Mercurial > repos > frogs > frogs_stat
diff FROGS_STAT.xml @ 0:6507a8d42a4f draft default tip
planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 78ca62b54aee22893d278d9c3d495527be405f8a
| author | frogs |
|---|---|
| date | Wed, 04 Feb 2026 13:16:44 +0000 |
| parents | |
| children |
line wrap: on
line diff
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/FROGS_STAT.xml Wed Feb 04 13:16:44 2026 +0000 @@ -0,0 +1,224 @@ +<tool id="FROGS_Stat" name="FROGS Stat" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" python_template_version="3.5" profile="24.0"> + <description>Analysis of community structure, composition, and differential abundances</description> + <macros> + <import>frogs_stat_macros.xml</import> + <import>phyloseq_import_macros.xml</import> + <import>phyloseq_composition_macros.xml</import> + <import>phyloseq_alpha_diversity_macros.xml</import> + <import>phyloseq_beta_diversity_macros.xml</import> + <import>phyloseq_clustering_macros.xml</import> + <import>phyloseq_structure_macros.xml</import> + <import>phyloseq_manova_macros.xml</import> + <import>deseq2_preprocess_macros.xml</import> + <import>deseq2_visualisation_macros.xml</import> + </macros> + + <expand macro="frogs_stat_requirements" /> + + <command detect_errors="exit_code"><![CDATA[ + #if $frogs_stat_tools.tool_name == "phyloseq_import": + @PHYLOSEQ_IMPORT_CMD_LINE@ + + #elif $frogs_stat_tools.tool_name == "phyloseq_composition": + @PHYLOSEQ_COMPOSITION_CMD_LINE@ + + #elif $frogs_stat_tools.tool_name == "phyloseq_alpha_diversity": + @PHYLOSEQ_ALPHA_DIVERSITY_CMD_LINE@ + + #elif $frogs_stat_tools.tool_name == "phyloseq_beta_diversity": + @PHYLOSEQ_BETA_DIVERSITY_CMD_LINE@ + + #elif $frogs_stat_tools.tool_name == "phyloseq_clustering": + @PHYLOSEQ_CLUSTERING_CMD_LINE@ + + #elif $frogs_stat_tools.tool_name == "phyloseq_structure": + @PHYLOSEQ_STRUCTURE_CMD_LINE@ + + #elif $frogs_stat_tools.tool_name == "phyloseq_manova": + @PHYLOSEQ_MANOVA_CMD_LINE@ + + #elif $frogs_stat_tools.tool_name == "deseq2_asv_preprocess": + @DESEQ2_ASV_PREPROCESS_CMD_LINE@ + + #elif $frogs_stat_tools.tool_name == "deseq2_fun_preprocess": + @DESEQ2_FUN_PREPROCESS_CMD_LINE@ + + #elif $frogs_stat_tools.tool_name == "deseq2_asv_visualisation": + @DESEQ2_ASV_VISUALISATION_CMD_LINE@ + + #elif $frogs_stat_tools.tool_name == "deseq2_fun_visualisation": + @DESEQ2_FUN_VISUALISATION_CMD_LINE@ + #end if + ]]> + </command> + + <inputs> + <conditional name="frogs_stat_tools"> + <param name="tool_name" type="select" display="radio" label="Select a tool from the FROGS Stat suite to run your analysis."> + <option value="" selected="true">-- Please select a tool --</option> + <option value="phyloseq_import">Phyloseq: Import data</option> + <option value="phyloseq_composition">Phyloseq: Taxonomic composition analysis</option> + <option value="phyloseq_alpha_diversity">Phyloseq: Alpha diversity analysis</option> + <option value="phyloseq_beta_diversity">Phyloseq: Beta diversity analysis</option> + <option value="phyloseq_clustering">Phyloseq: Sample clustering analysis</option> + <option value="phyloseq_structure">Phyloseq: Structure analysis (based on ordination methods)</option> + <option value="phyloseq_manova">Phyloseq: Multivariate Analysis of Variance</option> + <option value="deseq2_asv_preprocess">DESeq2: Preprocess for differential analysis of ASV</option> + <option value="deseq2_fun_preprocess">DESeq2: Preprocess for differential analysis of FUNCTION</option> + <option value="deseq2_asv_visualisation">DESeq2: Visualisation of differential analysis of ASV</option> + <option value="deseq2_fun_visualisation">DESeq2: Visualisation of differential analysis of FUNCTION</option> + </param> + <when value=""/> + <!-- ##################### phyloseq_import ##################### --> + <when value="phyloseq_import"> + <expand macro="phyloseq_import_inputs" /> + </when> + <!-- ##################### phyloseq_composition ##################### --> + <when value="phyloseq_composition"> + <expand macro="phyloseq_composition_inputs" /> + </when> + <!-- ##################### phyloseq_alpha_diversity ##################### --> + <when value="phyloseq_alpha_diversity"> + <expand macro="phyloseq_alpha_diversity_inputs" /> + </when> + <!-- ##################### phyloseq_beta_diversity ##################### --> + <when value="phyloseq_beta_diversity"> + <expand macro="phyloseq_beta_diversity_inputs" /> + </when> + <!-- ##################### phyloseq_clustering ##################### --> + <when value="phyloseq_clustering"> + <expand macro="phyloseq_clustering_inputs" /> + </when> + <!-- ##################### phyloseq_structure ##################### --> + <when value="phyloseq_structure"> + <expand macro="phyloseq_structure_inputs" /> + </when> + <!-- ##################### phyloseq_manova ##################### --> + <when value="phyloseq_manova"> + <expand macro="phyloseq_manova_inputs" /> + </when> + <!-- ##################### deseq2 preprocess on ASV ##################### --> + <when value="deseq2_asv_preprocess"> + <expand macro="deseq2_asv_preprocess_inputs" /> + </when> + <!-- ##################### deseq2 preprocess on Functions ##################### --> + <when value="deseq2_fun_preprocess"> + <expand macro="deseq2_fun_preprocess_inputs" /> + </when> + <!-- ##################### deseq2 visualisation on ASV ##################### --> + <when value="deseq2_asv_visualisation"> + <expand macro="deseq2_asv_visualisation_inputs" /> + </when> + <!-- ##################### deseq2 visualisation on Functions ##################### --> + <when value="deseq2_fun_visualisation"> + <expand macro="deseq2_fun_visualisation_inputs" /> + </when> + </conditional> + </inputs> + + <outputs> + <expand macro="frogs_stat_outputs" /> + </outputs> + + <tests> + <!-- ##################### 1 phyloseq_import ##################### --> + <test expect_num_outputs="2"> + <conditional name="frogs_stat_tools"> + <param name="tool_name" value="phyloseq_import"/> + <expand macro="phyloseq_import_test_input"/> + </conditional> + <expand macro="phyloseq_import_test_output"/> + </test> + <!-- ##################### 2 phyloseq_composition ##################### --> + <test expect_num_outputs="1"> + <conditional name="frogs_stat_tools"> + <param name="tool_name" value="phyloseq_composition"/> + <expand macro="phyloseq_composition_test_input"/> + </conditional> + <expand macro="phyloseq_composition_test_output"/> + </test> + <!-- ##################### 3 phyloseq_alpha_diversity ##################### --> + <test expect_num_outputs="2"> + <conditional name="frogs_stat_tools"> + <param name="tool_name" value="phyloseq_alpha_diversity"/> + <expand macro="phyloseq_alpha_diversity_test_input"/> + </conditional> + <expand macro="phyloseq_alpha_diversity_test_output"/> + </test> + <!-- ##################### 4 phyloseq_beta_diversity ##################### --> + <test expect_num_outputs="1"> + <conditional name="frogs_stat_tools"> + <param name="tool_name" value="phyloseq_beta_diversity"/> + <expand macro="phyloseq_beta_diversity_test_input"/> + </conditional> + <expand macro="phyloseq_beta_diversity_test_output"/> + </test> + <!-- ##################### 5 phyloseq_clustering ##################### --> + <test expect_num_outputs="1"> + <conditional name="frogs_stat_tools"> + <param name="tool_name" value="phyloseq_clustering"/> + <expand macro="phyloseq_clustering_test_input"/> + </conditional> + <expand macro="phyloseq_clustering_test_output"/> + </test> + <!-- ##################### 6 phyloseq_structure ##################### --> + <test expect_num_outputs="1"> + <conditional name="frogs_stat_tools"> + <param name="tool_name" value="phyloseq_structure"/> + <expand macro="phyloseq_structure_test_input"/> + </conditional> + <expand macro="phyloseq_structure_test_output"/> + </test> + <!-- ##################### 7 phyloseq_manova ##################### --> + <test expect_num_outputs="1"> + <conditional name="frogs_stat_tools"> + <param name="tool_name" value="phyloseq_manova"/> + <expand macro="phyloseq_manova_test_input"/> + </conditional> + <expand macro="phyloseq_manova_test_output"/> + </test> + <!-- ##################### 8 deseq2_asv_preprocess ##################### --> + <test expect_num_outputs="1"> + <conditional name="frogs_stat_tools"> + <param name="tool_name" value="deseq2_asv_preprocess"/> + <expand macro="deseq2_asv_preprocess_test_input"/> + </conditional> + <expand macro="deseq2_asv_preprocess_test_output"/> + </test> + <!-- ##################### 9 deseq2_fun_preprocess ##################### --> + <test expect_num_outputs="2"> + <conditional name="frogs_stat_tools"> + <param name="tool_name" value="deseq2_fun_preprocess"/> + <expand macro="deseq2_fun_preprocess_test_input"/> + </conditional> + <expand macro="deseq2_fun_preprocess_test_output"/> + </test> + <!-- ##################### 10 deseq2_asv_visualisation ##################### --> + <test expect_num_outputs="1"> + <conditional name="frogs_stat_tools"> + <param name="tool_name" value="deseq2_asv_visualisation"/> + <expand macro="deseq2_asv_visualisation_test_input"/> + </conditional> + <expand macro="deseq2_asv_visualisation_test_output"/> + </test> + <!-- ##################### 11 deseq2_fun_visualisation ##################### --> + <test expect_num_outputs="3"> + <conditional name="frogs_stat_tools"> + <param name="tool_name" value="deseq2_fun_visualisation"/> + <expand macro="deseq2_fun_visualisation_test_input"/> + </conditional> + <expand macro="deseq2_fun_visualisation_test_output"/> + </test> + </tests> + + <help><![CDATA[ + For more information and detailed documentation, visit the FROGS website https://frogs.inrae.fr. + ]]> + </help> + + <citations> + <citation type="doi">10.1093/bioinformatics/btx791</citation> + <citation type="doi">10.1093/bib/bbab318</citation> + </citations> + +</tool>