Mercurial > repos > dfornika > mash_screen
diff mash_screen.xml @ 0:f27853effdd6 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mash commit b1e065ba7e15f9f10b969db1d561b0e8fe6d4572-dirty"
author | dfornika |
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date | Fri, 14 Feb 2020 18:56:23 +0000 |
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children | 561dc2d84650 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/mash_screen.xml Fri Feb 14 18:56:23 2020 +0000 @@ -0,0 +1,102 @@ +<tool id="mash_screen" name="mash screen" version="@TOOL_VERSION@+galaxy1" profile="19.01"> + <description>determines how well query sequences are contained within a pool of sequences.</description> + <macros> + <import>macros.xml</import> + </macros> + <requirements> + <requirement type="package" version="@TOOL_VERSION@">mash</requirement> + </requirements> + <version_command>mash --version</version_command> + <command detect_errors="exit_code"><![CDATA[ + ln -s '$queries' queries.msh && + mash screen + $winner_takes_all + -i $minimum_identity_to_report + -v $maximum_p_value_to_report + queries.msh + #if str( $pool_input.pool_input_selector ) == "paired" + '$pool_input.pool_1' '$pool_input.pool_2' + #end if + #if str( $pool_input.pool_input_selector ) == "paired_collection" + '$pool_input.pool.forward' '$pool_input.pool.reverse' + #end if + #if str( $pool_input.pool_input_selector ) == "single" + '$pool_input.pool' + #end if + > '$output' + ]]></command> + <inputs> + <conditional name="pool_input"> + <param name="pool_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="pool_1" type="data" format="@INTYPES@" label="Select first set of reads" help="Specify dataset with forward reads"/> + <param name="pool_2" type="data" format="@INTYPES@" label="Select second set of reads" help="Specify dataset with reverse reads"/> + </when> + <when value="single"> + <param name="pool" type="data" format="@INTYPES@" label="Select fastq dataset" help="Specify dataset with single reads"/> + </when> + <when value="paired_collection"> + <param name="pool" 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> + <param name="queries" type="data" format="msh" /> + <param type="boolean" name="winner_takes_all" argument="-w" truevalue="-w" falsevalue=""/> + <param type="float" name="minimum_identity_to_report" argument="-i" value="0." min="-1." max="1." /> + <param type="float" name="maximum_p_value_to_report" argument="-v" value="1." min="0." max="1."/> + </inputs> + <outputs> + <data name="output" format="tabular" /> + </outputs> + <tests> + <test> + <param name="queries" value="NZ_MYON01000010.1.msh"/> + <param name="pool_input_selector" value="single"/> + <param name="pool" value="ERR024951_seqtk_sample_1000_1.fastq"/> + <output name="output" file="mash_screen_NZ_MYON01000010.1_ERR024951_seqtk_sample_1000_1.tsv"/> + </test> + <test> + <param name="queries" value="NZ_MYON01000010.1.msh"/> + <param name="pool_input_selector" value="single"/> + <param name="pool" value="ERR024951_seqtk_sample_1000_2.fastq"/> + <output name="output" file="mash_screen_NZ_MYON01000010.1_ERR024951_seqtk_sample_1000_2.tsv"/> + </test> + <test> + <param name="queries" value="NZ_MYON01000010.1.msh"/> + <param name="pool_input_selector" value="paired"/> + <param name="pool_1" value="ERR024951_seqtk_sample_1000_1.fastq"/> + <param name="pool_2" value="ERR024951_seqtk_sample_1000_2.fastq"/> + <output name="output" file="mash_screen_NZ_MYON01000010.1_ERR024951_seqtk_sample_1000_1and2.tsv"/> + </test> + </tests> + <help><![CDATA[ +Description: + + Determine how well query sequences are contained within a pool of sequences. + The queries must be formatted as a single Mash sketch file (.msh), created + with the `mash sketch` command. The <pool> files can be contigs or reads, in + fasta or fastq, gzipped or not, and "-" can be given for <pool> to read from + standard input. The <pool> sequences are assumed to be nucleotides, and will + be 6-frame translated if the <queries> are amino acids. The output fields are + [identity, shared-hashes, median-multiplicity, p-value, query-ID, + query-comment], where median-multiplicity is computed for shared hashes, based + on the number of observations of those hashes within the pool. + ]]></help> + <citations> + <citation type="bibtex"> +@article{ondov2016mash, + title={Mash: fast genome and metagenome distance estimation using MinHash}, + author={Ondov, Brian D and Treangen, Todd J and Melsted, P{\'a}ll and Mallonee, Adam B and Bergman, Nicholas H and Koren, Sergey and Phillippy, Adam M}, + journal={Genome biology}, + volume={17}, + number={1}, + pages={132}, + year={2016}, + publisher={BioMed Central} + } + </citation> + </citations> +</tool>