Mercurial > repos > iuc > mash_sketch
changeset 5:3852f36e3154 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mash commit 16d60f67e8fef6c51af1161d677c32d37cb0cab2
| author | iuc |
|---|---|
| date | Tue, 23 Sep 2025 13:48:37 +0000 |
| parents | c73c3dfe1af8 |
| children | 9de5319ad2db |
| files | mash_sketch.xml test-data/res_paste.msh |
| diffstat | 2 files changed, 29 insertions(+), 12 deletions(-) [+] |
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--- a/mash_sketch.xml Thu Sep 11 10:22:17 2025 +0000 +++ b/mash_sketch.xml Tue Sep 23 13:48:37 2025 +0000 @@ -1,4 +1,4 @@ -<tool id="mash_sketch" name="mash sketch" version="@TOOL_VERSION@+galaxy1" profile="@PROFILE@"> +<tool id="mash_sketch" name="mash sketch" version="@TOOL_VERSION@+galaxy2" profile="@PROFILE@"> <description>Create a reduced sequence representation based on min-hashes</description> <macros> <import>macros.xml</import> @@ -7,32 +7,49 @@ <expand macro="requirements" /> <expand macro="version_command" /> <command detect_errors="exit_code"><![CDATA[ + + #if str ( $reads_assembly.reads_assembly_selector ) == "reads": + #if str( $reads_assembly.reads_input.reads_input_selector ) == "paired": + ln -s '$reads_assembly.reads_input.reads_1' "${reads_assembly.reads_input.reads_1.element_identifier}" && + ln -s '$reads_assembly.reads_input.reads_2' "${reads_assembly.reads_input.reads_1.element_identifier}" && + #end if + #if str( $reads_assembly.reads_input.reads_input_selector ) == "paired_collection": + ln -s '$reads_assembly.reads_input.reads.forward' "${reads_assembly.reads_input.reads.forward.element_identifier}" && + ln -s '$reads_assembly.reads_input.reads.reverse' "${reads_assembly.reads_input.reads.reverse.element_identifier}" && + #end if + #if str( $reads_assembly.reads_input.reads_input_selector ) == "single": + ln -s '$reads_assembly.reads_input.reads' "${reads_assembly.reads_input.reads.element_identifier}" && + #end if + #elif str ( $reads_assembly.reads_assembly_selector ) == "assembly": + ln -s '${reads_assembly.assembly}' "${reads_assembly.assembly.element_identifier}" && + #end if + mash sketch -s '${sketch_size}' -k '${kmer_size}' -w '${prob_threshold}' - #if str ( $reads_assembly.reads_assembly_selector ) == "reads" + #if str( $reads_assembly.reads_assembly_selector ) == "reads": -m '${reads_assembly.minimum_kmer_copies}' -r - #if $reads_assembly.target_coverage + #if $reads_assembly.target_coverage : -c '${reads_assembly.target_coverage}' #end if - #if $reads_assembly.genome_size + #if $reads_assembly.genome_size : -g '${reads_assembly.genome_size}' #end if - #if str( $reads_assembly.reads_input.reads_input_selector ) == "paired" - '$reads_assembly.reads_input.reads_1' '$reads_assembly.reads_input.reads_2' + #if str( $reads_assembly.reads_input.reads_input_selector ) == "paired" : + "${reads_assembly.reads_input.reads_1.element_identifier}" "${reads_assembly.reads_input.reads_1.element_identifier}}" #end if - #if str( $reads_assembly.reads_input.reads_input_selector ) == "paired_collection" - '$reads_assembly.reads_input.reads.forward' '$reads_assembly.reads_input.reads.reverse' + #if str( $reads_assembly.reads_input.reads_input_selector ) == "paired_collection": + "${reads_assembly.reads_input.reads.forward.element_identifier}" "${reads_assembly.reads_input.reads.reverse.element_identifier}" #end if - #if str( $reads_assembly.reads_input.reads_input_selector ) == "single" - '$reads_assembly.reads_input.reads' + #if str( $reads_assembly.reads_input.reads_input_selector ) == "single": + "${reads_assembly.reads_input.reads.element_identifier}" #end if - #elif str ( $reads_assembly.reads_assembly_selector ) == "assembly" + #elif str( $reads_assembly.reads_assembly_selector ) == "assembly": -p \${GALAXY_SLOTS:-1} - '${assembly}' ${reads_assembly.individual_sequences} + "${reads_assembly.assembly.element_identifier}" #end if -o 'sketch' ]]></command>