Mercurial > repos > iuc > mash_sketch
changeset 6:9de5319ad2db draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/mash commit ff9564c2e6924fab084b6e02a3a196650041636a
| author | iuc |
|---|---|
| date | Thu, 16 Oct 2025 16:42:58 +0000 |
| parents | 3852f36e3154 |
| children | |
| files | mash_sketch.xml test-data/L1_R1.fastqsanger.gz test-data/L1_R2.fastqsanger.gz test-data/test_08_mash_sketch.msh |
| diffstat | 4 files changed, 24 insertions(+), 17 deletions(-) [+] |
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--- a/mash_sketch.xml Tue Sep 23 13:48:37 2025 +0000 +++ b/mash_sketch.xml Thu Oct 16 16:42:58 2025 +0000 @@ -1,4 +1,4 @@ -<tool id="mash_sketch" name="mash sketch" version="@TOOL_VERSION@+galaxy2" profile="@PROFILE@"> +<tool id="mash_sketch" name="mash sketch" version="@TOOL_VERSION@+galaxy3" profile="@PROFILE@"> <description>Create a reduced sequence representation based on min-hashes</description> <macros> <import>macros.xml</import> @@ -8,20 +8,24 @@ <expand macro="version_command" /> <command detect_errors="exit_code"><![CDATA[ + #import re #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}" && + #set safe_file_name = re.sub(r'[^\w\-_\.]', '_', $reads_assembly.reads_input.reads_1.element_identifier) + cat '$reads_assembly.reads_input.reads_1' '$reads_assembly.reads_input.reads_2' > '$safe_file_name' && #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}" && + #set safe_file_name = re.sub(r'[^\w\-_\.]', '_', $reads_assembly.reads_input.reads.element_identifier) + echo $no_extension && + cat '$reads_assembly.reads_input.reads.forward' '$reads_assembly.reads_input.reads.reverse' > '$safe_file_name' && #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}" && + #set safe_file_name = re.sub(r'[^\w\-_\.]', '_', $reads_assembly.reads_input.reads.element_identifier) + ln -s '$reads_assembly.reads_input.reads' '$safe_file_name' && #end if #elif str ( $reads_assembly.reads_assembly_selector ) == "assembly": - ln -s '${reads_assembly.assembly}' "${reads_assembly.assembly.element_identifier}" && + #set safe_file_name = re.sub(r'[^\w\-_\.]', '_', $reads_assembly.assembly.element_identifier) + ln -s '${reads_assembly.assembly}' '$safe_file_name' && #end if mash sketch @@ -37,20 +41,11 @@ #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.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.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.element_identifier}" - #end if #elif str( $reads_assembly.reads_assembly_selector ) == "assembly": -p \${GALAXY_SLOTS:-1} ${reads_assembly.individual_sequences} - "${reads_assembly.assembly.element_identifier}" #end if + '$safe_file_name' -o 'sketch' ]]></command> <inputs> @@ -177,6 +172,18 @@ </conditional> <output name="sketch" file="test_07_mash_sketch.msh" compare="sim_size" /> </test> + <test expect_num_outputs="1"> + <conditional name="reads_assembly"> + <param name="reads_assembly_selector" value="reads"/> + <conditional name="reads_input"> + <param name="reads_input_selector" value="paired"/> + <param name="reads_1" value="L1_R1.fastqsanger.gz"/> + <param name="reads_2" value="L1_R2.fastqsanger.gz"/> + </conditional> + <param name="minimum_kmer_copies" value="2"/> + </conditional> + <output name="sketch" file="test_08_mash_sketch.msh" compare="sim_size" /> + </test> </tests> <help><![CDATA[