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comparison small_rna_maps.xml @ 7:a96e6a7df2b7 draft

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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 06472d1bd1365e4f7b385d578a69f4646481e22f
author artbio
date Tue, 10 Oct 2017 18:48:37 -0400
parents a3be3601bcb3
children 1827b74f872b
comparison
equal deleted inserted replaced
6:a3be3601bcb3 7:a96e6a7df2b7
1 <tool id="small_rna_maps" name="small_rna_maps" version="2.1.0"> 1 <tool id="small_rna_maps" name="small_rna_maps" version="2.2.0">
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=r3.3.2_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=r3.3.2_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=r3.3.2_0">r-gridextra</requirement> 8 <requirement type="package" version="2.2.1=r3.3.2_0">r-gridextra</requirement>
9 <requirement type="package" version="1.4.2=r3.3.2_0">r-reshape2</requirement>
10
9 </requirements> 11 </requirements>
10 <stdio> 12 <stdio>
11 <exit_code range="1:" level="fatal" description="Tool exception" /> 13 <exit_code range="1:" level="fatal" description="Tool exception" />
12 </stdio> 14 </stdio>
13 <command detect_errors="exit_code"><![CDATA[ 15 <command detect_errors="exit_code"><![CDATA[
24 '$sample.name' 26 '$sample.name'
25 #end for 27 #end for
26 #if str($plots_options.plots_options_selector ) == "two_plot": 28 #if str($plots_options.plots_options_selector ) == "two_plot":
27 --plot_methods '${plots_options.first_plot}' '${plots_options.extra_plot}' 29 --plot_methods '${plots_options.first_plot}' '${plots_options.extra_plot}'
28 --outputs '$output_tab' '$extra_output_tab' && 30 --outputs '$output_tab' '$extra_output_tab' &&
31 #elif str($plots_options.plots_options_selector ) == "global":
32 --plot_methods 'Size'
33 --outputs '$output_tab' &&
29 #else: 34 #else:
30 --plot_methods '${plots_options.first_plot}' 35 --plot_methods '${plots_options.first_plot}'
31 --outputs '$output_tab' && 36 --outputs '$output_tab' &&
32 #end if 37 #end if
33 Rscript '$__tool_directory__'/small_rna_maps.r 38 Rscript '$__tool_directory__'/small_rna_maps.r
35 --extra_dataframe '$extra_output_tab' 40 --extra_dataframe '$extra_output_tab'
36 --normalization '$normalization' 41 --normalization '$normalization'
37 #if str($plots_options.plots_options_selector ) == "two_plot": 42 #if str($plots_options.plots_options_selector ) == "two_plot":
38 --first_plot_method '${plots_options.first_plot}' 43 --first_plot_method '${plots_options.first_plot}'
39 --extra_plot_method '${plots_options.extra_plot}' 44 --extra_plot_method '${plots_options.extra_plot}'
45 #elif str($plots_options.plots_options_selector ) == "global":
46 --first_plot_method 'Size'
47 --extra_plot_method ''
48 --global '${plots_options.mergestrands}'
40 #else: 49 #else:
41 --first_plot_method '${plots_options.first_plot}' 50 --first_plot_method '${plots_options.first_plot}'
42 --extra_plot_method '' 51 --extra_plot_method ''
43 #end if 52 #end if
44 --output_pdf '$output_pdf' 53 --output_pdf '$output_pdf'
45 ]]></command> 54 ]]></command>
46 <inputs> 55 <inputs>
47 <param name="inputs" type="data" format="bam" label="Select multiple alignments to parse" multiple="True"/> 56 <param name="inputs" type="data" format="bam" label="Select multiple alignments to parse" multiple="True"/>
48 <param name="normalization" type="text" label="Enter size/normalization factors as a space-separated list. Leave blank for no normalization (default)" 57 <param name="normalization" type="text" label="Enter size/normalization factors as a space-separated list. Leave blank for no normalization (default)"
49 help="e.g. '1 0.75 1.23'. Values of the list map to the above selected files from bottom to top" /> 58 help="e.g. '1 0.75 1.23'. Values of the list map to the above selected files from bottom to top" />
50 <conditional name="plots_options"> 59 <conditional name="plots_options">
51 <param name="plots_options_selector" type="select" label="Number of plots per chromosome"> 60 <param name="plots_options_selector" type="select" display="radio" label="Plot Options">
52 <option value="one_plot">Just one plot per chromosome</option> 61 <option value="one_plot">Just one plot per chromosome</option>
53 <option value="two_plot" selected="True">Two plots per chromosome</option> 62 <option value="two_plot" selected="True">Two plots per chromosome</option>
63 <option value="global">Global read size distributions of aligned reads</option>
54 </param> 64 </param>
55 <when value="two_plot"> 65 <when value="two_plot">
56 <param name="first_plot" type="select" label="Select the type of the first plot"> 66 <param name="first_plot" type="select" display="radio" label="Select the type of the first plot">
57 <option value="Counts">Counts</option> 67 <option value="Counts">Counts</option>
58 <option value="Coverage">Coverage</option> 68 <option value="Coverage">Coverage</option>
59 <option value="Mean">Mean Sizes</option> 69 <option value="Mean">Mean Sizes</option>
60 <option value="Median">Median Sizes</option> 70 <option value="Median">Median Sizes</option>
61 <option value="Size">Size Distributions</option> 71 <option value="Size">Size Distributions</option>
62 </param> 72 </param>
63 <param name="extra_plot" type="select" label="Select the type of the second plot"> 73 <param name="extra_plot" type="select" display="radio" label="Select the type of the second plot">
64 <option value="Counts">Counts</option> 74 <option value="Counts">Counts</option>
65 <option value="Coverage">Coverage</option> 75 <option value="Coverage">Coverage</option>
66 <option value="Mean">Mean Sizes</option> 76 <option value="Mean">Mean Sizes</option>
67 <option value="Median">Median Sizes</option> 77 <option value="Median">Median Sizes</option>
68 <option value="Size">Size Distributions</option> 78 <option value="Size">Size Distributions</option>
69 </param> 79 </param>
70 </when> 80 </when>
71 <when value="one_plot"> 81 <when value="one_plot">
72 <param name="first_plot" type="select" label="select the type of the first plot"> 82 <param name="first_plot" type="select" display="radio" label="select the type of the first plot">
73 <option value="Counts">Counts</option> 83 <option value="Counts">Counts</option>
74 <option value="Coverage">Coverage</option> 84 <option value="Coverage">Coverage</option>
75 <option value="Mean">Mean Sizes</option> 85 <option value="Mean">Mean Sizes</option>
76 <option value="Median">Median Sizes</option> 86 <option value="Median">Median Sizes</option>
77 <option value="Size">Size Distributions</option> 87 <option value="Size">Size Distributions</option>
78 </param> 88 </param>
79 </when> 89 </when>
90 <when value="global">
91 <param name="first_plot" type="hidden" value="Size"/>
92 <param name="mergestrands" type="select" display="radio" label="Whether forward and reverse aligned reads should be merged or not in the histogram">
93 <option value="nomerge">Do not merge</option>
94 <option value="merge">Merge forward and reverse reads</option>
95 </param>
96 </when>
80 </conditional> 97 </conditional>
81 </inputs> 98 </inputs>
82 99
83 <outputs> 100 <outputs>
84 <data format="tabular" name="output_tab" label="Read Count dataframe" /> 101 <data format="tabular" name="output_tab" label="$plots_options.first_plot dataframe" />
85 <data format="tabular" name="extra_output_tab" label="$plots_options.extra_plot dataframe"> 102 <data format="tabular" name="extra_output_tab" label="$plots_options.extra_plot dataframe">
86 <filter>plots_options['plots_options_selector'] == 'two_plot'</filter> 103 <filter>plots_options['plots_options_selector'] == 'two_plot'</filter>
87 </data> 104 </data>
88 <data format="pdf" name="output_pdf" label="PDF file" /> 105 <data format="pdf" name="output_pdf" label="small RNA maps" />
89
90 </outputs> 106 </outputs>
91 107
92 <tests> 108 <tests>
109 <test>
110 <param name="inputs" value="input1.bam,input2.bam" ftype="bam"/>
111 <param name="plots_options_selector" value="global" />
112 <param name="mergestrands" value="nomerge" />
113 <param name="first_plot" value="Size" />
114 <param name="normalization" value="1 1" />
115 <output file="size.tab" name="output_tab" />
116 <output file="global_nomerge.pdf" name="output_pdf" />
117 </test>
118 <test>
119 <param name="inputs" value="input1.bam,input2.bam" ftype="bam"/>
120 <param name="plots_options_selector" value="global" />
121 <param name="mergestrands" value="merge" />
122 <param name="first_plot" value="Size" />
123 <param name="normalization" value="1 1" />
124 <output file="size.tab" name="output_tab" />
125 <output file="global_merge.pdf" name="output_pdf" />
126 </test>
93 <test> 127 <test>
94 <param name="inputs" value="input1.bam,input2.bam" ftype="bam"/> 128 <param name="inputs" value="input1.bam,input2.bam" ftype="bam"/>
95 <param name="plots_options_selector" value="two_plot" /> 129 <param name="plots_options_selector" value="two_plot" />
96 <param name="first_plot" value="Counts" /> 130 <param name="first_plot" value="Counts" />
97 <param name="extra_plot" value="Mean" /> 131 <param name="extra_plot" value="Mean" />