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<tool id="ctat_analyze_differential_expression" name="ctat_analyze_differential_expression" version="1.0.0" profile="17.05">
<description>Analyze differential expression</description>
<requirements>
<requirement type="package" version="2.7">python</requirement>
<requirement type="package">subprocess32</requirement>
<requirement type="package">bzip2</requirement>
<requirement type="package" version="1.3.0">rsem</requirement>
<requirement type="package" version="3">bioconductor-edger</requirement>
<requirement type="package" version="2">bioconductor-qvalue</requirement>
<requirement type="package">r-cluster</requirement>
<requirement type="package">r-fastcluster</requirement>
<requirement type="package" version="2.6.6">trinity</requirement>
</requirements>
<command detect_errors="exit_code">
<![CDATA[
python $__tool_directory__/ctat_analyze_differential_expression.py $EdgeRTarGz $Counts_matrix $Pvalue $Cvalue
]]>
</command>
<inputs>
<param name="EdgeRTarGz" label="EdgeR tar gz file" type="data" format="txt"/>
<param name="Counts_matrix" label="Counts Matrix" type="data" format="tabular" />
<param name="Pvalue" label="P-value" value="0.05" type="float" />
<param name="Cvalue" label="C-value" value="0" type="float" />
</inputs>
<outputs>
<data format="data" name="diffExpr_matrix" label="${tool.name} on ${on_string}: Matrix" from_work_dir="diffExpr.matrix"/>
<data format="data" name="diffExpr_correlation_matrix" label="${tool.name} on ${on_string}: Sample_Correlation_Matrix" from_work_dir="diffExpr.matrix.log2.sample_cor.dat"/>
<data format="data" name="diffExpr_correlation_matrix_pdf" label="${tool.name} on ${on_string}: Sample_Correlation_Matrix_PDF" from_work_dir="diffExpr.matrix.log2.sample_cor_matrix.pdf"/>
<data format="data" name="Heatmap" label="${tool.name} on ${on_string}: Heatmap" from_work_dir="diffExpr.matrix.log2.centered.genes_vs_samples_heatmap.pdf"/>
</outputs>
<tests>
<test>
<param name="EdgeRTarGz" value="Sp.edgeR.tar.gz" ftype="tar" />
<param name="TMM_Matrix_FPKM" value="Sp.TMM.EXPR.matrix" />
<param name="Pvalue" value="0.05" />
<param name="Cvalue" value="0.0" />
<output name="diffExpr_matrix" >
<assert_contents>
<has_line_matching expression=".+" />
<has_line line="Sp_ds	Sp_hs" />
<has_line_matching expression="TRINITY_DN.+" />
</assert_contents>
</output>
<output name="diffExpr_correlation_matrix" file="Sp.diffExpr.matrix.log2.sample_cor.dat" />
<output name="diffExpr_correlation_matrix_pdf" >
<assert_contents>
<has_line_matching expression=".+" />
</assert_contents>
</output>
<output name="Heatmap" >
<assert_contents>
<has_line_matching expression=".+" />
</assert_contents>
</output>
</test>
</tests>
<help>
.. class:: infomark
This tool filters differentially expressed transcripts derived from edgeR using a minimum fold change (C-value) which will be log2 transformed before use and a required significance (P-value) in the pairwise sample comparisons (after false discovery rate correction).
If you are following the Trinity RNA-seq protocol please go here_ for a galaxy tool walk through or the Nature Protocols paper_.
.. _here: https://github.com/trinityrnaseq/GalaxyTrinityProtocol/wiki
.. _paper: http://www.nature.com/nprot/journal/v8/n8/full/nprot.2013.084.html
</help>
<citations>
<citation type="doi">10.1038/nbt.1883</citation>
</citations>
</tool>