Mercurial > repos > iuc > picrust2_pipeline

annotate picrust2_pipeline.xml @ 1:d6bb2e3febda draft default tip

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planemo upload for repository https://github.com/picrust/picrust2 commit f8c32a316582ff102c9b7edf3817000691ef9eea
author iuc
date Tue, 13 Aug 2024 12:10:47 +0000
parents 540aedfc81c7
children
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540aedfc81c7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
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1 <tool id="picrust2_pipeline" name="PICRUSt2 Full pipeline" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
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2 <description></description>
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
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6 <expand macro="bio_tool"/>
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7 <expand macro="requirements"/>
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8 <version_command>picrust2_pipeline.py -v</version_command>
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9 <command detect_errors="exit_code"><![CDATA[
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10 @VAR_ACCESS_FOO@
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11 @PLACE_SEQS_PREPROCESSING@
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12 @PREPARE_METAGENOME_PIPELINE_PARAMS@
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13
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14 picrust2_pipeline.py
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15 ## place_seqs parameters
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16 @PLACE_SEQS_PARAMS@
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17
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18 ## hsp parameters
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19 @HSP_PARAMS@
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20
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21 ## metagenome_pipeline parameters
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22 @METAGENOME_PIPELINE_PARAMS@
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23
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24 ## pathway_pipeline parameters
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25 #if $predict_pathways.no_pathways == ''
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26 @PATHWAY_PIPELINE_PARAMS@
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27 --reaction_func '$predict_pathways.reaction_map_file.reaction_func'
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28 #end if
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29
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30 #if $remove_intermediate is None
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31 --remove_intermediate
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32 #end if
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33
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34 --output 'full_pipeline_output'
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35 --processes "\${GALAXY_SLOTS:-1}"
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36 ## unzip all (potential) output files
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37 &&
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38 find full_pipeline_output -name "*.gz" -exec gunzip {} \;
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39 ## rename all tsv files to tabular to simplify discovery
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40 &&
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41 find full_pipeline_output -name "*.tsv" -exec sh -c 'mv {} \$(dirname {})/\$(basename {} .tsv).tabular' \;
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42 ## flatten metagenome output dirs ro simplify/enable discovery
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43 &&
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44 for d in full_pipeline_output/*_metagenome_out; do
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45 D=\$(basename \$d);
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46 for i in \$d/*; do
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47 I=\$(basename \$i);
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48 mv "\$i" "full_pipeline_output/""\$D""_""\$I";
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49 done;
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50 done;
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51 ]]></command>
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52 <inputs>
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53 <!-- place_seqs parameters -->
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54 <section name="place_seqs_section" title="Sequence placement options" expanded="true">
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55 <expand macro="place_seqs_params"/>
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56 </section>
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57
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58 <!-- hsp parameters -->
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59 <section name="hsp_section" title="Hidden state prediction (HSP) options" expanded="true">
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60 <expand macro="hsp_params" nsti_falsevalue="--skip_nsti" nsti_checked="true" in_trait_arg="--in_traits" in_trait_multiple="true" in_trait_label_suff="(s)" in_traits_help="Note that EC numbers will always be predicted unless --no_pathways is set">
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61 <token name="custom_traits">
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62 <!-- both go separately into hsp observed_trait_table -->
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63 <param argument="--custom_trait_tables" type="data" multiple="true" format="tabular" label="Customized trait table(s)" help="with gene families as columns and genomes as rows"/>
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64 <!-- by default 16S is used also goes into observed_trait_table -->
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65 <param argument="--marker_gene_table" type="data" format="tabular" optional="true" label="Table of predicted marker gene (16S or other) copy numbers" />
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66 </token>
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67 </expand>
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68 </section>
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69
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70 <!-- metagenome_pipeline parameters -->
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71 <section name="metagenome_pipeline_section" title="Metagenome prediction options" expanded="true">
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72 <expand macro="metagenome_pipeline_params" stratified_arg="--stratified"/>
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73 </section>
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74
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75 <!-- pathway_pipeline parameters -->
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76 <conditional name="predict_pathways">
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77 <param argument="--no_pathways" type="select" truevalue="" falsevalue="--no_pathways" checked="true" label="Infer pathways">
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78 <option value="">Yes</option>
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79 <option value="--no_pathways">No</option>
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80 </param>
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81 <when value="">
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82 <expand macro="pathway_pipeline_params" mapargument="--pathway_map"/>
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83 <conditional name="reaction_map_file">
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84 <param name="selector" type="select" label="Functional database to use as reactions for inferring pathway abundances">
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85 <option value="default" selected="true">Default functional database</option>
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86 <option value="custom">Customized reation functional map file</option>
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87 </param>
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88 <when value="default">
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89 <param argument="--reaction_func" type="select" label="Default functional database">
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90 <option value="COG">Clusters of Orthologous Genes database (COG)</option>
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91 <option value="EC" selected="true">Enzyme Commission number database (EC number)</option>
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92 <option value="KO">KEGG Orthology database (KO)</option>
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93 <option value="PFAM">Pfam database</option>
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94 <option value="TIGRFAM">TIGRFAM database</option>
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95 </param>
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96 </when>
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97 <when value="custom">
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98 <param argument="--reaction_func" type="data" format="tabular" label="Custom mapping table" help="An input 2 column map table linking function ids to descriptions for each function"/>
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99 </when>
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100 </conditional>
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101 </when>
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102 <when value="--no_pathways"/>
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103 </conditional>
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104 <param argument="--remove_intermediate" type="select" multiple="true" optional="true" label="Keep intermediate files of">
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105 <option value="place_seqs">place_seqs</option>
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106 <option value="pathways">pathways_pipeline</option>
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107 </param>
540aedfc81c7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
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diff changeset
108 </inputs>
540aedfc81c7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
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diff changeset
109 <outputs>
540aedfc81c7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
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diff changeset
110 <!-- place seqs outputs -->
540aedfc81c7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
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diff changeset
111 <expand macro="place_seqs_output" from_work_dir="full_pipeline_output/" label_suffix="(place_seqs)">
540aedfc81c7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
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diff changeset
112 <filter>remove_intermediate and "place_seqs" in remove_intermediate</filter>
540aedfc81c7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
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diff changeset
113 </expand>
540aedfc81c7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
114
540aedfc81c7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
115 <!-- hsp output -->
540aedfc81c7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
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diff changeset
116 <collection name="hsp_output" type="list" label="${tool.name} on ${on_string}: predicted copy numbers" >
540aedfc81c7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
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diff changeset
117 <discover_datasets pattern="(?P&lt;designation&gt;.+)_predicted\.tabular" directory="full_pipeline_output/" format="tabular"/>
540aedfc81c7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
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diff changeset
118 </collection>
540aedfc81c7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
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diff changeset
119
540aedfc81c7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
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diff changeset
120 <!-- metagenome output -->
540aedfc81c7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
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diff changeset
121 <collection name="metagenome_output" type="list:list" label="${tool.name} on ${on_string}: metagenome output" >
540aedfc81c7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
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diff changeset
122 <discover_datasets pattern="(?P&lt;identifier_0&gt;.+)_metagenome_out_(?P&lt;identifier_1&gt;.+)\.tabular" directory="full_pipeline_output/" format="tabular"/>
540aedfc81c7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
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diff changeset
123 </collection>
540aedfc81c7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
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diff changeset
124
540aedfc81c7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
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diff changeset
125 <!-- pathways output -->
540aedfc81c7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
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diff changeset
126 <expand macro="pathways_output" from_work_dir="full_pipeline_output/" label_suffix="pathways">
540aedfc81c7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
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diff changeset
127 <filter>predict_pathways["no_pathways"] == ""</filter>
540aedfc81c7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
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diff changeset
128 <token name="intermediate_filter">
540aedfc81c7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
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diff changeset
129 <filter>remove_intermediate and "pathways" in remove_intermediate</filter>
540aedfc81c7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
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diff changeset
130 </token>
540aedfc81c7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
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diff changeset
131 <token name="coverage_filter">
540aedfc81c7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
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132 <filter>predict_pathways["coverage"]</filter>
540aedfc81c7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
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133 </token>
540aedfc81c7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
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diff changeset
134 <token name="per_sequence_filter">
540aedfc81c7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
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diff changeset
135 <filter>predict_pathways["strat_output"]["per_sequence_contrib"]</filter>
540aedfc81c7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
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diff changeset
136 </token>
540aedfc81c7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
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diff changeset
137 </expand>
540aedfc81c7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
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diff changeset
138 </outputs>
540aedfc81c7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
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diff changeset
139 <tests>
540aedfc81c7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
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diff changeset
140 <test expect_num_outputs="5">
540aedfc81c7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
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diff changeset
141 <!-- place_seq -->
540aedfc81c7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
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diff changeset
142 <param name="study_fasta" value="study_seqs_full.fasta"/>
540aedfc81c7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
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diff changeset
143 <param name="placement_tool" value="sepp"/>
540aedfc81c7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
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diff changeset
144 <param name="min_align" value="0.0"/>
540aedfc81c7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
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diff changeset
145 <!-- hsp -->
540aedfc81c7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
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diff changeset
146 <conditional name="trait_input">
540aedfc81c7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
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diff changeset
147 <param name="selector" value="default"/>
540aedfc81c7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
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diff changeset
148 <param name="in_traits" value="EC,COG"/>
540aedfc81c7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
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diff changeset
149 </conditional>
540aedfc81c7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
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diff changeset
150 <param name="skip_nsti" value="false"/>
540aedfc81c7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
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diff changeset
151 <!-- metagenome -->
540aedfc81c7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
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parents:
diff changeset
152 <param name="input" value="workflow_seq_abun.biom"/>
540aedfc81c7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
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parents:
diff changeset
153 <conditional name="input_options">
540aedfc81c7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
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diff changeset
154 <param name="selector" value="ASV"/>
540aedfc81c7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
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diff changeset
155 <param name="min_reads" value="1"/>
540aedfc81c7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
156 <param name="min_samples" value="1"/>
540aedfc81c7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
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diff changeset
157 </conditional>
540aedfc81c7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
158 <param name="max_nsti" value="2.0"/>
540aedfc81c7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
159 <param name="skip_norm" value="false"/>
540aedfc81c7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
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parents:
diff changeset
160 <!-- pathway -->
540aedfc81c7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
161 <param name="skip_minpath" value="false"/>
540aedfc81c7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
162 <param name="no_gap_fill" value="true"/>
540aedfc81c7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
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diff changeset
163
540aedfc81c7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
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diff changeset
164 <param name="remove_intermediate" value="place_seqs"/>
540aedfc81c7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
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diff changeset
165 <output name="out_tree" ftype="newick">
540aedfc81c7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
166 <assert_contents>
540aedfc81c7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
167 <has_text text="643348582"/>
540aedfc81c7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
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diff changeset
168 <has_n_lines n="1"/>
540aedfc81c7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
169 </assert_contents>
540aedfc81c7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
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diff changeset
170 </output>
540aedfc81c7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
171 <output_collection name="place_seqs_intermediate_output" type="list" count="2">
540aedfc81c7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
172 <element name="query_align" ftype="stockholm">
540aedfc81c7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
173 <assert_contents>
540aedfc81c7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
174 <has_text text="STOCKHOLM 1.0"/>
540aedfc81c7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
175 <has_n_lines n="160106"/>
540aedfc81c7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
176 </assert_contents>
540aedfc81c7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
177 </element>
540aedfc81c7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
178 <element name="study_seqs_filtered" ftype="fasta">
540aedfc81c7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
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parents:
diff changeset
179 <assert_contents>
540aedfc81c7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
180 <has_text text="02905cfb87861c837dde629596d9272b"/>
540aedfc81c7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
181 <has_n_lines n="10"/>
540aedfc81c7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
182 </assert_contents>
540aedfc81c7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
183 </element>
540aedfc81c7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
184 </output_collection>
540aedfc81c7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
185 <output_collection name="hsp_output" type="list" count="3">
540aedfc81c7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
186 <element name="COG">
540aedfc81c7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
187 <assert_contents>
540aedfc81c7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
188 <has_text text="COG0001"/>
540aedfc81c7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
189 <has_n_lines n="6"/>
540aedfc81c7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
190 </assert_contents>
540aedfc81c7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
191 </element>
540aedfc81c7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
192 <element name="EC">
540aedfc81c7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
193 <assert_contents>
540aedfc81c7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
194 <has_text text="EC:1.1.1.1"/>
540aedfc81c7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
195 <has_n_lines n="6"/>
540aedfc81c7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
196 </assert_contents>
540aedfc81c7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
197 </element>
540aedfc81c7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
198 <element name="marker">
540aedfc81c7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
199 <assert_contents>
540aedfc81c7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
200 <has_text text="16S_rRNA_Count"/>
540aedfc81c7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
201 <has_n_lines n="6"/>
540aedfc81c7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
202 </assert_contents>
540aedfc81c7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
203 </element>
540aedfc81c7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
204 </output_collection>
540aedfc81c7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
205 <output_collection name="metagenome_output" type="list:list" count="2">
540aedfc81c7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
206 <element name="COG">
540aedfc81c7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
207 <element name="pred_metagenome_unstrat">
540aedfc81c7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
208 <assert_contents>
540aedfc81c7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
209 <has_text text="function"/>
540aedfc81c7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
210 <has_n_lines n="1793"/>
540aedfc81c7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
211 </assert_contents>
540aedfc81c7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
212 </element>
540aedfc81c7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
213 <element name="seqtab_norm">
540aedfc81c7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
214 <assert_contents>
540aedfc81c7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
215 <has_text text="normalized"/>
540aedfc81c7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
216 <has_n_lines n="6"/>
540aedfc81c7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
217 </assert_contents>
540aedfc81c7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
218 </element>
540aedfc81c7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
219 </element>
540aedfc81c7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
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parents:
diff changeset
220 <element name="EC">
540aedfc81c7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
221 <element name="pred_metagenome_unstrat">
540aedfc81c7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
222 <assert_contents>
540aedfc81c7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
223 <has_text text="function"/>
540aedfc81c7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
224 <has_n_lines n="768"/>
540aedfc81c7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
225 </assert_contents>
540aedfc81c7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
226 </element>
540aedfc81c7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
227 <element name="seqtab_norm">
540aedfc81c7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
228 <assert_contents>
540aedfc81c7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
229 <has_text text="normalized"/>
540aedfc81c7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
230 <has_n_lines n="6"/>
540aedfc81c7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
231 </assert_contents>
540aedfc81c7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
232 </element>
540aedfc81c7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
233 </element>
540aedfc81c7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
234 </output_collection>
540aedfc81c7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
235 <output name="pathways_output" ftype="tabular">
540aedfc81c7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
236 <assert_contents>
540aedfc81c7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
237 <has_text text="pathway"/>
540aedfc81c7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
238 <has_n_lines n="149"/>
540aedfc81c7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
239 <has_n_columns n="3"/>
540aedfc81c7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
240 </assert_contents>
540aedfc81c7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
241 </output>
540aedfc81c7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
242 </test>
540aedfc81c7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
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diff changeset
243 <!-- same as test 1, but only COG as in_traits (which has the same result since EC is added automatically), and test the other intermediate result -->
540aedfc81c7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
244 <test expect_num_outputs="5">
540aedfc81c7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
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diff changeset
245 <!-- place_seq -->
540aedfc81c7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
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diff changeset
246 <param name="study_fasta" value="study_seqs_full.fasta"/>
540aedfc81c7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
247 <param name="placement_tool" value="sepp"/>
540aedfc81c7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
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diff changeset
248 <param name="min_align" value="0.0"/>
540aedfc81c7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
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diff changeset
249 <!-- hsp -->
540aedfc81c7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
250 <conditional name="trait_input">
540aedfc81c7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
251 <param name="selector" value="default"/>
540aedfc81c7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
252 <param name="in_traits" value="COG"/>
540aedfc81c7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
253 </conditional>
540aedfc81c7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
254 <param name="skip_nsti" value="false"/>
540aedfc81c7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
255 <!-- metagenome -->
540aedfc81c7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
256 <param name="input" value="workflow_seq_abun.biom"/>
540aedfc81c7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
257 <conditional name="input_options">
540aedfc81c7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
258 <param name="selector" value="ASV"/>
540aedfc81c7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
259 <param name="min_reads" value="1"/>
540aedfc81c7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
260 <param name="min_samples" value="1"/>
540aedfc81c7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
261 </conditional>
540aedfc81c7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
262 <param name="max_nsti" value="2.0"/>
540aedfc81c7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
263 <param name="skip_norm" value="false"/>
540aedfc81c7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
264 <!-- pathway -->
540aedfc81c7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
265 <param name="skip_minpath" value="false"/>
540aedfc81c7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
266 <param name="no_gap_fill" value="true"/>
540aedfc81c7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
267
540aedfc81c7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
268 <param name="remove_intermediate" value="pathways"/>
540aedfc81c7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
269 <output name="out_tree" ftype="newick">
540aedfc81c7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
270 <assert_contents>
540aedfc81c7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
271 <has_text text="643348582"/>
540aedfc81c7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
272 <has_n_lines n="1"/>
540aedfc81c7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
273 </assert_contents>
540aedfc81c7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
274 </output>
540aedfc81c7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
275 <output_collection name="hsp_output" type="list" count="3">
540aedfc81c7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
276 <element name="COG" ftype="tabular">
540aedfc81c7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
277 <assert_contents>
540aedfc81c7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
278 <has_text text="COG0001"/>
540aedfc81c7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
279 <has_n_lines n="6"/>
540aedfc81c7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
280 <has_n_columns n="4599"/>
540aedfc81c7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
281 </assert_contents>
540aedfc81c7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
282 </element>
540aedfc81c7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
283 <element name="EC" ftype="tabular">
540aedfc81c7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
284 <assert_contents>
540aedfc81c7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
285 <has_text text="EC:1.1.1.1"/>
540aedfc81c7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
286 <has_n_lines n="6"/>
540aedfc81c7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
287 <has_n_columns n="2914"/>
540aedfc81c7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
288 </assert_contents>
540aedfc81c7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
289 </element>
540aedfc81c7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
290 <element name="marker" ftype="tabular">
540aedfc81c7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
291 <assert_contents>
540aedfc81c7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
292 <has_text text="16S_rRNA_Count"/>
540aedfc81c7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
293 <has_n_lines n="6"/>
540aedfc81c7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
294 <has_n_columns n="2"/>
540aedfc81c7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
295 </assert_contents>
540aedfc81c7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
296 </element>
540aedfc81c7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
297 </output_collection>
540aedfc81c7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
298
540aedfc81c7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
299 <output_collection name="metagenome_output" type="list:list" count="2">
540aedfc81c7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
300 <element name="COG">
540aedfc81c7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
301 <element name="pred_metagenome_unstrat" ftype="tabular">
540aedfc81c7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
302 <assert_contents>
540aedfc81c7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
303 <has_text text="function"/>
540aedfc81c7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
304 <has_n_lines n="1793"/>
540aedfc81c7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
305 <has_n_columns n="3"/>
540aedfc81c7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
306 </assert_contents>
540aedfc81c7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
307 </element>
540aedfc81c7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
308 <element name="seqtab_norm" ftype="tabular">
540aedfc81c7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
309 <assert_contents>
540aedfc81c7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
310 <has_text text="normalized"/>
540aedfc81c7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
311 <has_n_lines n="6"/>
540aedfc81c7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
312 <has_n_columns n="3"/>
540aedfc81c7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
313 </assert_contents>
540aedfc81c7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
314 </element>
540aedfc81c7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
315 </element>
540aedfc81c7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
316 <element name="EC">
540aedfc81c7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
317 <element name="pred_metagenome_unstrat" ftype="tabular">
540aedfc81c7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
318 <assert_contents>
540aedfc81c7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
319 <has_text text="function"/>
540aedfc81c7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
320 <has_n_lines n="768"/>
540aedfc81c7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
321 <has_n_columns n="3"/>
540aedfc81c7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
322 </assert_contents>
540aedfc81c7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
323 </element>
540aedfc81c7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
324 <element name="seqtab_norm" ftype="tabular">
540aedfc81c7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
325 <assert_contents>
540aedfc81c7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
326 <has_text text="normalized"/>
540aedfc81c7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
327 <has_n_lines n="6"/>
540aedfc81c7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
328 <has_n_columns n="3"/>
540aedfc81c7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
329 </assert_contents>
540aedfc81c7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
330 </element>
540aedfc81c7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
331 </element>
540aedfc81c7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
332 </output_collection>
540aedfc81c7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
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333 <output name="pathways_output" ftype="tabular">
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334 <assert_contents>
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335 <has_text text="pathway"/>
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336 <has_n_lines n="149"/>
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337 <has_n_columns n="3"/>
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338 </assert_contents>
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339 </output>
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340 <output_collection name="pathways_intermediate_output" type="list" count="1">
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341 <element name="regrouped_infile" ftype="tabular">
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342 <assert_contents>
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343 <has_text text="function"/>
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344 <has_n_lines n="1509"/>
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345 <has_n_columns n="3"/>
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346 </assert_contents>
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347 </element>
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348 </output_collection>
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349 </test>
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350 <!-- due to the long test times the other pathways_outputs
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351 have been tested manually -->
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352 </tests>
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353 <help><![CDATA[
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354 @HELP_HEADER@
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355
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356 PICRUSt2 full pipeline
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357 ======================
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358 Run sequence placement with EPA-NG and GAPPA to place study sequences (i.e. OTUs and ASVs) into a reference tree. Then runs hidden-state prediction with the castor R package to predict genome for each study sequence. Metagenome profiles are then generated, which can be optionally stratified by the contributing sequence. Finally, pathway abundances are predicted based on metagenome profiles. By default, output files include predictions for Enzyme Commission (EC) numbers, KEGG Orthologs (KOs), and MetaCyc pathway abundances. However, the tool enables users to use custom reference and trait tables to customize analyses.
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359
540aedfc81c7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
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360 Note
540aedfc81c7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
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361 ====
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362 The standard pipeline will generate metagenome predictions for 16S rRNA gene data.
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363
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364 Input
540aedfc81c7 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
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365 =====
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366 1. A FASTA of amplicon sequences variants (ASVs; i.e. your representative sequences, not your raw reads)
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367 2. A BIOM table of the abundance of each ASV across each sample.
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368
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369 Output
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370 ======
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371 1. Output tree with placed study sequences.
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372 2. Metagenome Predictions
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373 3. Pathway level predictions
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374
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375 ]]></help>
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376 <citations>
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377 <citation type="doi">10.1038/s41587-020-0548-6</citation>
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378 </citations>
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379 </tool>