Mercurial > repos > marpiech > rnaseq_pro_workflow_tools
comparison plotheatmap.xml @ 3:db5d126bf8d0 draft
planemo upload
| author | marpiech |
|---|---|
| date | Thu, 22 Dec 2016 18:19:53 -0500 |
| parents | ddde82ae5dea |
| children | 4cdaf6059e84 |
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| 2:27e62af48a5a | 3:db5d126bf8d0 |
|---|---|
| 3 <stdio> | 3 <stdio> |
| 4 <exit_code range="1:" /> | 4 <exit_code range="1:" /> |
| 5 </stdio> | 5 </stdio> |
| 6 <command> | 6 <command> |
| 7 <![CDATA[ | 7 <![CDATA[ |
| 8 $__tool_directory__/tools/script.R $count_matrix $stats_matrix $log_fc $log_cpm $pvalue $fdr > $rscript_log 2> $rerror_log | 8 $__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 |
| 9 | 9 |
| 10 ]]> | 10 ]]> |
| 11 </command> | 11 </command> |
| 12 <inputs> | 12 <inputs> |
| 13 <param name="count_matrix" type="data" format="data" label=""/> | 13 <section name="main" title="Main parameters" expanded="True"> |
| 14 <param name="stats_matrix" type="data" format="data" label=""/> | 14 <param name="count_matrix" type="data" format="data" label=""/> |
| 15 <param name="log_fc" type="float" value="0.5" label=""/> | 15 <param name="stats_matrix" type="data" format="data" label=""/> |
| 16 <param name="log_cpm" type="float" value="0.5" label=""/> | 16 <param name="log_fc" type="float" value="0.5" label=""/> |
| 17 <param name="pvalue" type="float" value="0.5" label=""/> | 17 <param name="log_cpm" type="float" value="0.5" label=""/> |
| 18 <param name="fdr" type="float" value="0.5" label=""/> | 18 <param name="pvalue" type="float" value="0.5" label=""/> |
| 19 <param name="fdr" type="float" value="0.5" label=""/> | |
| 20 </section> | |
| 21 | |
| 22 <section name="heatmap" title="Heatmap parameters"> | |
| 23 <param name="cluster_row" type="select" label="Determines if the row dendrogram should be reordered"> | |
| 24 <option value="No" >No </option> | |
| 25 <option value="Yes" selected="true" >Yes </option> | |
| 26 </param> | |
| 27 <param name="cluster_col" type="select" label="Determines if the column dendrogram should be reordered"> | |
| 28 <option value="No" selected="true">No </option> | |
| 29 <option value="Yes" >Yes </option> | |
| 30 </param> | |
| 31 | |
| 32 <param name="hclust_method" type="select" label="Hierarchical clustering method"> | |
| 33 <option value="ward.D" >ward.D </option> | |
| 34 <option value="ward.D2" >ward.D2 </option> | |
| 35 <option value="single" >single </option> | |
| 36 <option value="complete" >complete </option> | |
| 37 <option value="average" selected="true">average </option> | |
| 38 <option value="mcquitty" >mcquitty </option> | |
| 39 <option value="median" >median </option> | |
| 40 <option value="centroid" >centroid </option> | |
| 41 </param> | |
| 42 </section> | |
| 43 | |
| 44 | |
| 45 <section name="plotparm" title="Plot parameters"> | |
| 46 <param name="col_marg" type="float" value="7" label="Margins or column names"/> | |
| 47 <param name="row_marg" type="float" value="8" label="Margins or row names"/> | |
| 48 <param name="pdf_width" type="float" value="7" label="Width of the graphics region in inches" /> | |
| 49 <param name="pdf_height" type="float" value="7" label="Height of the graphics region in inches" /> | |
| 50 </section> | |
| 51 | |
| 52 | |
| 19 | 53 |
| 20 </inputs> | 54 </inputs> |
| 21 <outputs> | 55 <outputs> |
| 22 <data format="pdf" name="haetamappdf" from_work_dir="heatmap.pdf" > | 56 <data format="pdf" name="haetamappdf" from_work_dir="heatmap.pdf" > |
| 23 <filter>(outftype == 'pdf')</filter> | 57 <filter>(outftype == 'pdf')</filter> |
| 41 </test> | 75 </test> |
| 42 | 76 |
| 43 </tests> | 77 </tests> |
| 44 <help> | 78 <help> |
| 45 <![CDATA[ | 79 <![CDATA[ |
| 80 | |
| 46 ]]> | 81 ]]> |
| 47 </help> | 82 </help> |
| 48 <citations> | 83 <citations> |
| 49 </citations> | 84 </citations> |
| 50 </tool> | 85 </tool> |