Mercurial > repos > iuc > coverm_genome
changeset 5:847f274a60da draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 339c91447e45305efa0eed6952ef391db8e5d207
| author | iuc |
|---|---|
| date | Sun, 12 Nov 2023 14:30:30 +0000 |
| parents | 0ff4b0e5a3bc |
| children | 73b667038f46 |
| files | coverm_genome.xml macros.xml test-data/all_fasta.loc |
| diffstat | 3 files changed, 16 insertions(+), 13 deletions(-) [+] |
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--- a/coverm_genome.xml Fri Aug 18 09:23:39 2023 +0000 +++ b/coverm_genome.xml Sun Nov 12 14:30:30 2023 +0000 @@ -33,10 +33,8 @@ ln -s '$genome' '$fn' && #end for #else - #for $i, $genome in enumerate($mapped.genome.genomic.genome_fasta_files) - #set $fn = re.sub('[^\s\w\-\\.]', '_', str($genome.fields.path.element_identifier)) - #silent $genome_fp.append( $fn ) -ln -s '$genome' '$fn' && + #for $genome in $mapped.genome.genomic.genome_fasta_files + #silent $genome_fp.append($genome) #end for #end if #end if @@ -455,8 +453,8 @@ <conditional name="genome"> <param name="ref_or_genome" value="genomic"/> <conditional name="genomic"> - <param name="source" value="history"/> - <param name="genome_fasta_files" value="500kb.fna,1mbp.fna"/> + <param name="source" value="builtin"/> + <param name="genome_fasta_files" value="500kb_name,1mbp_name"/> </conditional> </conditional> <param name="sharded" value="" />
--- a/macros.xml Fri Aug 18 09:23:39 2023 +0000 +++ b/macros.xml Sun Nov 12 14:30:30 2023 +0000 @@ -1,6 +1,6 @@ <macros> <token name="@TOOL_VERSION@">0.6.1</token> - <token name="@VERSION_SUFFIX@">2</token> + <token name="@VERSION_SUFFIX@">3</token> <token name="@PROFILE@">22.01</token> <xml name="requirements"> <requirements> @@ -74,7 +74,10 @@ </when> <when value="builtin"> <param argument="--genome-fasta-files" type="select" multiple="true" label="Reference genome(s)"> - <options from_data_table="all_fasta" /> + <options from_data_table="all_fasta"> + <column name="name" index="2"/> + <column name="value" index="3"/> + </options> </param> </when> </conditional> @@ -178,6 +181,8 @@ ln -s '$ref' '${fn}' && ]]></token> <token name="@GENOME_FOR_READS@"><![CDATA[ + echo "GENOME_FOR_READS mapped.mode.genome.genomic.source=$mapped.mode.genome.genomic.source" && + echo "GENOME_FOR_READS mapped.mode.genome.genomic.genome_fasta_files=$mapped.mode.genome.genomic.genome_fasta_files" && #if $mapped.mode.genome.genomic.source == 'history' #for $i, $genome in enumerate($mapped.mode.genome.genomic.genome_fasta_files) #set $fn = re.sub('[^\s\w\-\\.]', '_', str($genome.element_identifier)) @@ -185,10 +190,8 @@ ln -s '$genome' '$fn' && #end for #else - #for $i, $genome in enumerate($mapped.mode.genome.genomic.genome_fasta_files) - #set $fn = re.sub('[^\s\w\-\\.]', '_', str($genome.fields.path.element_identifier)) - #silent $genome_fp.append( $fn ) -ln -s '$genome' '$fn' && + #for $genome in $mapped.mode.genome.genomic.genome_fasta_files + #silent $genome_fp.append($genome) #end for #end if ]]></token>
--- a/test-data/all_fasta.loc Fri Aug 18 09:23:39 2023 +0000 +++ b/test-data/all_fasta.loc Sun Nov 12 14:30:30 2023 +0000 @@ -27,4 +27,6 @@ #hg18full hg18 Human (Homo sapiens): hg18 Full /depot/data2/galaxy/hg18/hg18full.fasta #hg19canon hg19 Human (Homo sapiens): hg19 Canonical /depot/data2/galaxy/hg19/hg19canon.fasta #hg19full hg19 Human (Homo sapiens): hg19 Full /depot/data2/galaxy/hg19/hg19full.fasta -test1tg01 "TestGenome" ${__HERE__}/reference.fasta \ No newline at end of file +500kb_value 50kb_dbkey 500kb_name ${__HERE__}/500kb.fna +1mbp_value 1mbp_dbkey 1mbp_name ${__HERE__}/1mbp.fna +1mbp \ No newline at end of file