Mercurial > repos > marpiech > rnaseq_pro_workflow_tools

comparison plotheatmap.xml @ 1:ddde82ae5dea draft

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planemo upload
author marpiech
date Sun, 11 Dec 2016 18:57:58 -0500
parents c5a812cdf478
children db5d126bf8d0
comparison
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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>