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1 <tool id="mt_for_mq" name="MT_for_MQ" version="1.0">
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2 <description>Tool to prepare outputs from ASaiM for Metaquantome</description>
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3 <requirements>
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4 <requirement type="package" version="1.2.1">r-tidyverse</requirement>
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5 <requirement type="package" version="1.0.0">r-dplyr</requirement>
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6 <requirement type="package" version="1.3.1">r-readr</requirement>
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7 </requirements>
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8 <command detect_errors="exit_code"><![CDATA[
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9
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10 #if $options.mode == "f" or $options.mode == "ft":
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11 Rscript '$__tool_directory__/MT_for_iMQ.R' '$options.input_files' '$options.mode' $options.ontology $mq_output
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12 #elif $options.mode == "t":
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13 mkdir in_dir
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14 #for $input in $options.input_files:
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15 && cp '$input' 'in_dir/${input.name.rsplit('.',1)[0]}'
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16 #end for
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17 && Rscript '$__tool_directory__/MT_for_iMQ.R' in_dir t NA $mq_output
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18 #end if
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19
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20 ]]>
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21 </command>
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22
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23 <inputs>
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24 <conditional name="options">
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25 <param type="select" display="radio" name="mode" label="Mode">
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26 <option value="f">Functional</option>
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27 <option value="t" selected="true">Taxonomic</option>
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28 <option value="ft">Functional-Taxonomic</option>
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29 </param>
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30 <when value="t">
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31 <param name="ontology" type="hidden" value="NA" />
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32 <param type="data" name="input_files" format="tsv,tabular,txt" label="Files from ASaiM for all samples (named after sample)" multiple="true" />
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33 </when>
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34 <when value="f">
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35 <param type="select" name="ontology" label="GO namespace" multiple="true" optional="false">
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36 <option value="molecular_function">molecular function</option>
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37 <option value="biological_process">biological proces</option>
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38 <option value="cellular_component">cellular component</option>
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39 </param>
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40 <param type="data" name="input_files" format="tsv,tabular,txt" label="File from HIUMAnN2 renormalize function" />
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41 </when>
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42 <when value="ft">
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43 <param type="select" name="ontology" label="GO namespace" multiple="true" optional="false">
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44 <option value="molecular_function">molecular function</option>
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45 <option value="biological_process">biological proces</option>
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46 <option value="cellular_component">cellular component</option>
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47 </param>
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48 <param type="data" name="input_files" format="tsv,tabular,txt" label="File from HIUMAnN2 renormalize function" />
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49 </when>
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50 </conditional>
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51 </inputs>
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52
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53 <outputs>
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54 <data name="mq_output" format="tabular" label="mq_${options.mode}_input.tabular"/>
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55 </outputs>
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56
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57
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58 <tests>
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59 <test>
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60 <param name="input_files" value="T4A.tsv,T4B.tsv,T4C.tsv,T7A.tsv,T7B.tsv,T7C.tsv" ftype="tsv"/>
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61 <param name="mode" value="f"/>
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62 <param name="ontology" value="molecular_function,biological_process"/>
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63 <output name="mq_output" file="mq_input.tabular">
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64 <assert_contents>
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65 <has_text text="namespace"/>
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66 </assert_contents>
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67 </output>
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68 </test>
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69 </tests>
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70
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71
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72
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73 <help><![CDATA[
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74
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75 **MT2MQ**: Metatranscriptomics to Metaquantome
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76
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77 MT2MQ is a tool to prepare metatrascriptomic results for further analysis with MetaQuantome, which currently only supports metaproteomic data.
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78 This tool takes in tabular files with taxonomic or functional results acquired from metatranscriptomic data. If taxonomic, the data should be the genus-level MetaPhlan results. If functional, the data should be the gene families output from HUMAnN2. Each sample and replicate should be contained in a single file, which must be named as the sample is.
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79
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80 **Outputs**:
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81
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82 MT2MQ produces a single tabular output, formatted to be used as input for Metaquantome.
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83
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84 ]]></help>
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85
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86 <citations>
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87 <citation type="bibtex">
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88 @misc{MT_for_MQ,
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89 author={Crane, Marie},
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90 year={2020},
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91 title={ASaiM to MetaQuantome}
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92 }
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93 </citation>
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94 </citations>
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95 </tool> |
