--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/cemitool.xml	Mon Oct 10 16:55:19 2022 +0000
@@ -0,0 +1,352 @@
+<tool id="cemitool" name="CEMiTool" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
+    <description>gene co-expression network analyses</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro='xrefs'/>
+    <expand macro="requirements" />
+    <command detect_errors="exit_code"><![CDATA[
+        Rscript '$__tool_directory__/CEMiTool.R'
+            -M '$expression_matrix'
+        #if $annotation
+            -A '$annotation'
+        #end if
+        #if $pathways
+            -P '$pathways'
+        #end if
+        #if $interactions
+            -I '$interactions'
+        #end if
+        -f $advanced_parameters.filter
+        -i $advanced_parameters.filter_pval
+        -a $advanced_parameters.apply_vst
+        -n $advanced_parameters.n_genes
+        -e $advanced_parameters.eps
+        -c $advanced_parameters.cor_method
+        -y $advanced_parameters.cor_function
+        -x $advanced_parameters.network_type
+        -t $advanced_parameters.tom_type
+        -m $advanced_parameters.merge_similar
+        -r $advanced_parameters.rank_method
+        -g $advanced_parameters.min_ngen
+        -d $advanced_parameters.diss_thresh
+        -h $advanced_parameters.center_func
+        -o $advanced_parameters.ora_pval
+        -l $advanced_parameters.gsea_scale
+        -w $advanced_parameters.gsea_min_size
+        -z $advanced_parameters.gsea_max_size
+        -v $advanced_parameters.sample_column_name
+    ]]></command>
+    <inputs>
+        <param name="expression_matrix" type="data" format="tabular" label="Expression matrix"/>
+        <param name="annotation" type="data" format="tabular" optional="true" label="Sample annotation" 
+            help="It allows to build a more complete object and generate richer reports about the 
+                expression data. Sample annotation can be supplied in a data.frame that specifies a 
+                class for each sample. Classes can represent different conditions, phenotypes, cell lines, 
+                time points, etc. " />
+        <param name="pathways" type="data" format="tabular,txt" label="Pathways list" optional="true" help="CEMiTool can 
+            determine which biological functions are associated with the modules by performing an over 
+            representation analysis (ORA). To do this you must provide a pathway list in the form of GMT 
+            file. CEMiTool will then analyze how these pathways are represented in the modules." />
+        <param name="interactions" type="data" format="tabular" optional="true" label="Interactions data" help="Interaction data, 
+            such as protein-protein interactions can be added in order to generate annotated module graphs. 
+            Interaction files contains two columns for interacting pairs of genes"/>
+        <param name="outputs" type="select" multiple="true" display="checkboxes" label="Outputs selector">
+            <option value="report" selected="true">Report</option>
+            <option value="tables">Tables</option>
+            <option value="plots">Plots</option>
+        </param>
+        <section name="advanced_parameters" title="Advanced parameters">
+            <param argument="filter" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="True" label="Filter" help="If enabled, it will filter expression data" />
+            <param argument="filter_pval" type="float" min="0" max="1" value="0.1" label="Filter P-value" help="P-value threshold for filtering" />
+            <param argument="apply_vst" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="false" label="VST" help="If enabled, it apply Variance Stabilizing Transform before filtering genes" />
+            <param argument="n_genes" type="integer" min="0" value="1000" label="Number of genes" help="Number of genes left after filtering" />
+            <param argument="eps" type="float" min="0" max="1" value="0.1" label="EPS" help="A value for accepted R-squared interval between subsequent beta values" />
+            <param name="cor_method" type="select" label="Correlation method" help="Correlation coefficient to be computed">
+                <option value="pearson">Pearson</option>
+                <option value="spearman">Spearman</option>
+            </param>
+            <param name="cor_function" type="select" label="Correlation function" help="Correlation function to be used">
+                <option value="cor">Correlation (cor)</option>
+                <option value="bicor">Biweight Midcorrelation (bicor)</option>
+            </param>
+            <param name="network_type" type="select" label="Network type" help="Indicates if network type should be computed as 'signed' or 'unsigned'">
+                <option value="signed">Signed</option>
+                <option value="unsigned" selected="true">Unsigned</option>
+            </param>
+            <param name="tom_type" type="select" label="TOM type" help="Indicates if TOM type should be computed as 'signed' or 'unsigned'">
+                <option value="signed">Signed</option>
+                <option value="unsigned">Unsigned</option>
+            </param>
+            <param argument="merge_similar" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="false" label="Merge similar" help="If enabled, merge similar modules" />
+            <param argument="rank_method" type="select" label="Rank method" help="Indicate how to rank genes">
+                <option value="mean">Mean</option>
+                <option value="median">Median</option>
+            </param>
+            <param argument="min_ngen" type="integer" min="0" value="30" label="Minimal number of genes per module"/>
+            <param argument="diss_thresh" type="float" min="0" max="1" value="0.8" label="Merging correlation threshold" help="Module merging correlation threshold for eigengene similarity" />
+            <param argument="center_func" type="select" label="Cetrality measure to show in the plot">
+                <option value="mean">Mean</option>
+                <option value="median">Median</option>
+            </param>
+            <param argument="ora_pval" type="float" min="0" max="1" value="0.05" label="P-value for overrepresentation analysis"/>
+            <param argument="gsea_scale" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="true" label="Z-score transformation for GSEA analysis" help="If enabled, it applies z-score transformation" />
+            <param argument="gsea_min_size" type="integer" min="0" value="15" label="Minimum size of gene sets for GSEA analysis"/>
+            <param argument="gsea_max_size" type="integer" min="0" value="1000" label="Maximum size of gene sets for GSEA analysis"/>
+            <param argument="sample_column_name" type="text" value="SampleName" label="Sample column name" help="This is only required if an annotation file is provided">
+                <sanitizer invalid_char="">
+                    <valid initial="string.letters,string.digits">
+                        <add value="_" />
+                        <add value="-" />
+                        <add value=":" />
+                    </valid>
+                </sanitizer>
+                <validator type="regex">[0-9a-zA-Z:-_]+</validator>
+            </param>
+        </section>
+    </inputs>
+    <outputs>
+        <collection name="plots" type="list" label="${tool.name} on ${on_string}: Plots">
+            <discover_datasets pattern="__designation_and_ext__" format="pdf" directory="Plots" />
+            <filter>"plots" in outputs</filter>
+        </collection>
+        <data name="module" format="tabular" from_work_dir="Tables/module.tsv" label="${tool.name} on ${on_string}: Module">
+            <filter>"tables" in outputs</filter>
+        </data>
+        <data name="modules_genes" format="tabular" from_work_dir="Tables/modules_genes.gmt" label="${tool.name} on ${on_string}: Module genes">
+            <filter>"tables" in outputs</filter>
+        </data>
+        <data name="parameters" format="tabular" from_work_dir="Tables/parameters.tsv" label="${tool.name} on ${on_string}: Parameters">
+            <filter>"tables" in outputs</filter>
+        </data>
+        <data name="selected_genes" format="txt" from_work_dir="Tables/selected_genes.txt" label="${tool.name} on ${on_string}: Selected genes">
+            <filter>"tables" in outputs</filter>
+        </data>
+        <data name="summary_eigengene" format="tabular" from_work_dir="Tables/summary_eigengene.tsv" label="${tool.name} on ${on_string}: Summary eigengenes">
+            <filter>"tables" in outputs</filter>
+        </data>
+        <data name="summary_mean" format="tabular" from_work_dir="Tables/summary_mean.tsv" label="${tool.name} on ${on_string}: Summary mean">
+            <filter>"tables" in outputs</filter>
+        </data>
+        <data name="summary_median" format="tabular" from_work_dir="Tables/summary_median.tsv" label="${tool.name} on ${on_string}: Summary median">
+            <filter>"tables" in outputs</filter>
+        </data>
+        <data name="interactions_output" format="tabular" from_work_dir="Tables/interactions.tsv" label="${tool.name} on ${on_string}: Interactions">
+            <filter>"tables" in outputs</filter>
+            <filter>interactions</filter>
+        </data>
+        <data name='output_html' format='html' from_work_dir="Reports/Report/report.html" label="${tool.name} on ${on_string}: HTML report">
+            <filter>"report" in outputs</filter>
+        </data>
+    </outputs>
+    <tests>
+        <test expect_num_outputs="1">
+            <!--Test expression matrix input-->
+            <param name="expression_matrix" value="expression_matrix.tab"/>
+            <param name="outputs" value="report"/>
+            <section name="advanced_parameters">
+                <param name="filter" value="True"/>
+                <param name="filter_pval" value="0.1"/>
+                <param name="apply_vst" value="false"/>
+                <param name="n_genes" value="1000"/>
+                <param name="eps" value="0.1"/>
+                <param name="cor_method" value="pearson"/>
+                <param name="cor_function" value="cor"/>
+                <param name="network_type" value="signed"/>
+                <param name="tom_type" value="signed"/>
+                <param name="merge_similar" value="false"/>
+                <param name="rank_method" value="mean"/>
+                <param name="min_ngen" value="30"/>
+                <param name="diss_thresh" value="0.8"/>
+                <param name="center_func" value="mean"/>
+                <param name="ora_pval" value="0.05"/>
+                <param name="gsea_scale" value="true"/>
+                <param name="gsea_min_size" value="15"/>
+                <param name="gsea_max_size" value="1000"/>
+            </section>
+            <output name="output_html">
+                <assert_contents>
+                    <has_text text="EPSTI1"/>
+                    <has_text text="RSAD2"/>
+                    <has_text text="XAF1"/>
+                    <has_text text="OAS2"/>
+                    <has_text text="Gene Set Enrichment Analysis"/>
+                    <has_text text="SPARC"/>
+                </assert_contents>
+            </output>
+        </test>
+        
+        <test expect_num_outputs="8">
+            <!--Test all inputs and output tables-->
+            <param name="expression_matrix" value="expression_matrix.tab"/>
+            <param name="annotation" value="sample_annotation.tab"/>
+            <param name="pathways" value="pathways.gmt"/>
+            <param name="interactions" value="interactions.tab"/>
+            <param name="outputs" value="tables"/>
+            <section name="advanced_parameters">
+                <param name="filter" value="True"/>
+                <param name="filter_pval" value="0.1"/>
+                <param name="apply_vst" value="false"/>
+                <param name="n_genes" value="1000"/>
+                <param name="eps" value="0.1"/>
+                <param name="cor_method" value="pearson"/>
+                <param name="cor_function" value="cor"/>
+                <param name="network_type" value="signed"/>
+                <param name="tom_type" value="signed"/>
+                <param name="merge_similar" value="false"/>
+                <param name="rank_method" value="mean"/>
+                <param name="min_ngen" value="30"/>
+                <param name="diss_thresh" value="0.8"/>
+                <param name="center_func" value="mean"/>
+                <param name="ora_pval" value="0.05"/>
+                <param name="gsea_scale" value="true"/>
+                <param name="gsea_min_size" value="15"/>
+                <param name="gsea_max_size" value="1000"/>
+            </section>
+            <output name="module">
+                <assert_contents>
+                    <has_n_lines n="110"/>
+                    <has_size value="2250" delta="200"/>
+                </assert_contents>
+            </output>
+            <output name="modules_genes">
+                <assert_contents>
+                    <has_n_lines n="1"/>
+                    <has_size value="216" delta="10"/>
+                </assert_contents>
+            </output>
+            <output name="parameters">
+                <assert_contents>
+                    <has_n_lines n="12"/>
+                    <has_size value="234" delta="10"/>
+                </assert_contents>
+            </output>
+            <output name="selected_genes">
+                <assert_contents>
+                    <has_n_lines n="1000"/>
+                    <has_size value="6496" delta="10"/>
+                </assert_contents>
+            </output>
+            <output name="summary_eigengene">
+                <assert_contents>
+                    <has_n_lines n="3"/>
+                    <has_size value="2241" delta="10"/>
+                </assert_contents>
+            </output>
+            <output name="summary_mean">
+                <assert_contents>
+                    <has_n_lines n="3"/>
+                    <has_size value="2044" delta="50"/>
+                </assert_contents>
+            </output>
+            <output name="summary_median">
+                <assert_contents>
+                    <has_n_lines n="3"/>
+                    <has_size value="1621" delta="10"/>
+                </assert_contents>
+            </output>
+            <output name="interactions_output">
+                <assert_contents>
+                    <has_n_lines n="277"/>
+                    <has_size value="7736" delta="200"/>
+                </assert_contents>
+            </output>
+        </test>
+
+        <test expect_num_outputs="10">
+            <!--Test custom inputs and plots-->
+            <param name="expression_matrix" value="expression_matrix.tab"/>
+            <param name="annotation" value="sample_annotation.tab"/>
+            <param name="pathways" value="pathways.gmt"/>
+            <param name="interactions" value="interactions.tab"/>
+            <param name="outputs" value="report,tables,plots"/>
+            <section name="advanced_parameters">
+                <param name="filter" value="false"/>
+                <param name="filter_pval" value="0.2"/>
+                <param name="apply_vst" value="true"/>
+                <param name="n_genes" value="2000"/>
+                <param name="eps" value="0.1"/>
+                <param name="cor_method" value="spearman"/>
+                <param name="cor_function" value="bicor"/>
+                <param name="network_type" value="unsigned"/>
+                <param name="tom_type" value="unsigned"/>
+                <param name="merge_similar" value="true"/>
+                <param name="rank_method" value="median"/>
+                <param name="min_ngen" value="35"/>
+                <param name="diss_thresh" value="0.7"/>
+                <param name="center_func" value="median"/>
+                <param name="ora_pval" value="0.07"/>
+                <param name="gsea_scale" value="false"/>
+                <param name="gsea_min_size" value="10"/>
+                <param name="gsea_max_size" value="1100"/>
+            </section>
+            <output name="module">
+                <assert_contents>
+                    <has_n_lines n="1929"/>
+                    <has_size value="26528" delta="200"/>
+                </assert_contents>
+            </output>
+            <output name="modules_genes">
+                <assert_contents>
+                    <has_n_lines n="10"/>
+                    <has_size value="15814" delta="200"/>
+                </assert_contents>
+            </output>
+            <output name="parameters">
+                <assert_contents>
+                    <has_n_lines n="12"/>
+                    <has_size value="234" delta="10"/>
+                </assert_contents>
+            </output>
+            <output name="selected_genes">
+                <assert_contents>
+                    <has_n_lines n="1928"/>
+                    <has_size value="12570" delta="200"/>
+                </assert_contents>
+            </output>
+            <output name="summary_eigengene">
+                <assert_contents>
+                    <has_n_lines n="12"/>
+                    <has_size value="9963" delta="200"/>
+                </assert_contents>
+            </output>
+            <output name="summary_mean">
+                <assert_contents>
+                    <has_n_lines n="12"/>
+                    <has_size value="8898" delta="200"/>
+                </assert_contents>
+            </output>
+            <output name="summary_median">
+                <assert_contents>
+                    <has_n_lines n="12"/>
+                    <has_size value="6574" delta="200"/>
+                </assert_contents>
+            </output>
+            <output name="interactions_output">
+                <assert_contents>
+                    <has_n_lines n="2579"/>
+                    <has_size value="55341" delta="200"/>
+                </assert_contents>
+            </output>
+            <output_collection name="plots" type="list" count="10">
+                <element name="profile" file="profiles.pdf" compare="sim_size" delta="100"/>
+            </output_collection>
+        </test>
+
+    </tests>
+    <help><![CDATA[
+
+.. class:: infomark
+
+**Purpose**
+
+The CEMiTool R package provides users with an easy-to-use method to automatically implement gene co-expression network analyses, obtain key information about the 
+discovered gene modules using additional downstream analyses and retrieve publication-ready results via a high-quality interactive report.
+
+.. class:: infomark
+
+**Purpose**
+
+    ]]></help>
+    <expand macro="citations" />
+</tool>