Mercurial > repos > iuc > abyss
changeset 12:a929ce596a34 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit c083399ddb31b026aaab1d600d8789bf56cf4d4b
| author | iuc |
|---|---|
| date | Mon, 18 Sep 2023 11:05:22 +0000 |
| parents | 7547fcab5d19 |
| children | 0124fce4654a |
| files | abyss-pe.xml |
| diffstat | 1 files changed, 6 insertions(+), 5 deletions(-) [+] |
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--- a/abyss-pe.xml Tue May 09 10:13:25 2023 +0000 +++ b/abyss-pe.xml Mon Sep 18 11:05:22 2023 +0000 @@ -2,7 +2,7 @@ <description>de novo sequence assembler</description> <macros> <token name="@TOOL_VERSION@">2.3.6</token> - <token name="@VERSION_SUFFIX@">0</token> + <token name="@VERSION_SUFFIX@">1</token> <xml name="reads_conditional"> <conditional name="reads"> <param name="reads_selector" type="select" label="Type of paired-end datasets"> @@ -85,7 +85,8 @@ abyss-pe name=abyss j=\${GALAXY_SLOTS:-1} -B=\${GALAXY_MEMORY_MB:-2048}M +B=\$((\${GALAXY_MEMORY_MB:-2048} * 9 /10 ))M + k=$k #if str($K) @@ -227,7 +228,7 @@ </outputs> <tests> - <test> + <test expect_num_outputs="5"> <repeat name="lib_repeat"> <conditional name="reads"> <param name="reads_selector" value="paired" /> @@ -242,14 +243,14 @@ <output name="indels" file="empty_file.fasta" /> <output name="stats" file="abyss-stats1.tab" /> </test> - <test> + <test expect_num_outputs="3"> <param name="se_reads" ftype="fastq.gz" value="assembly_sample-R1.fastq.gz,assembly_sample-R2.fastq.gz" /> <param name="k" value="50" /> <output name="unitigs" file="abyss-unitigs2.fa" /> <output name="indels" file="empty_file.fasta" /> <output name="stats" file="abyss-stats2.tab" /> </test> - <test> + <test expect_num_outputs="4"> <param name="se_reads" ftype="fasta" value="assembly_sample-R1.fasta,assembly_sample-R2.fasta" /> <param name="long_seqs" ftype="fasta" value="assembly_sample-R2.fasta" /> <param name="k" value="50" />