Mercurial > repos > artbio > small_rna_maps

comparison small_rna_maps.xml @ 5:12c14642e6ac draft

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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 24a21619d79d83b38cef7f1a7b858c621e4c8449
author artbio
date Sun, 08 Oct 2017 17:56:13 -0400
parents a6b9a081064b
children a3be3601bcb3
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4:a6b9a081064b 5:12c14642e6ac
1 <tool id="small_rna_maps" name="small_rna_maps" version="1.1.0"> 1 <tool id="small_rna_maps" name="small_rna_maps" version="2.0.0">
2 <description></description> 2 <description></description>
3 <requirements> 3 <requirements>
4 <requirement type="package" version="1.11.2=py27_0">numpy</requirement> 4 <requirement type="package" version="1.11.2=py27_0">numpy</requirement>
5 <requirement type="package" version="0.11.2.1=py27_0">pysam</requirement> 5 <requirement type="package" version="0.11.2.1=py27_0">pysam</requirement>
6 <requirement type="package" version="1.3.2=r3.3.1_0">r-optparse</requirement> 6 <requirement type="package" version="1.3.2=r3.3.2_0">r-optparse</requirement>
7 <requirement type="package" version="0.6_28=r3.3.1_0">r-latticeextra</requirement> 7 <requirement type="package" version="0.6_28=r3.3.2_0">r-latticeextra</requirement>
8 <requirement type="package" version="2.2.1=r3.3.1_0">r-gridextra</requirement> 8 <requirement type="package" version="2.2.1=r3.3.2_0">r-gridextra</requirement>
9 </requirements> 9 </requirements>
10 <stdio> 10 <stdio>
11 <exit_code range="1:" level="fatal" description="Tool exception" /> 11 <exit_code range="1:" level="fatal" description="Tool exception" />
12 </stdio> 12 </stdio>
13 <command detect_errors="exit_code"><![CDATA[ 13 <command detect_errors="exit_code"><![CDATA[
21 #end for 21 #end for
22 --sample_names 22 --sample_names
23 #for $sample in $inputs 23 #for $sample in $inputs
24 '$sample.name' 24 '$sample.name'
25 #end for 25 #end for
26 --plot_methods Counts '$extra_plot' 26 #if str($plots_options.plots_options_selector ) == "two_plot":
27 --plot_methods '${plots_options.first_plot}' '${plots_options.extra_plot}'
27 --outputs '$output_tab' '$extra_output_tab' && 28 --outputs '$output_tab' '$extra_output_tab' &&
29 #else:
30 --plot_methods '${plots_options.first_plot}'
31 --outputs '$output_tab' &&
32 #end if
28 Rscript '$__tool_directory__'/small_rna_maps.r 33 Rscript '$__tool_directory__'/small_rna_maps.r
29 --first_dataframe '$output_tab' 34 --first_dataframe '$output_tab'
30 --extra_dataframe '$extra_output_tab' 35 --extra_dataframe '$extra_output_tab'
31 --extra_plot_method '$extra_plot' 36 #if str($plots_options.plots_options_selector ) == "two_plot":
37 --first_plot_method '${plots_options.first_plot}'
38 --extra_plot_method '${plots_options.extra_plot}'
39 #else:
40 --first_plot_method '${plots_options.first_plot}'
41 --extra_plot_method ''
42 #end if
32 --output_pdf '$output_pdf' 43 --output_pdf '$output_pdf'
33 ]]></command> 44 ]]></command>
34 <inputs> 45 <inputs>
35 <param name="inputs" type="data" format="bam" label="Select multiple alignments to parse" multiple="True"/> 46 <param name="inputs" type="data" format="bam" label="Select multiple alignments to parse" multiple="True"/>
36 <param name="extra_plot" type="select" label="select the type of extra plot in addition to read map"> 47 <conditional name="plots_options">
37 <option value="Coverage">Coverage</option> 48 <param name="plots_options_selector" type="select" label="Number of plots per chromosome">
38 <option value="Mean">Mean Sizes</option> 49 <option value="one_plot">Just one plot per chromosome</option>
39 <option value="Median">Median Sizes</option> 50 <option value="two_plot" selected="True">Two plots per chromosome</option>
40 <option value="Size">Size Distributions</option> 51 </param>
41 </param> 52 <when value="two_plot">
53 <param name="first_plot" type="select" label="select the type of the first plot">
54 <option value="Counts">Counts</option>
55 <option value="Coverage">Coverage</option>
56 <option value="Mean">Mean Sizes</option>
57 <option value="Median">Median Sizes</option>
58 <option value="Size">Size Distributions</option>
59 </param>
60 <param name="extra_plot" type="select" label="select the type of the second plot">
61 <option value="Counts">Counts</option>
62 <option value="Coverage">Coverage</option>
63 <option value="Mean">Mean Sizes</option>
64 <option value="Median">Median Sizes</option>
65 <option value="Size">Size Distributions</option>
66 </param>
67 </when>
68 <when value="one_plot">
69 <param name="first_plot" type="select" label="select the type of the first plot">
70 <option value="Counts">Counts</option>
71 <option value="Coverage">Coverage</option>
72 <option value="Mean">Mean Sizes</option>
73 <option value="Median">Median Sizes</option>
74 <option value="Size">Size Distributions</option>
75 </param>
76 </when>
77 </conditional>
42 </inputs> 78 </inputs>
43 79
44 <outputs> 80 <outputs>
45 <data format="tabular" name="output_tab" label="Read Count dataframe" /> 81 <data format="tabular" name="output_tab" label="Read Count dataframe" />
46 <data format="tabular" name="extra_output_tab" label="$extra_plot dataframe" /> 82 <data format="tabular" name="extra_output_tab" label="$plots_options.extra_plot dataframe">
83 <filter>plots_options['plots_options_selector'] == 'two_plot'</filter>
84 </data>
47 <data format="pdf" name="output_pdf" label="PDF file" /> 85 <data format="pdf" name="output_pdf" label="PDF file" />
48 86
49 </outputs> 87 </outputs>
50 88
51 <tests> 89 <tests>
52 <test> 90 <test>
53 <param name="inputs" value="input1.bam,input2.bam" ftype="bam"/> 91 <param name="inputs" value="input1.bam,input2.bam" ftype="bam"/>
92 <param name="plots_options_selector" value="two_plot" />
93 <param name="first_plot" value="Counts" />
54 <param name="extra_plot" value="Mean" /> 94 <param name="extra_plot" value="Mean" />
55 <output file="readmap.tab" name="output_tab" /> 95 <output file="count.tab" name="output_tab" />
56 <output file="mean.tab" name="extra_output_tab" /> 96 <output file="mean.tab" name="extra_output_tab" />
57 <output file="mean.pdf" name="output_pdf" /> 97 <output file="count-mean.pdf" name="output_pdf" />
58 </test> 98 </test>
59 <test> 99 <test>
60 <param name="inputs" value="input1.bam,input1.bam" ftype="bam"/> 100 <param name="inputs" value="input1.bam,input1.bam" ftype="bam"/>
101 <param name="plots_options_selector" value="two_plot" />
102 <param name="first_plot" value="Counts" />
61 <param name="extra_plot" value="Mean" /> 103 <param name="extra_plot" value="Mean" />
62 <output file="doubled_readmap.tab" name="output_tab" /> 104 <output file="doubled_count.tab" name="output_tab" />
63 <output file="double_mean.tab" name="extra_output_tab" /> 105 <output file="doubled_mean.tab" name="extra_output_tab" />
64 <output file="doubled_mean.pdf" name="output_pdf" /> 106 <output file="doubled_count-mean.pdf" name="output_pdf" />
65 </test> 107 </test>
66 <test> 108 <test>
67 <param name="inputs" value="input1.bam,input2.bam" ftype="bam"/> 109 <param name="inputs" value="input1.bam,input2.bam" ftype="bam"/>
110 <param name="plots_options_selector" value="two_plot" />
111 <param name="first_plot" value="Counts" />
68 <param name="extra_plot" value="Median" /> 112 <param name="extra_plot" value="Median" />
69 <output file="readmap.tab" name="output_tab" /> 113 <output file="count.tab" name="output_tab" />
70 <output file="median.tab" name="extra_output_tab" /> 114 <output file="median.tab" name="extra_output_tab" />
71 <output file="median.pdf" name="output_pdf" /> 115 <output file="count-median.pdf" name="output_pdf" />
72 </test> 116 </test>
73 <test> 117 <test>
74 <param name="inputs" value="input1.bam,input2.bam" ftype="bam"/> 118 <param name="inputs" value="input1.bam,input2.bam" ftype="bam"/>
119 <param name="plots_options_selector" value="two_plot" />
120 <param name="first_plot" value="Counts" />
75 <param name="extra_plot" value="Coverage" /> 121 <param name="extra_plot" value="Coverage" />
76 <output file="readmap.tab" name="output_tab" /> 122 <output file="count.tab" name="output_tab" />
77 <output file="coverage.tab" name="extra_output_tab" /> 123 <output file="coverage.tab" name="extra_output_tab" />
124 <output file="count-coverage.pdf" name="output_pdf" />
125 </test>
126 <test>
127 <param name="inputs" value="input1.bam,input2.bam" ftype="bam"/>
128 <param name="plots_options_selector" value="two_plot" />
129 <param name="first_plot" value="Counts" />
130 <param name="extra_plot" value="Size" />
131 <output file="count.tab" name="output_tab" />
132 <output file="size.tab" name="extra_output_tab" />
133 <output file="count-size.pdf" name="output_pdf" />
134 </test>
135 <test>
136 <param name="inputs" value="input1.bam,input2.bam" ftype="bam"/>
137 <param name="plots_options_selector" value="two_plot" />
138 <param name="first_plot" value="Size" />
139 <param name="extra_plot" value="Counts" />
140 <output file="size.tab" name="output_tab" />
141 <output file="count.tab" name="extra_output_tab" />
142 <output file="size-count.pdf" name="output_pdf" />
143 </test>
144 <test>
145 <param name="inputs" value="input1.bam,input2.bam" ftype="bam"/>
146 <param name="plots_options_selector" value="one_plot" />
147 <param name="first_plot" value="Counts" />
148 <output file="count.tab" name="output_tab" />
149 <output file="count.pdf" name="output_pdf" />
150 </test>
151 <test>
152 <param name="inputs" value="input1.bam,input2.bam" ftype="bam"/>
153 <param name="plots_options_selector" value="one_plot" />
154 <param name="first_plot" value="Size" />
155 <output file="size.tab" name="output_tab" />
156 <output file="size.pdf" name="output_pdf" />
157 </test>
158 <test>
159 <param name="inputs" value="input1.bam,input2.bam" ftype="bam"/>
160 <param name="plots_options_selector" value="one_plot" />
161 <param name="first_plot" value="Coverage" />
162 <output file="coverage.tab" name="output_tab" />
78 <output file="coverage.pdf" name="output_pdf" /> 163 <output file="coverage.pdf" name="output_pdf" />
79 </test>
80 <test>
81 <param name="inputs" value="input1.bam,input2.bam" ftype="bam"/>
82 <param name="extra_plot" value="Size" />
83 <output file="readmap.tab" name="output_tab" />
84 <output file="size.tab" name="extra_output_tab" />
85 <output file="sizes.pdf" name="output_pdf" />
86 </test> 164 </test>
87 </tests> 165 </tests>
88 166
89 167
90 <help> 168 <help>