Mercurial > repos > iuc > data_manager_mash_sketch_builder

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mash_sketch_builder/ commit 096286097ed5cdf189a1b68c3fc34d10f4142e54
author iuc
date Sun, 16 Apr 2023 08:30:43 +0000
parents 2af9137ba067
children
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1 <?xml version="1.0"?>
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2 <tool id="mash_sketch_builder" name="Mash Sketch" tool_type="manage_data" version="@TOOL_VERSION@+galaxy0" profile="18.09">
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3 <description>builder</description>
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4 <requirements>
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5 <requirement type="package" version="@TOOL_VERSION@">mash</requirement>
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6 <requirement type="package" version="3.7">python</requirement>
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7 </requirements>
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8 <macros>
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9 <token name="@TOOL_VERSION@">2.1</token>
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10 </macros>
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11 <version_command>mash --version</version_command>
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12 <command detect_errors="exit_code">
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13 <![CDATA[
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14 python '$__tool_directory__/mash_sketch_builder.py'
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15 '${out_file}'
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16 --threads \${GALAXY_SLOTS:-1}
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17 #if str( $input_sequence_source.input_sequence_source_selector ) == "tool_data_table":
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18 --fasta '${input_sequence_source.input_sequence.fields.path}'
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19 #elif str( $input_sequence_source.input_sequence_source_selector ) == 'history':
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20 --fasta '${input_sequence_source.input_sequence}'
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21 #end if
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22 --sketch-name '${sketch_name}'
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23 --sketch-size '${sketch_size}'
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24 --kmer-size '${kmer_size}'
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25 --probability-threshold '${probability_threshold}'
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26 ${individual_sequences}
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27 ]]>
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28 </command>
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29 <inputs>
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30 <conditional name="input_sequence_source">
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31 <param name="input_sequence_source_selector" type="select"
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32 label="Select a sequence from your history or use one from a tool data table?">
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33 <option value="tool_data_table">Sequence from tool data table</option>
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34 <option selected="True" value="history">Sequence from history</option>
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35 </param>
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36 <when value="tool_data_table">
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37 <param name="input_sequence" type="select" label="Source FASTA Sequence">
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38 <options from_data_table="all_fasta"/>
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39 </param>
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40 </when>
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41 <when value="history">
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42 <param name="input_sequence" type="data" format="fasta" label="Input sequence" help=""/>
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43 </when>
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44 </conditional>
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45 <param type="text" name="sketch_name" label="Sketch name" help="Human-readable description of the sketch"/>
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46 <param type="integer" name="sketch_size" value="1000" min="10" max="1000000" label="Sketch size" help="Each sketch will have at most this many non-redundant min-hashes."/>
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47 <param type="integer" name="kmer_size" value="21" min="1" max="32" label="K-mer size" help="Hashes will be based on strings of this many nucleotides."/>
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48 <param type="float" name="probability_threshold" value="0.01" min="0." max="1." label="Probability threshold for warning about low k-mer size." />
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49 <param type="boolean" name="individual_sequences" truevalue="--individual-sequences" falsevalue="" label="Sketch individual sequences" help="e.g. for multi-fastas of single-chromosome genomes or pair-wise gene comparisons."/>
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50 </inputs>
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51 <outputs>
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52 <data name="out_file" format="data_manager_json" />
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53 </outputs>
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54 <tests>
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55 <test>
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56 <param name="input_sequence_source_selector" value="history"/>
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57 <param name="input_sequence" value="test_assembly.fasta"/>
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58 <param name="sketch_name" value="Test Sketch" />
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59 <output name="out_file" value="mash_sketch_data_manager.json" compare="sim_size" />
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60 </test>
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61 </tests>
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62 <help><![CDATA[
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63
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64 **What it does**
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65
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66 Create a sketch file, which is a reduced representation of a sequence or set
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67 of sequences (based on min-hashes) that can be used for fast distance
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68 estimations. For output, one sketch file will be generated, but it can have
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69 multiple sketches within it, divided by sequences or files.
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70 ]]></help>
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71 <citations>
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72 <citation type="doi">10.1186/s13059-016-0997-x</citation>
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73 </citations>
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74 </tool>