Mercurial > repos > marpiech > rnaseq_pro_workflow_tools

comparison plotheatmap.xml @ 3:db5d126bf8d0 draft

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planemo upload
author marpiech
date Thu, 22 Dec 2016 18:19:53 -0500
parents ddde82ae5dea
children 4cdaf6059e84
comparison
equal deleted inserted replaced
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>