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annotate mash_screen.xml @ 3:6d63b05cfea8 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mash commit 24f4271bd62a3d96fec812eae2ad607f6a7f723c"
author iuc
date Sun, 16 Feb 2020 22:02:43 +0000
parents 7305a1d87e99
children d9fb7a9bce28
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3
6d63b05cfea8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mash commit 24f4271bd62a3d96fec812eae2ad607f6a7f723c"
iuc
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1 <tool id="mash_screen" name="mash screen" version="@TOOL_VERSION@+galaxy2" profile="19.01">
2
7305a1d87e99 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mash commit 463a12a276cab461734ad7d04440e0d52d6cf91e-dirty"
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2 <description>determines how well query sequences are contained within a pool of sequences</description>
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
3
6d63b05cfea8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mash commit 24f4271bd62a3d96fec812eae2ad607f6a7f723c"
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6 <expand macro="requirements" />
6d63b05cfea8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mash commit 24f4271bd62a3d96fec812eae2ad607f6a7f723c"
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7 <expand macro="version_command" />
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8 <command detect_errors="exit_code"><![CDATA[
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9 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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10 mash screen
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11 $winner_takes_all
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12 -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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13 -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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14 queries.msh
1
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15 #if str( $pool_input.pool_input_selector ) == "paired"
4f453db80800 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mash commit 91435d801528addac840722e9a0092b2d342b8bb
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16 '$pool_input.pool_1' '$pool_input.pool_2'
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17 #end if
4f453db80800 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mash commit 91435d801528addac840722e9a0092b2d342b8bb
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18 #if str( $pool_input.pool_input_selector ) == "paired_collection"
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19 '$pool_input.pool.forward' '$pool_input.pool.reverse'
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20 #end if
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21 #if str( $pool_input.pool_input_selector ) == "single"
4f453db80800 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mash commit 91435d801528addac840722e9a0092b2d342b8bb
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22 '$pool_input.pool'
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23 #end if
0
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24 > '$output'
867692ec85aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mash commit 500478e8adcabf5249941012f78fe2140ecc7264
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25 ]]></command>
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26 <inputs>
1
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27 <conditional name="pool_input">
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28 <param name="pool_input_selector" type="select" label="Single or Paired-end reads" help="Select between paired and single end data">
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29 <option value="paired">Paired</option>
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30 <option value="single">Single</option>
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31 <option value="paired_collection">Paired Collection</option>
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32 </param>
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33 <when value="paired">
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34 <param name="pool_1" type="data" format="@INTYPES@" label="Select first set of reads" help="Specify dataset with forward reads"/>
4f453db80800 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mash commit 91435d801528addac840722e9a0092b2d342b8bb
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35 <param name="pool_2" type="data" format="@INTYPES@" label="Select second set of reads" help="Specify dataset with reverse reads"/>
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36 </when>
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37 <when value="single">
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38 <param name="pool" type="data" format="@INTYPES@" label="Select fastq dataset" help="Specify dataset with single reads"/>
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39 </when>
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40 <when value="paired_collection">
4f453db80800 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mash commit 91435d801528addac840722e9a0092b2d342b8bb
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41 <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"/>
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42 </when>
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43 </conditional>
0
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44 <param name="queries" type="data" format="msh" />
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45 <param name="winner_takes_all" argument="-w" type="boolean" checked="true" truevalue="-w" falsevalue="" label="'Winner takes all' to remove redundancy in the result"
6d63b05cfea8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mash commit 24f4271bd62a3d96fec812eae2ad607f6a7f723c"
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46 help="If this option is not enabled, every matching strain from the same species of the reference database is reported in the result."/>
6d63b05cfea8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mash commit 24f4271bd62a3d96fec812eae2ad607f6a7f723c"
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47 <param type="float" name="minimum_identity_to_report" argument="-i" value="0." min="-1." max="1." label="Minimum identity to report" />
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48 <param type="float" name="maximum_p_value_to_report" argument="-v" value="1." min="0." max="1." label="Maximum p-value to report" />
0
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49 </inputs>
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50 <outputs>
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51 <data name="output" format="tabular" />
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52 </outputs>
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53 <tests>
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54 <test>
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55 <param name="queries" value="NZ_MYON01000010.1.msh"/>
1
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56 <param name="pool_input_selector" value="single"/>
0
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57 <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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58 <output name="output" file="mash_screen_NZ_MYON01000010.1_ERR024951_seqtk_sample_1000_1.tsv"/>
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59 </test>
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60 <test>
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61 <param name="queries" value="NZ_MYON01000010.1.msh"/>
1
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62 <param name="pool_input_selector" value="single"/>
0
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63 <param name="pool" value="ERR024951_seqtk_sample_1000_2.fastq"/>
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64 <output name="output" file="mash_screen_NZ_MYON01000010.1_ERR024951_seqtk_sample_1000_2.tsv"/>
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65 </test>
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66 <test>
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67 <param name="queries" value="NZ_MYON01000010.1.msh"/>
1
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68 <param name="pool_input_selector" value="paired"/>
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69 <param name="pool_1" value="ERR024951_seqtk_sample_1000_1.fastq"/>
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70 <param name="pool_2" value="ERR024951_seqtk_sample_1000_2.fastq"/>
0
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71 <output name="output" file="mash_screen_NZ_MYON01000010.1_ERR024951_seqtk_sample_1000_1and2.tsv"/>
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72 </test>
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73 </tests>
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74 <help><![CDATA[
3
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75
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76 **What it does**
0
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77
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78 Determine how well query sequences are contained within a pool of sequences.
867692ec85aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mash commit 500478e8adcabf5249941012f78fe2140ecc7264
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79 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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80 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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81 fasta or fastq, gzipped or not, and "-" can be given for <pool> to read from
867692ec85aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mash commit 500478e8adcabf5249941012f78fe2140ecc7264
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82 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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83 be 6-frame translated if the <queries> are amino acids. The output fields are
867692ec85aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mash commit 500478e8adcabf5249941012f78fe2140ecc7264
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84 [identity, shared-hashes, median-multiplicity, p-value, query-ID,
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85 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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86 on the number of observations of those hashes within the pool.
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87 ]]></help>
3
6d63b05cfea8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mash commit 24f4271bd62a3d96fec812eae2ad607f6a7f723c"
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88 <expand macro="citations"/>
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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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89 </tool>