Mercurial > repos > oinizan > frogs_func

annotate FROGS_FUNC.xml @ 0:7275d6a514d2 draft default tip

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planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 0e048f8e3dfce3c6abe2facd83ab95d62d42dab8
author oinizan
date Wed, 28 Jan 2026 16:20:19 +0000
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1 <tool id="FROGS_Func" name="FROGS Func" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" python_template_version="3.5" profile="24.0">
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2 <description>Prediction of functional abundances using marker gene sequences</description>
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3 <macros>
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4 <import>frogs_func_macros.xml</import>
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5 <import>picrust2_placeseq_and_copynumber_macros.xml</import>
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6 <import>picrust2_functions_macros.xml</import>
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7 <import>picrust2_pathways_macros.xml</import>
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8 </macros>
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10 <expand macro="frogs_func_requirements" />
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11
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12 <command detect_errors="exit_code"><![CDATA[
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13 #if $frogs_func_tools.tool_name == "picrust2_placeseq_and_copynumber"
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14 @PICRUST2_PLACESEQ_AND_COPYNUMBER_CMD_LINE@
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15
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16 #elif $frogs_func_tools.tool_name == "picrust2_functions"
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17 @PICRUST2_FUNCTIONS_CMD_LINE@
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19 #elif $frogs_func_tools.tool_name == "picrust2_pathways"
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20 @PICRUST2_PATHWAYS_CMD_LINE@
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21 #end if
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22 ]]>
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23 </command>
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24
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25 <inputs>
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26 <conditional name="frogs_func_tools">
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27 <param name="tool_name" type="select" display="radio" label="Select a tool from the FROGS Func suite to run your analysis.">
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28 <option value="" selected="true">-- Please select a tool --</option>
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29 <option value="picrust2_placeseq_and_copynumber"> Tool 1: sequence placement and gene copy number estimation (PICRUSt2)</option>
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30 <option value="picrust2_functions">Tool 2: functional abundance estimation (PICRUSt2)</option>
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31 <option value="picrust2_pathways">Tool 3: pathway abundance estimation (PICRUSt2)</option>
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32 </param>
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33 <when value=""/>
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34 <!-- ##################### picrust2_placeseq_and_copynumber ##################### -->
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35 <when value="picrust2_placeseq_and_copynumber">
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36 <expand macro="picrust2_placeseq_and_copynumber_inputs" />
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37 </when>
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38 <!-- ##################### picrust2_functions ##################### -->
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39 <when value="picrust2_functions">
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40 <expand macro="picrust2_functions_inputs" />
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41 </when>
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42 <!-- ##################### picrust2_pathways ##################### -->
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43 <when value="picrust2_pathways">
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44 <expand macro="picrust2_pathways_inputs" />
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45 </when>
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46 </conditional>
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47 </inputs>
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48
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49 <outputs>
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50 <expand macro="frogs_func_outputs" />
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51 </outputs>
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52
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53 <tests>
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54 <!-- ##################### 1 picrust2_placeseq_and_copynumber ##################### -->
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55 <test expect_num_outputs="7">
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56 <conditional name="frogs_func_tools">
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57 <param name="tool_name" value="picrust2_placeseq_and_copynumber"/>
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58 <expand macro="picrust2_placeseq_and_copynumber_test_input"/>
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59 </conditional>
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60 <expand macro="picrust2_placeseq_and_copynumber_test_output"/>
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61 </test>
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62 <!-- ##################### 2 picrust2_functions ##################### -->
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63 <test expect_num_outputs="8">
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64 <conditional name="frogs_func_tools">
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65 <param name="tool_name" value="picrust2_functions"/>
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66 <expand macro="picrust2_functions_test_input"/>
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67 </conditional>
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68 <expand macro="picrust2_functions_test_output"/>
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69 </test>
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70 <!-- ##################### 3 picrust2_pathways ##################### -->
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71 <test expect_num_outputs="2">
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72 <conditional name="frogs_func_tools">
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73 <param name="tool_name" value="picrust2_pathways"/>
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74 <expand macro="picrust2_pathways_test_input"/>
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75 </conditional>
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76 <expand macro="picrust2_pathways_test_output"/>
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77 </test>
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78 </tests>
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79
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80 <help><![CDATA[
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81 For more information and detailed documentation, visit the FROGS website https://frogs.inrae.fr.
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82 ]]>
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83 </help>
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84
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85 <citations>
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86 <citation type="doi">10.1093/bioinformatics/btx791</citation>
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87 <citation type="doi">10.1093/bib/bbab318</citation>
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88 </citations>
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89
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90 </tool>