Mercurial > repos > marpiech > rnaseq_pro_workflow_tools
comparison plotheatmap.xml @ 1:ddde82ae5dea draft
planemo upload
| author | marpiech |
|---|---|
| date | Sun, 11 Dec 2016 18:57:58 -0500 |
| parents | c5a812cdf478 |
| children | db5d126bf8d0 |
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| 0:c5a812cdf478 | 1:ddde82ae5dea |
|---|---|
| 1 <tool id="plotheatmap" name="plotheatmap" version="1.0"> | 1 <tool id="plotheatmap" name="plotHeatmap" version="1.0"> |
| 2 <description>Make a count matrix for edgeR</description> | 2 <description>Plot heatmap</description> |
| 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 $count_matrix $stats_matrix $log_fc $log_cpm $pvalue $fdr > $rscript_log 2> $rerror_log |
| 9 | |
| 10 | |
| 11 | 9 |
| 12 ]]> | 10 ]]> |
| 13 </command> | 11 </command> |
| 14 <inputs> | 12 <inputs> |
| 15 <param name="count_matrix" type="data" format="data" label=""/> | 13 <param name="count_matrix" type="data" format="data" label=""/> |
| 19 <param name="pvalue" type="float" value="0.5" label=""/> | 17 <param name="pvalue" type="float" value="0.5" label=""/> |
| 20 <param name="fdr" type="float" value="0.5" label=""/> | 18 <param name="fdr" type="float" value="0.5" label=""/> |
| 21 | 19 |
| 22 </inputs> | 20 </inputs> |
| 23 <outputs> | 21 <outputs> |
| 24 <!-- <data name="output" format="data" /> --> | |
| 25 <data format="pdf" name="haetamappdf" from_work_dir="heatmap.pdf" > | 22 <data format="pdf" name="haetamappdf" from_work_dir="heatmap.pdf" > |
| 26 <filter>(outftype == 'pdf')</filter> | 23 <filter>(outftype == 'pdf')</filter> |
| 27 </data> | 24 </data> |
| 28 <data name="rscript_log" format="data" /> | 25 <data name="rscript_log" format="data" /> |
| 29 <data name="rerror_log" format="data" /> | 26 <data name="rerror_log" format="data" /> |
| 35 <param name="stats_matrix" value="stats.data"/> | 32 <param name="stats_matrix" value="stats.data"/> |
| 36 <param name="log_fc" value="1"/> | 33 <param name="log_fc" value="1"/> |
| 37 <param name="log_cpm" value="2"/> | 34 <param name="log_cpm" value="2"/> |
| 38 <param name="pvalue" value="0.05"/> | 35 <param name="pvalue" value="0.05"/> |
| 39 <param name="fdr" value="0.1"/> | 36 <param name="fdr" value="0.1"/> |
| 40 <!-- <output name="output" file="done"/> --> | |
| 41 <output name="haetamappdf" file="heatmap.pdf" ftype="pdf" compare="sim_size" /> | 37 <output name="haetamappdf" file="heatmap.pdf" ftype="pdf" compare="sim_size" /> |
| 42 <output name="rscript_log" file="rscript.log"/> | 38 <output name="rscript_log" file="rscript.log"/> |
| 43 <output name="rerror_log" file="rerror.log"/> | 39 <output name="rerror_log" file="rerror.log"/> |
| 44 | 40 |
| 45 </test> | 41 </test> |
| 46 | 42 |
| 47 </tests> | 43 </tests> |
| 48 <help> | 44 <help> |
| 49 <![CDATA[ | 45 <![CDATA[ |
| 50 | |
| 51 tutaj cos bedzie | |
| 52 ]]> | 46 ]]> |
| 53 </help> | 47 </help> |
| 54 <citations> | 48 <citations> |
| 55 | |
| 56 </citations> | 49 </citations> |
| 57 </tool> | 50 </tool> |