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comparison ks_distribution.xml @ 1:56f42cc1dd58 draft

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author greg
date Wed, 28 Jun 2017 11:20:17 -0400
parents c5846258c458
children 2c8e564adede
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0:c5846258c458 1:56f42cc1dd58
1 <tool id="ks_distribution" name="KsDistribution" version="1.0.0"> 1 <tool id="ks_distribution" name="KsDistribution" version="1.0.1">
2 <description>plots the distribution of synonymous substitution (Ks) rates and fits significant component(s)</description> 2 <description>plots the distribution of synonymous substitution (Ks) rates and fits significant component(s)</description>
3 <macros> 3 <macros>
4 <import>macros.xml</import> 4 <import>macros.xml</import>
5 </macros> 5 </macros>
6 <expand macro="requirements_ks_distribution" /> 6 <expand macro="requirements_ks_distribution" />
7 <command detect_errors="exit_code"><![CDATA[ 7 <command detect_errors="exit_code"><![CDATA[
8 Rscript $__tool_directory__/ks_distribution.R 8 Rscript $__tool_directory__/ks_distribution.R
9 -k '$input' 9 -k '$input'
10 -c '$components' 10 -c '$components'
11 -n $components.metadata.number_comp
11 -o '$output' 12 -o '$output'
13 #if str($choose_colors_cond.choose_colors) == 'yes':
14 #set specified_colors = list()
15 #for $selection in $choose_colors_cond.colors:
16 $specified_colors.append(str($selection.color))
17 #end for
18 #set specified_colors = ",".join($specified_colors)
19 -s '$specified_colors'
20 #end if
12 ]]></command> 21 ]]></command>
13 <inputs> 22 <inputs>
14 <param name="input" format="tabular" type="data" label="KaKsAnalysis tabular file" /> 23 <param name="input" format="tabular" type="data" label="KaKsAnalysis tabular file" />
15 <param name="components" format="tabular" type="data" label="Significant components" /> 24 <param name="components" format="ptkscmp" type="data" label="Significant components" />
25 <conditional name="choose_colors_cond">
26 <param name="choose_colors" type="select" label="Choose colors for significant components">
27 <option value="no" selected="true">No</option>
28 <option value="yes">Yes</option>
29 </param>
30 <when value="no" />
31 <when value="yes">
32 <repeat name="colors" title="Component colors" min="1">
33 <param name="color" type="select" label="Color">
34 <option value="red" selected="True">red</option>
35 <option value="green">green</option>
36 <option value="blue">blue</option>
37 <option value="yellow">yellow</option>
38 <option value="darkorange">dark orange</option>
39 <option value="black">black</option>
40 </param>
41 </repeat>
42 </when>
43 </conditional>
16 </inputs> 44 </inputs>
17 <outputs> 45 <outputs>
18 <data name="output" format="pdf"/> 46 <data name="output" format="pdf"/>
19 </outputs> 47 </outputs>
20 <tests> 48 <tests>
21 <test> 49 <test>
22 <param name="input" value="kaks_input1.tabular" ftype="tabular" /> 50 <param name="input" value="kaks_input1.tabular" ftype="tabular" />
23 <param name="components" value="components.tabular" ftype="tabular" /> 51 <param name="components" value="components.ptkscmp" ftype="ptkscmp" />
24 <output name="output" file="output.pdf" ftype="pdf" compare="contains" /> 52 <output name="output" file="output.pdf" ftype="pdf" compare="contains" />
25 </test> 53 </test>
26 </tests> 54 </tests>
27 <help> 55 <help>
28 **What it does** 56 **What it does**
35 63
36 **Options** 64 **Options**
37 65
38 * **Synonymous substitution rates** - estimated synonymous substitution (Ks) rates output file produced by the KaKsAnalysis tool selected from your history. 66 * **Synonymous substitution rates** - estimated synonymous substitution (Ks) rates output file produced by the KaKsAnalysis tool selected from your history.
39 * **Synonymous components** - estimated significant component(s) output file produced by the KaKsAnalysis tool selected from your history. 67 * **Synonymous components** - estimated significant component(s) output file produced by the KaKsAnalysis tool selected from your history.
68 * **Choose colors for significant components** - select 'Yes' to specify component colors or 'No' for colors chosen randlomly.
69
70 * **Component colors** - select a color from the palette for each component (colors will be chosen randomly for unspecified components).
40 </help> 71 </help>
41 <citations> 72 <citations>
42 <expand macro="citation1" /> 73 <expand macro="citation1" />
43 <citation type="bibtex"> 74 <citation type="bibtex">
44 @article{Wall2008, 75 @article{Wall2008,