Mercurial > repos > dfornika > mash
changeset 16:13516965dc59 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mash commit d12104bf41c388c45b1188c55928c9e678063bc7-dirty"
| author | dfornika |
|---|---|
| date | Thu, 13 Feb 2020 22:10:20 +0000 |
| parents | 3a8ef132023c |
| children | 34869670b2d0 |
| files | mash_sketch.xml test-data/test_assembly.fasta |
| diffstat | 2 files changed, 54 insertions(+), 28 deletions(-) [+] |
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--- a/mash_sketch.xml Thu Feb 13 20:25:09 2020 +0000 +++ b/mash_sketch.xml Thu Feb 13 22:10:20 2020 +0000 @@ -11,37 +11,54 @@ <version_command>mash --version</version_command> <command detect_errors="exit_code"><![CDATA[ mash sketch - -s '${sketch_size}' - -k '${kmer_size}' - -m '${minimum_kmer_copies}' - -r - #if str( $input.input_selector ) == "paired" - '$input.reads_1' '$input.reads_2' - #end if - #if str( $input.input_selector ) == "paired_collection" - '$input.reads.forward' '$input.reads.reverse' - #end if - #if str( $input.input_selector ) == "single" - '$input.reads' - #end if - -o 'sketch' + -s '${sketch_size}' + -k '${kmer_size}' + -m '${minimum_kmer_copies}' + #if str ( $reads_assembly.reads_assembly_selector ) == "reads" + -r + #if str( $reads_assembly.reads_input.reads_input_selector ) == "paired" + '$reads_input.reads_1' '$reads_input.reads_2' + #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' + #end if + #if str( $reads_assembly.reads_input.reads_input_selector ) == "single" + '$reads_assembly.reads_input.reads' + #end if + #elif str ( $reads_assembly.reads_assembly_selector ) == "assembly" + '${assembly}' + ${reads_assembly.individual_sequences} + #end if + -o 'sketch' ]]></command> <inputs> - <conditional name="input"> - <param name="input_selector" type="select" label="Single or Paired-end reads" help="Select between paired and single end data"> - <option value="paired">Paired</option> - <option value="single">Single</option> - <option value="paired_collection">Paired Collection</option> + <conditional name="reads_assembly"> + <param name="reads_assembly_selector" type="select" label="Input: Reads or Assemblies"> + <option selected="True" value="reads">Reads</option> + <option value="assembly">Assembly</option> </param> - <when value="paired"> - <param name="reads_1" type="data" format="@INTYPES@" label="Select first set of reads" help="Specify dataset with forward reads"/> - <param name="reads_2" type="data" format="@INTYPES@" label="Select second set of reads" help="Specify dataset with reverse reads"/> + <when value="reads"> + <conditional name="reads_input"> + <param name="reads_input_selector" type="select" label="Single or Paired-end reads" help="Select between paired and single end data"> + <option value="paired">Paired</option> + <option value="single">Single</option> + <option value="paired_collection">Paired Collection</option> + </param> + <when value="paired"> + <param name="reads_1" type="data" format="@INTYPES@" label="Select first set of reads" help="Specify dataset with forward reads"/> + <param name="reads_2" type="data" format="@INTYPES@" label="Select second set of reads" help="Specify dataset with reverse reads"/> + </when> + <when value="single"> + <param name="reads" type="data" format="@INTYPES@" label="Select fastq dataset" help="Specify dataset with single reads"/> + </when> + <when value="paired_collection"> + <param name="reads" format="@INTYPES@" type="data_collection" collection_type="paired" label="Select a paired collection" help="See help section for an explanation of dataset collections"/> + </when> + </conditional> </when> - <when value="single"> - <param name="reads" type="data" format="@INTYPES@" label="Select fastq dataset" help="Specify dataset with single reads"/> - </when> - <when value="paired_collection"> - <param name="reads" format="@INTYPES@" type="data_collection" collection_type="paired" label="Select a paired collection" help="See help section for an explanation of dataset collections"/> + <when value="assembly"> + <param name="assembly" type="data" format="fasta,fasta.gz" label="Assembly"/> + <param type="boolean" name="individual_sequences" truevalue="-i" falsevalue="" label="Sketch individual Sequences"/> </when> </conditional> <param type="integer" name="sketch_size" argument="-s" value="1000" min="10" max="1000000" /> @@ -53,10 +70,16 @@ </outputs> <tests> <test> - <param name="input_selector" value="single"/> + <param name="reads_assembly_selector" value="reads" /> + <param name="reads_input_selector" value="single"/> <param name="reads" value="ERR024951_seqtk_sample_1000_1.fastq"/> <assert_stderr has_text="Estimated genome size:"/> </test> + <test> + <param name="reads_assembly_selector" value="assembly" /> + <param name="assembly" value="test_assembly.fasta"/> + <assert_stderr has_text="Sketching"/> + </test> </tests> <help><![CDATA[ Description: