| Previous changeset 4:2fee8da6aabb (2016-12-23) |
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Commit message:
planemo upload |
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modified:
countmatrixforedger.xml plotheatmap.xml |
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| diff -r 2fee8da6aabb -r 4cdaf6059e84 countmatrixforedger.xml --- a/countmatrixforedger.xml Fri Dec 23 06:42:19 2016 -0500 +++ b/countmatrixforedger.xml Wed Feb 01 10:29:17 2017 -0500 |
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| @@ -20,9 +20,9 @@ </command> <inputs> <repeat name="sample" title=""> - <param name="sample_data" type="data" format="data" label="" help="" /> - <param name="sample_name" type="text" label="" help="" /> - <param name="sample_group" type="text" label="" help="" /> + <param name="sample_data" type="data" format="data" label="Output matrix from EDGE-pro (out_rpkm)" /> + <param name="sample_name" type="text" label="" help="Sample name" /> + <param name="sample_group" type="text" label="" help="Sample group name- it has to be the same string for each sample of this group" /> </repeat> </inputs> <outputs> @@ -54,6 +54,7 @@ </tests> <help> <![CDATA[ + ]]> </help> <citations> |
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| diff -r 2fee8da6aabb -r 4cdaf6059e84 plotheatmap.xml --- a/plotheatmap.xml Fri Dec 23 06:42:19 2016 -0500 +++ b/plotheatmap.xml Wed Feb 01 10:29:17 2017 -0500 |
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| @@ -1,24 +1,32 @@ <tool id="plotheatmap" name="plotHeatmap" version="1.0"> <description>Plot heatmap</description> + <requirements> + <requirement type="package" version="3.0.1">r-gplots</requirement> + </requirements> <stdio> <exit_code range="1:" /> </stdio> <command> <![CDATA[ - $__tool_directory__/tools/script.R $main.count_matrix $main.stats_matrix $main.log_fc $main.log_cpm $main.pvalue $main.fdr $heatmap.cluster_row $heatmap.cluster_col $heatmap.hclust_method $plotparm.col_marg $plotparm.row_marg $plotparm.pdf_width $plotparm.pdf_height > $rscript_log 2> $rerror_log + $__tool_directory__/tools/script.R $main.count_matrix $main.stats_matrix $filter.log_fc $filter.log_cpm $filter.pvalue $filter.fdr $heatmap.cluster_row $heatmap.cluster_col $heatmap.hclust_method $plotparm.col_marg $plotparm.row_marg $plotparm.pdf_width $plotparm.pdf_height > $rscript_log 2> $rerror_log ]]> </command> <inputs> <section name="main" title="Main parameters" expanded="True"> - <param name="count_matrix" type="data" format="data" label=""/> - <param name="stats_matrix" type="data" format="data" label=""/> - <param name="log_fc" type="float" value="0.5" label=""/> - <param name="log_cpm" type="float" value="0.5" label=""/> - <param name="pvalue" type="float" value="0.5" label=""/> - <param name="fdr" type="float" value="0.5" label=""/> + <param name="count_matrix" type="data" format="data" label="Output dataset 'count_matrix' from tool countMatrixForEdger"/> + <param name="stats_matrix" type="data" format="data" label="Output dataset 'output' from tool edgeR"/> </section> - + <section name="filter" title="Filtering parameters" expanded="True"> + <param name="log_fc" type="float" value="0.5" label="A log FC threshold"/> + <param name="log_cpm" type="float" value="0.5" label="A log CPM threshold"/> + <param name="pvalue" type="float" value="0.5" label="A PValue threshold"> + <validator type="in_range" min="0" max="1" /> + </param> + <param name="fdr" type="float" value="0.5" label="A FDR threshold"> + <validator type="in_range" min="0" max="1" /> + </param> + </section> <section name="heatmap" title="Heatmap parameters"> <param name="cluster_row" type="select" label="Determines if the row dendrogram should be reordered"> <option value="No" >No </option> @@ -43,14 +51,12 @@ <section name="plotparm" title="Plot parameters"> - <param name="col_marg" type="float" value="7" label="Margins or column names"/> - <param name="row_marg" type="float" value="8" label="Margins or row names"/> - <param name="pdf_width" type="float" value="7" label="Width of the graphics region in inches" /> - <param name="pdf_height" type="float" value="7" label="Height of the graphics region in inches" /> + <param name="col_marg" type="float" value="7" label="Margins for column names"/> + <param name="row_marg" type="float" value="8" label="Margins for row names"/> + <param name="pdf_width" type="float" value="7" label="Width of the graphics region in inches (pdf width)" /> + <param name="pdf_height" type="float" value="7" label="Height of the graphics region in inches (pdf height)" /> </section> - - </inputs> <outputs> <data format="pdf" name="haetamappdf" from_work_dir="heatmap.pdf" > @@ -77,7 +83,19 @@ </tests> <help> <![CDATA[ - +**What it does** +It takes a list of genes basen on set filtering criteria and draws them on heatmap. +**Example** +The following filtering options: +A log FC threshold = 0.5 +A log CPM threshold = 0.5 +A PValue threshold = 0.05 +A FDR threshold = 0.1 +mean that you select genes whose values in output table from edgeR are: +* absolute value of logFC is greater than or equal 0.5 +* logCPM is greater than or equal 0.5 +* PValue is less than or equal to 0.05 +* FDR is less than or equal to 0.1 ]]> </help> <citations> |