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1 <?xml version="1.0"?>
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2 <tool name="BloomTree Manager - Query" id="btman_query" version="1.0.0">
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3 <description>the Sequence Bloom Tree</description>
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4 <requirements>
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5 <requirement type="package" version="2.7.10">python</requirement>
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6 <requirement type="package" version="2.18.4">requests</requirement>
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7 </requirements>
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8 <command detect_errors="exit_code">
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9 <![CDATA[
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10 python '$__tool_directory__/query.py'
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11
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4
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12 --tree 1
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13 --search 'rrr'
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14 --sthreshold ${sthreshold}
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10
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15 --sort ${sortcontrol}
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16 --exact 0
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17
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18 #if $conditional_input.inputtype == '0':
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19 #set file_paths = ','.join( [ str( $f ) for $f in $conditional_input.txtfiles ] )
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20 #if $file_paths is not 'None':
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21 --files '${file_paths}'
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22 #set file_names = ','.join( [ str( $f.name ) for $f in $conditional_input.txtfiles ] )
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23 --names '${file_names}'
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24 #end if
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25 #elif $conditional_input.inputtype == '1':
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26 --sequences '${conditional_input.sequences}'
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27 #end if
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28
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29 --outputdir 'collection_content'
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30 ]]>
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31 </command>
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32 <inputs>
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33 <conditional name="conditional_input">
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34 <param name="inputtype" type="select" label="Input mode" help="Select a mode based on how do you want to specify the input">
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35 <option value="0" selected="true">By file</option>
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36 <option value="1">By manually inserted text</option>
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37 </param>
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38 <when value="0">
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2
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39 <param format="tabular" name="txtfiles" type="data" label="Select files" multiple="true" optional="false" help="Select one or more tabular files containing (ID, TRANSCRIPT) couples for each line. The content of these files will be merged and the result will represent a query to the Sequence Bloom Tree that will return a collection containing a file for each ID. The content of these files as result of the tool will be a list of accession numbers." />
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40 </when>
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41 <when value="1">
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2
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42 <param name="sequences" type="text" area="True" size="5x25" label="Manually insert sequences" optional="false" help="Insert a list of (ID, TRANSCRIPT) couples in a tab delimited format, one for each line. The content of this text box will represent a query to the Sequence Bloom Tree that will return a collection containing a file for each ID. The content of these files as result of the tool will be a list of accession numbers." />
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43 </when>
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44 </conditional>
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45 <param name="sthreshold" size="3" type="float" value="0.7" min="0.0" max="1.0" label="Search threshold" help="This threshold controls the specificity. Lower values will produce more hits to the query. Higher values are more stringent and will produce fewer hits." />
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46 <param name="sortcontrol" type="boolean" checked="true" truevalue="1" falsevalue="0" label="Sort the result by the number of hits per transcript." />
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47 </inputs>
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48 <outputs>
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49 <collection name="output_collect" type="list" label="BloomTree Manager - Query result collection">
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50 <discover_datasets pattern="(?P<identifier_0>[^_]+)_(?P<ext>[^_]+)" directory="collection_content" ext="auto" />
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51 </collection>
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52 </outputs>
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53
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54 <help><![CDATA[
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55 This Query tool is part of the BloomTree Manager Framework that allow to rapidly identify all publicly available
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56 sequenced samples which express a transcript of interest.
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57
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58 ----
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59
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60 The input for this tool is a list of (ID, TRANSCRIPT) couples, one for each line,
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61 in a tab delimited format::
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62
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63 id0 CCAACCAAAGGGAAAACTTTTTTCCGACTTTGGCCTAAAGGGTTTAACGGCCAAGTCAGAAGGGAAAAAGTTGCGCCA
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64 id1 TTAATGACAGGGCCACATGATGTGAAAAAAAATCAGAAACCGAGTCAACGTGAGAAGATAGTACGTACTACCGCAAAT
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65 ...
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66 idn CAATTAATGATAAATATTTTATAAGGTGCGGAAATAAAGTGAGGAATATCTTTTAAATTCAAGTTCAATTCTGAAAGC
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67
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68 The ID can contain alphanumeric characters in addition to spaces, dots, dashes, and round and square brackets.
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69 Any additional character will be trimmed out.
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70
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71 The output of the tool is a collection that contains a file for each ID with a list of
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72 accession numbers representing the samples that express one particular transcript.
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73
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74 ----
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75
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76 .. class:: infomark
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77
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78 **Notes**
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79
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80 This Galaxy tool has been developed by Fabio Cumbo.
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81
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82 Please visit this GithHub_repository_ for more information about the BloomTree Manager
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83
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84 .. _GithHub_repository: https://github.com/fabio-cumbo/bloomtree-manager
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85 ]]></help>
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86
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87 <citations>
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88 <citation type="doi">10.1101/090464</citation>
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89 </citations>
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90 </tool>
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