Mercurial > repos > iuc > picrust2_pipeline

annotate picrust2_pipeline.xml @ 1:33770798ef12 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 12:09:11 +0000
parents 37918ad187d3
children
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37918ad187d3 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
37918ad187d3 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
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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
37918ad187d3 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
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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 &&
37918ad187d3 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
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38 find full_pipeline_output -name "*.gz" -exec gunzip {} \;
37918ad187d3 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
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39 ## rename all tsv files to tabular to simplify discovery
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40 &&
37918ad187d3 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
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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;
37918ad187d3 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
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50 done;
37918ad187d3 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
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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">
37918ad187d3 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
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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>
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108 </inputs>
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109 <outputs>
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110 <!-- place seqs outputs -->
37918ad187d3 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
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111 <expand macro="place_seqs_output" from_work_dir="full_pipeline_output/" label_suffix="(place_seqs)">
37918ad187d3 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
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112 <filter>remove_intermediate and "place_seqs" in remove_intermediate</filter>
37918ad187d3 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
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113 </expand>
37918ad187d3 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
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diff changeset
114
37918ad187d3 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
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diff changeset
115 <!-- hsp output -->
37918ad187d3 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
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116 <collection name="hsp_output" type="list" label="${tool.name} on ${on_string}: predicted copy numbers" >
37918ad187d3 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
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117 <discover_datasets pattern="(?P&lt;designation&gt;.+)_predicted\.tabular" directory="full_pipeline_output/" format="tabular"/>
37918ad187d3 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
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118 </collection>
37918ad187d3 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
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diff changeset
119
37918ad187d3 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
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diff changeset
120 <!-- metagenome output -->
37918ad187d3 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
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121 <collection name="metagenome_output" type="list:list" label="${tool.name} on ${on_string}: metagenome output" >
37918ad187d3 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"/>
37918ad187d3 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
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123 </collection>
37918ad187d3 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
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diff changeset
124
37918ad187d3 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
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diff changeset
125 <!-- pathways output -->
37918ad187d3 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
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126 <expand macro="pathways_output" from_work_dir="full_pipeline_output/" label_suffix="pathways">
37918ad187d3 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
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127 <filter>predict_pathways["no_pathways"] == ""</filter>
37918ad187d3 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
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128 <token name="intermediate_filter">
37918ad187d3 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
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129 <filter>remove_intermediate and "pathways" in remove_intermediate</filter>
37918ad187d3 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
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130 </token>
37918ad187d3 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
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131 <token name="coverage_filter">
37918ad187d3 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
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132 <filter>predict_pathways["coverage"]</filter>
37918ad187d3 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
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133 </token>
37918ad187d3 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
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134 <token name="per_sequence_filter">
37918ad187d3 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
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135 <filter>predict_pathways["strat_output"]["per_sequence_contrib"]</filter>
37918ad187d3 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
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136 </token>
37918ad187d3 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
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diff changeset
137 </expand>
37918ad187d3 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
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138 </outputs>
37918ad187d3 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
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139 <tests>
37918ad187d3 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
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140 <test expect_num_outputs="5">
37918ad187d3 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
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141 <!-- place_seq -->
37918ad187d3 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
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142 <param name="study_fasta" value="study_seqs_full.fasta"/>
37918ad187d3 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
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143 <param name="placement_tool" value="sepp"/>
37918ad187d3 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
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144 <param name="min_align" value="0.0"/>
37918ad187d3 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
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145 <!-- hsp -->
37918ad187d3 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
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diff changeset
146 <conditional name="trait_input">
37918ad187d3 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
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147 <param name="selector" value="default"/>
37918ad187d3 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
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148 <param name="in_traits" value="EC,COG"/>
37918ad187d3 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
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149 </conditional>
37918ad187d3 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
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150 <param name="skip_nsti" value="false"/>
37918ad187d3 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
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diff changeset
151 <!-- metagenome -->
37918ad187d3 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
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diff changeset
152 <param name="input" value="workflow_seq_abun.biom"/>
37918ad187d3 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
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diff changeset
153 <conditional name="input_options">
37918ad187d3 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
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154 <param name="selector" value="ASV"/>
37918ad187d3 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
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155 <param name="min_reads" value="1"/>
37918ad187d3 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
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diff changeset
156 <param name="min_samples" value="1"/>
37918ad187d3 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
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157 </conditional>
37918ad187d3 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
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diff changeset
158 <param name="max_nsti" value="2.0"/>
37918ad187d3 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
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diff changeset
159 <param name="skip_norm" value="false"/>
37918ad187d3 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
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diff changeset
160 <!-- pathway -->
37918ad187d3 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
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diff changeset
161 <param name="skip_minpath" value="false"/>
37918ad187d3 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
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diff changeset
162 <param name="no_gap_fill" value="true"/>
37918ad187d3 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
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diff changeset
163
37918ad187d3 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"/>
37918ad187d3 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
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diff changeset
165 <output name="out_tree" ftype="newick">
37918ad187d3 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
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166 <assert_contents>
37918ad187d3 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
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167 <has_text text="643348582"/>
37918ad187d3 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
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168 <has_n_lines n="1"/>
37918ad187d3 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
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diff changeset
169 </assert_contents>
37918ad187d3 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
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diff changeset
170 </output>
37918ad187d3 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
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diff changeset
171 <output_collection name="place_seqs_intermediate_output" type="list" count="2">
37918ad187d3 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
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diff changeset
172 <element name="query_align" ftype="stockholm">
37918ad187d3 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
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diff changeset
173 <assert_contents>
37918ad187d3 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
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diff changeset
174 <has_text text="STOCKHOLM 1.0"/>
37918ad187d3 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
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diff changeset
175 <has_n_lines n="160106"/>
37918ad187d3 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
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diff changeset
176 </assert_contents>
37918ad187d3 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
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diff changeset
177 </element>
37918ad187d3 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
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diff changeset
178 <element name="study_seqs_filtered" ftype="fasta">
37918ad187d3 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
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diff changeset
179 <assert_contents>
37918ad187d3 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
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diff changeset
180 <has_text text="02905cfb87861c837dde629596d9272b"/>
37918ad187d3 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
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diff changeset
181 <has_n_lines n="10"/>
37918ad187d3 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
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diff changeset
182 </assert_contents>
37918ad187d3 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
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diff changeset
183 </element>
37918ad187d3 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
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diff changeset
184 </output_collection>
37918ad187d3 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
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diff changeset
185 <output_collection name="hsp_output" type="list" count="3">
37918ad187d3 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
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diff changeset
186 <element name="COG">
37918ad187d3 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
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diff changeset
187 <assert_contents>
37918ad187d3 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
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diff changeset
188 <has_text text="COG0001"/>
37918ad187d3 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
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diff changeset
189 <has_n_lines n="6"/>
37918ad187d3 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
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diff changeset
190 </assert_contents>
37918ad187d3 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
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diff changeset
191 </element>
37918ad187d3 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
192 <element name="EC">
37918ad187d3 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
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parents:
diff changeset
193 <assert_contents>
37918ad187d3 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
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diff changeset
194 <has_text text="EC:1.1.1.1"/>
37918ad187d3 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
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diff changeset
195 <has_n_lines n="6"/>
37918ad187d3 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
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parents:
diff changeset
196 </assert_contents>
37918ad187d3 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
197 </element>
37918ad187d3 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
198 <element name="marker">
37918ad187d3 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
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diff changeset
199 <assert_contents>
37918ad187d3 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
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diff changeset
200 <has_text text="16S_rRNA_Count"/>
37918ad187d3 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
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diff changeset
201 <has_n_lines n="6"/>
37918ad187d3 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
202 </assert_contents>
37918ad187d3 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
203 </element>
37918ad187d3 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
204 </output_collection>
37918ad187d3 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">
37918ad187d3 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
206 <element name="COG">
37918ad187d3 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
207 <element name="pred_metagenome_unstrat">
37918ad187d3 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
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diff changeset
208 <assert_contents>
37918ad187d3 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
209 <has_text text="function"/>
37918ad187d3 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
210 <has_n_lines n="1793"/>
37918ad187d3 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
211 </assert_contents>
37918ad187d3 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
212 </element>
37918ad187d3 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
213 <element name="seqtab_norm">
37918ad187d3 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
214 <assert_contents>
37918ad187d3 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
215 <has_text text="normalized"/>
37918ad187d3 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
216 <has_n_lines n="6"/>
37918ad187d3 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
217 </assert_contents>
37918ad187d3 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
218 </element>
37918ad187d3 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
219 </element>
37918ad187d3 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
220 <element name="EC">
37918ad187d3 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
221 <element name="pred_metagenome_unstrat">
37918ad187d3 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
222 <assert_contents>
37918ad187d3 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
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diff changeset
223 <has_text text="function"/>
37918ad187d3 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
224 <has_n_lines n="768"/>
37918ad187d3 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
225 </assert_contents>
37918ad187d3 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
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diff changeset
226 </element>
37918ad187d3 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
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diff changeset
227 <element name="seqtab_norm">
37918ad187d3 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
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diff changeset
228 <assert_contents>
37918ad187d3 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
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diff changeset
229 <has_text text="normalized"/>
37918ad187d3 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
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diff changeset
230 <has_n_lines n="6"/>
37918ad187d3 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
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diff changeset
231 </assert_contents>
37918ad187d3 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
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diff changeset
232 </element>
37918ad187d3 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
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diff changeset
233 </element>
37918ad187d3 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
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diff changeset
234 </output_collection>
37918ad187d3 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
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diff changeset
235 <output name="pathways_output" ftype="tabular">
37918ad187d3 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
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diff changeset
236 <assert_contents>
37918ad187d3 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
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diff changeset
237 <has_text text="pathway"/>
37918ad187d3 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
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diff changeset
238 <has_n_lines n="149"/>
37918ad187d3 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
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diff changeset
239 <has_n_columns n="3"/>
37918ad187d3 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
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diff changeset
240 </assert_contents>
37918ad187d3 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
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diff changeset
241 </output>
37918ad187d3 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
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diff changeset
242 </test>
37918ad187d3 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
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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 -->
37918ad187d3 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
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diff changeset
244 <test expect_num_outputs="5">
37918ad187d3 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
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diff changeset
245 <!-- place_seq -->
37918ad187d3 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
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diff changeset
246 <param name="study_fasta" value="study_seqs_full.fasta"/>
37918ad187d3 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
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diff changeset
247 <param name="placement_tool" value="sepp"/>
37918ad187d3 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
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diff changeset
248 <param name="min_align" value="0.0"/>
37918ad187d3 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
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249 <!-- hsp -->
37918ad187d3 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
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diff changeset
250 <conditional name="trait_input">
37918ad187d3 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
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diff changeset
251 <param name="selector" value="default"/>
37918ad187d3 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
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diff changeset
252 <param name="in_traits" value="COG"/>
37918ad187d3 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
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diff changeset
253 </conditional>
37918ad187d3 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
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diff changeset
254 <param name="skip_nsti" value="false"/>
37918ad187d3 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
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diff changeset
255 <!-- metagenome -->
37918ad187d3 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
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parents:
diff changeset
256 <param name="input" value="workflow_seq_abun.biom"/>
37918ad187d3 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
257 <conditional name="input_options">
37918ad187d3 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
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diff changeset
258 <param name="selector" value="ASV"/>
37918ad187d3 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
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diff changeset
259 <param name="min_reads" value="1"/>
37918ad187d3 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
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diff changeset
260 <param name="min_samples" value="1"/>
37918ad187d3 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
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diff changeset
261 </conditional>
37918ad187d3 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
262 <param name="max_nsti" value="2.0"/>
37918ad187d3 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
263 <param name="skip_norm" value="false"/>
37918ad187d3 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
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diff changeset
264 <!-- pathway -->
37918ad187d3 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
265 <param name="skip_minpath" value="false"/>
37918ad187d3 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
266 <param name="no_gap_fill" value="true"/>
37918ad187d3 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
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diff changeset
267
37918ad187d3 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
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diff changeset
268 <param name="remove_intermediate" value="pathways"/>
37918ad187d3 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
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diff changeset
269 <output name="out_tree" ftype="newick">
37918ad187d3 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
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diff changeset
270 <assert_contents>
37918ad187d3 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
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diff changeset
271 <has_text text="643348582"/>
37918ad187d3 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
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diff changeset
272 <has_n_lines n="1"/>
37918ad187d3 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
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diff changeset
273 </assert_contents>
37918ad187d3 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
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diff changeset
274 </output>
37918ad187d3 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">
37918ad187d3 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
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diff changeset
276 <element name="COG" ftype="tabular">
37918ad187d3 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
277 <assert_contents>
37918ad187d3 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
278 <has_text text="COG0001"/>
37918ad187d3 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
279 <has_n_lines n="6"/>
37918ad187d3 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
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diff changeset
280 <has_n_columns n="4599"/>
37918ad187d3 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
281 </assert_contents>
37918ad187d3 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
282 </element>
37918ad187d3 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
283 <element name="EC" ftype="tabular">
37918ad187d3 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
284 <assert_contents>
37918ad187d3 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
285 <has_text text="EC:1.1.1.1"/>
37918ad187d3 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
286 <has_n_lines n="6"/>
37918ad187d3 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
287 <has_n_columns n="2914"/>
37918ad187d3 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
288 </assert_contents>
37918ad187d3 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
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diff changeset
289 </element>
37918ad187d3 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
290 <element name="marker" ftype="tabular">
37918ad187d3 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
291 <assert_contents>
37918ad187d3 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
292 <has_text text="16S_rRNA_Count"/>
37918ad187d3 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
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diff changeset
293 <has_n_lines n="6"/>
37918ad187d3 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
294 <has_n_columns n="2"/>
37918ad187d3 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
295 </assert_contents>
37918ad187d3 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
296 </element>
37918ad187d3 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
297 </output_collection>
37918ad187d3 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
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diff changeset
298
37918ad187d3 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">
37918ad187d3 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
300 <element name="COG">
37918ad187d3 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
301 <element name="pred_metagenome_unstrat" ftype="tabular">
37918ad187d3 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
302 <assert_contents>
37918ad187d3 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
303 <has_text text="function"/>
37918ad187d3 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
304 <has_n_lines n="1793"/>
37918ad187d3 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
305 <has_n_columns n="3"/>
37918ad187d3 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
306 </assert_contents>
37918ad187d3 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
307 </element>
37918ad187d3 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
308 <element name="seqtab_norm" ftype="tabular">
37918ad187d3 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
309 <assert_contents>
37918ad187d3 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
310 <has_text text="normalized"/>
37918ad187d3 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
311 <has_n_lines n="6"/>
37918ad187d3 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
312 <has_n_columns n="3"/>
37918ad187d3 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
313 </assert_contents>
37918ad187d3 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
314 </element>
37918ad187d3 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
315 </element>
37918ad187d3 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
316 <element name="EC">
37918ad187d3 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
317 <element name="pred_metagenome_unstrat" ftype="tabular">
37918ad187d3 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
318 <assert_contents>
37918ad187d3 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
319 <has_text text="function"/>
37918ad187d3 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
320 <has_n_lines n="768"/>
37918ad187d3 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
321 <has_n_columns n="3"/>
37918ad187d3 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
322 </assert_contents>
37918ad187d3 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
323 </element>
37918ad187d3 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
324 <element name="seqtab_norm" ftype="tabular">
37918ad187d3 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
325 <assert_contents>
37918ad187d3 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
326 <has_text text="normalized"/>
37918ad187d3 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
327 <has_n_lines n="6"/>
37918ad187d3 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
328 <has_n_columns n="3"/>
37918ad187d3 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
329 </assert_contents>
37918ad187d3 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
330 </element>
37918ad187d3 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
331 </element>
37918ad187d3 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
332 </output_collection>
37918ad187d3 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
333 <output name="pathways_output" ftype="tabular">
37918ad187d3 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
334 <assert_contents>
37918ad187d3 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
335 <has_text text="pathway"/>
37918ad187d3 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
diff changeset
336 <has_n_lines n="149"/>
37918ad187d3 planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
iuc
parents:
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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
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360 Note
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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
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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>