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annotate mash_screen.xml @ 0:867692ec85aa draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mash commit 500478e8adcabf5249941012f78fe2140ecc7264
author iuc
date Mon, 07 Jan 2019 15:09:31 -0500
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867692ec85aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mash commit 500478e8adcabf5249941012f78fe2140ecc7264
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1 <tool id="mash_screen" name="mash screen" version="@TOOL_VERSION@+galaxy0" profile="19.01">
867692ec85aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mash commit 500478e8adcabf5249941012f78fe2140ecc7264
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2 <description>determines how well query sequences are contained within a pool of sequences.</description>
867692ec85aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mash commit 500478e8adcabf5249941012f78fe2140ecc7264
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3 <macros>
867692ec85aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mash commit 500478e8adcabf5249941012f78fe2140ecc7264
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4 <import>macros.xml</import>
867692ec85aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mash commit 500478e8adcabf5249941012f78fe2140ecc7264
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5 </macros>
867692ec85aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mash commit 500478e8adcabf5249941012f78fe2140ecc7264
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6 <requirements>
867692ec85aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mash commit 500478e8adcabf5249941012f78fe2140ecc7264
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7 <requirement type="package" version="@TOOL_VERSION@">mash</requirement>
867692ec85aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mash commit 500478e8adcabf5249941012f78fe2140ecc7264
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8 </requirements>
867692ec85aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mash commit 500478e8adcabf5249941012f78fe2140ecc7264
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9 <version_command>mash --version</version_command>
867692ec85aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mash commit 500478e8adcabf5249941012f78fe2140ecc7264
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10 <command detect_errors="exit_code"><![CDATA[
867692ec85aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mash commit 500478e8adcabf5249941012f78fe2140ecc7264
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11 ln -s '$queries' queries.msh &&
867692ec85aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mash commit 500478e8adcabf5249941012f78fe2140ecc7264
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12 mash screen
867692ec85aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mash commit 500478e8adcabf5249941012f78fe2140ecc7264
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13 $winner_takes_all
867692ec85aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mash commit 500478e8adcabf5249941012f78fe2140ecc7264
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14 -i $minimum_identity_to_report
867692ec85aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mash commit 500478e8adcabf5249941012f78fe2140ecc7264
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15 -v $maximum_p_value_to_report
867692ec85aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mash commit 500478e8adcabf5249941012f78fe2140ecc7264
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16 queries.msh
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17 '${ str($pool).replace(',', '\' \'') }'
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18 > '$output'
867692ec85aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mash commit 500478e8adcabf5249941012f78fe2140ecc7264
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19 ]]></command>
867692ec85aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mash commit 500478e8adcabf5249941012f78fe2140ecc7264
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20 <inputs>
867692ec85aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mash commit 500478e8adcabf5249941012f78fe2140ecc7264
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21 <param name="queries" type="data" format="msh" />
867692ec85aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mash commit 500478e8adcabf5249941012f78fe2140ecc7264
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22 <param type="data" multiple="true" name="pool" format="@INTYPES@" />
867692ec85aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mash commit 500478e8adcabf5249941012f78fe2140ecc7264
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23 <param type="boolean" name="winner_takes_all" argument="-w" truevalue="-w" falsevalue=""/>
867692ec85aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mash commit 500478e8adcabf5249941012f78fe2140ecc7264
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24 <param type="float" name="minimum_identity_to_report" argument="-i" value="0." min="-1." max="1." />
867692ec85aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mash commit 500478e8adcabf5249941012f78fe2140ecc7264
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25 <param type="float" name="maximum_p_value_to_report" argument="-v" value="1." min="0." max="1."/>
867692ec85aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mash commit 500478e8adcabf5249941012f78fe2140ecc7264
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26 </inputs>
867692ec85aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mash commit 500478e8adcabf5249941012f78fe2140ecc7264
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27 <outputs>
867692ec85aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mash commit 500478e8adcabf5249941012f78fe2140ecc7264
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28 <data name="output" format="tabular" />
867692ec85aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mash commit 500478e8adcabf5249941012f78fe2140ecc7264
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29 </outputs>
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30 <tests>
867692ec85aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mash commit 500478e8adcabf5249941012f78fe2140ecc7264
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31 <test>
867692ec85aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mash commit 500478e8adcabf5249941012f78fe2140ecc7264
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32 <param name="queries" value="NZ_MYON01000010.1.msh"/>
867692ec85aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mash commit 500478e8adcabf5249941012f78fe2140ecc7264
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33 <param name="pool" value="ERR024951_seqtk_sample_1000_1.fastq"/>
867692ec85aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mash commit 500478e8adcabf5249941012f78fe2140ecc7264
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34 <output name="output" file="mash_screen_NZ_MYON01000010.1_ERR024951_seqtk_sample_1000_1.tsv"/>
867692ec85aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mash commit 500478e8adcabf5249941012f78fe2140ecc7264
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35 </test>
867692ec85aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mash commit 500478e8adcabf5249941012f78fe2140ecc7264
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36 <test>
867692ec85aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mash commit 500478e8adcabf5249941012f78fe2140ecc7264
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37 <param name="queries" value="NZ_MYON01000010.1.msh"/>
867692ec85aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mash commit 500478e8adcabf5249941012f78fe2140ecc7264
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38 <param name="pool" value="ERR024951_seqtk_sample_1000_2.fastq"/>
867692ec85aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mash commit 500478e8adcabf5249941012f78fe2140ecc7264
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39 <output name="output" file="mash_screen_NZ_MYON01000010.1_ERR024951_seqtk_sample_1000_2.tsv"/>
867692ec85aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mash commit 500478e8adcabf5249941012f78fe2140ecc7264
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40 </test>
867692ec85aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mash commit 500478e8adcabf5249941012f78fe2140ecc7264
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41 <test>
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42 <param name="queries" value="NZ_MYON01000010.1.msh"/>
867692ec85aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mash commit 500478e8adcabf5249941012f78fe2140ecc7264
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43 <param name="pool" value="ERR024951_seqtk_sample_1000_1.fastq,ERR024951_seqtk_sample_1000_2.fastq"/>
867692ec85aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mash commit 500478e8adcabf5249941012f78fe2140ecc7264
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44 <output name="output" file="mash_screen_NZ_MYON01000010.1_ERR024951_seqtk_sample_1000_1and2.tsv"/>
867692ec85aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mash commit 500478e8adcabf5249941012f78fe2140ecc7264
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45 </test>
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46 </tests>
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47 <help><![CDATA[
867692ec85aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mash commit 500478e8adcabf5249941012f78fe2140ecc7264
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48 Description:
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49
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50 Determine how well query sequences are contained within a pool of sequences.
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51 The queries must be formatted as a single Mash sketch file (.msh), created
867692ec85aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mash commit 500478e8adcabf5249941012f78fe2140ecc7264
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52 with the `mash sketch` command. The <pool> files can be contigs or reads, in
867692ec85aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mash commit 500478e8adcabf5249941012f78fe2140ecc7264
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53 fasta or fastq, gzipped or not, and "-" can be given for <pool> to read from
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54 standard input. The <pool> sequences are assumed to be nucleotides, and will
867692ec85aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mash commit 500478e8adcabf5249941012f78fe2140ecc7264
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55 be 6-frame translated if the <queries> are amino acids. The output fields are
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56 [identity, shared-hashes, median-multiplicity, p-value, query-ID,
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57 query-comment], where median-multiplicity is computed for shared hashes, based
867692ec85aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mash commit 500478e8adcabf5249941012f78fe2140ecc7264
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58 on the number of observations of those hashes within the pool.
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59 ]]></help>
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60 <citations>
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61 <citation type="bibtex">
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62 @article{ondov2016mash,
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63 title={Mash: fast genome and metagenome distance estimation using MinHash},
867692ec85aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mash commit 500478e8adcabf5249941012f78fe2140ecc7264
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64 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},
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65 journal={Genome biology},
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66 volume={17},
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67 number={1},
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68 pages={132},
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69 year={2016},
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70 publisher={BioMed Central}
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71 }
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72 </citation>
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73 </citations>
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74 </tool>