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cemitool.xml
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cemitool.xml
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<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>