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comparison small_rna_maps.xml @ 2:507383cce5a8 draft

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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit edbb53cb13b52bf8e71c562fa8acc2c3be2fb270
author artbio
date Mon, 14 Aug 2017 05:52:34 -0400
parents 40972a8dfab9
children ed8b0142538d
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1:40972a8dfab9 2:507383cce5a8
1 <tool id="small_rna_maps" name="small_rna_maps" version="0.9.1"> 1 <tool id="small_rna_maps" name="small_rna_maps" version="1.0.0">
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=r3.3.1_0">r-optparse</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[
14 #for $file in $input 14 #for $file in $inputs
15 samtools index '$file' && 15 samtools index '$file' &&
16 #end for 16 #end for
17 python '$__tool_directory__'/small_rna_maps.py 17 python '$__tool_directory__'/small_rna_maps.py
18 --input 18 --inputs
19 #for $file in $input 19 #for $file in $inputs
20 '$file' 20 '$file'
21 #end for 21 #end for
22 --sample_name 22 --sample_names
23 #for $sample in $input 23 #for $sample in $inputs
24 '$sample.name' 24 '$sample.name'
25 #end for 25 #end for
26 #if $extra_plot == 'Sizes': 26 --plot_methods Counts $extra_plot
27 --sizes '$output_sizes' 27 --outputs $output_tab $extra_output_tab &&
28 #end if 28 Rscript '$__tool_directory__'/small_rna_maps.r
29 --output '$output_tab' && 29 --first_dataframe '$output_tab'
30 Rscript '$__tool_directory__'/small_rna_maps.r --output_tab '$output_tab' 30 --extra_dataframe '$extra_output_tab'
31 --output_pdf '$output_pdf' 31 --extra_plot_method '$extra_plot'
32 #if $extra_plot != 'Sizes': 32 --output_pdf '$output_pdf'
33 --extra_plot '$extra_plot'
34 #else
35 --sizes $output_sizes
36 #end if
37 ]]></command> 33 ]]></command>
38 <inputs> 34 <inputs>
39 <param name="input" type="data" format="bam" label="Select multiple alignments to parse" multiple="True"/> 35 <param name="inputs" type="data" format="bam" label="Select multiple alignments to parse" multiple="True"/>
40 <param name="extra_plot" type="select" label="select the type of extra plot in addition to read map"> 36 <param name="extra_plot" type="select" label="select the type of extra plot in addition to read map">
41 <option value="Coverage">Coverage</option> 37 <option value="Coverage">Coverage</option>
42 <option value="Mean">Mean Sizes</option> 38 <option value="Mean">Mean Sizes</option>
43 <option value="Median">Median Sizes</option> 39 <option value="Median">Median Sizes</option>
44 <option value="Sizes">Size Distributions</option> 40 <option value="Size">Size Distributions</option>
45 </param> 41 </param>
46 </inputs> 42 </inputs>
47 43
48 <outputs> 44 <outputs>
49 <data format="tabular" name="output_tab" label="Map dataframe" /> 45 <data format="tabular" name="output_tab" label="Read Count dataframe" />
50 <data format="tabular" name="output_sizes" label="Size dataframe" > 46 <data format="tabular" name="extra_output_tab" label="$extra_plot dataframe" />
51 <filter>extra_plot == "Sizes"</filter>
52 </data>
53 <data format="pdf" name="output_pdf" label="PDF file" /> 47 <data format="pdf" name="output_pdf" label="PDF file" />
54 48
55 </outputs> 49 </outputs>
56 50
57 <tests> 51 <tests>
58 <test> 52 <test>
59 <param name="input" value="input1.bam,input2.bam" ftype="bam"/> 53 <param name="inputs" value="input1.bam,input2.bam" ftype="bam"/>
60 <param name="extra_plot" value="Mean" /> 54 <param name="extra_plot" value="Mean" />
61 <output file="output.tab" name="output_tab" /> 55 <output file="readmap.tab" name="output_tab" />
56 <output file="mean.tab" name="extra_output_tab" />
62 <output file="mean.pdf" name="output_pdf" /> 57 <output file="mean.pdf" name="output_pdf" />
63 </test> 58 </test>
64 <test> 59 <test>
65 <param name="input" value="input1.bam,input1.bam" ftype="bam"/> 60 <param name="inputs" value="input1.bam,input1.bam" ftype="bam"/>
66 <param name="extra_plot" value="Mean" /> 61 <param name="extra_plot" value="Mean" />
67 <output file="doubled.tab" name="output_tab" /> 62 <output file="doubled_readmap.tab" name="output_tab" />
63 <output file="double_mean.tab" name="extra_output_tab" />
68 <output file="doubled_mean.pdf" name="output_pdf" /> 64 <output file="doubled_mean.pdf" name="output_pdf" />
69 </test> 65 </test>
70 <test> 66 <test>
71 <param name="input" value="input1.bam,input2.bam" ftype="bam"/> 67 <param name="inputs" value="input1.bam,input2.bam" ftype="bam"/>
72 <param name="extra_plot" value="Median" /> 68 <param name="extra_plot" value="Median" />
73 <output file="output.tab" name="output_tab" /> 69 <output file="readmap.tab" name="output_tab" />
70 <output file="median.tab" name="extra_output_tab" />
74 <output file="median.pdf" name="output_pdf" /> 71 <output file="median.pdf" name="output_pdf" />
75 </test> 72 </test>
76 <test> 73 <test>
77 <param name="input" value="input1.bam,input2.bam" ftype="bam"/> 74 <param name="inputs" value="input1.bam,input2.bam" ftype="bam"/>
78 <param name="extra_plot" value="Coverage" /> 75 <param name="extra_plot" value="Coverage" />
79 <output file="output.tab" name="output_tab" /> 76 <output file="readmap.tab" name="output_tab" />
77 <output file="coverage.tab" name="extra_output_tab" />
80 <output file="coverage.pdf" name="output_pdf" /> 78 <output file="coverage.pdf" name="output_pdf" />
81 </test> 79 </test>
82 <test> 80 <test>
83 <param name="input" value="input1.bam,input2.bam" ftype="bam"/> 81 <param name="inputs" value="input1.bam,input2.bam" ftype="bam"/>
84 <param name="extra_plot" value="Sizes" /> 82 <param name="extra_plot" value="Size" />
85 <output file="output.tab" name="output_tab" /> 83 <output file="readmap.tab" name="output_tab" />
86 <output file="sizes.tab" name="output_sizes" /> 84 <output file="size.tab" name="extra_output_tab" />
87 <output file="sizes.pdf" name="output_pdf" /> 85 <output file="sizes.pdf" name="output_pdf" />
88 </test> 86 </test>
89 </tests> 87 </tests>
90 88
91 89
97 95
98 In addition to the read counts (lower graphs), median size, mean size and coverage depth of reads(lower graphs) mapping at a given position are plotted. 96 In addition to the read counts (lower graphs), median size, mean size and coverage depth of reads(lower graphs) mapping at a given position are plotted.
99 97
100 **Inputs** 98 **Inputs**
101 99
102 bam alignment files that *must* be 100 bam alignment files that must be
103 101
104 - single-read 102 - single-read
105 - sorted 103 - sorted
106 - mapping to the same reference 104 - mapping to the same reference
107 105