="@TOOL_VERSION@">spades</requirement> @@ -148,6 +148,7 @@ <token name="@RESOURCES@"><![CDATA[ -t \${GALAXY_SLOTS:-4} -m \$((\${GALAXY_MEMORY_MB:-8192}/1024)) +--tmp-dir \${TMPDIR} ]]></token> <token name="@INPUT_READS_MAIN@"><![CDATA[ @@ -384,16 +385,16 @@ <token name="@STATS@"><![CDATA[ #if 'cs' in $optional_output - && test -f 'output/contigs.fasta' && python '$__tool_directory__/write_tsv_script.py' < 'output/contigs.fasta' > '$out_cs' || echo 'No contigs.fasta.' + && (test -f 'output/contigs.fasta' && python '$__tool_directory__/write_tsv_script.py' < 'output/contigs.fasta' > '$out_cs' || echo 'No contigs.fasta.') #end if #if 'ss' in $optional_output - && test -f 'output/scaffolds.fasta' && python '$__tool_directory__/write_tsv_script.py' < 'output/scaffolds.fasta' > '$out_ss' || echo 'No scaffolds.fasta.' + && (test -f 'output/scaffolds.fasta' && python '$__tool_directory__/write_tsv_script.py' < 'output/scaffolds.fasta' > '$out_ss' || echo 'No scaffolds.fasta.') #end if ]]></token> <token name="@CORRECTED@"><![CDATA[ #if 'corrected' in $optional_output - && test -d 'output/corrected' && zip -q -r 'corrected.zip' 'output/corrected/*.fastq.gz' || echo 'No output files for corrected reads.' + && (test -d 'output/corrected' && zip -q -r 'corrected.zip' 'output/corrected/*.fastq.gz' || echo 'No output files for corrected reads.') #end if ]]></token> @@ -504,10 +505,6 @@ </param> <when value="true"> <expand macro="input_files_paired" format="fastq,fastq.gz,fastqsanger.gz,fasta,fasta.gz" label="FASTA/FASTQ file(s)" help="@HELP@"/> - <param name="library_number" type="select" label="The samples belong to the same library" help="If the reads have been generated from the sample sample, it means that they belong to the same library."> - <option value="true" selected="true">True</option> - <option value="false">False</option> - </param> </when> <when value="false"/> </conditional>
--- a/metaspades.xml Tue Aug 23 07:55:55 2022 +0000 +++ b/metaspades.xml Mon Mar 03 11:06:18 2025 +0000 @@ -3,6 +3,9 @@ <macros> <import>macros.xml</import> </macros> + <xrefs> + <xref type="bio.tools">metaspades</xref> + </xrefs> <expand macro="requirements"/> <expand macro="stdio"/> <expand macro="version_command"/> @@ -41,9 +44,6 @@ <section name="arf" title="Additional read files"> <expand macro="nanopore_pacbio"/> </section> - <section name="arf" title="Additional read files"> - <expand macro="nanopore_pacbio"/> - </section> <expand macro="kmer"/> <expand macro="phred"/> <expand macro="pipeline_options">