Mercurial > repos > artbio > small_rna_map

annotate small_rna_map.xml @ 3:2e0dc6032a98 draft

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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_map commit 93f212712d9846c7aaa389de60babb332d38363e
author artbio
date Tue, 18 Jul 2017 13:34:36 -0400
parents 7feee0446c5c
children 6ff925458e05
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1 <tool id="small_rna_map" name="small rna map" version="0.3.0">
0
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2 <description></description>
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3 <requirements>
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4 <requirement type="package" version="1.11.2=py27_0">numpy</requirement>
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5 <requirement type="package" version="0.11.2.1=py27_0">pysam</requirement>
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6 <requirement type="package" version="1.3.2=r3.3.1_0">r-optparse</requirement>
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7 <requirement type="package" version="2.2.1=r3.3.1_0">r-ggplot2</requirement>
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8 <requirement type="package" version="0.6_28=r3.3.1_0">r-latticeextra</requirement>
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9 <requirement type="package" version="2.2.1=r3.3.1_0">r-gridextra</requirement>
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10 </requirements>
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11 <stdio>
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12 <exit_code range="1:" level="fatal" description="Tool exception" />
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13 </stdio>
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14 <command detect_errors="exit_code"><![CDATA[
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15 python '$__tool_directory__'/small_rna_map.py
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16 --input
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17 #for $file in $input
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18 '$file'
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19 #end for
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20 --sample_name
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21 #for $sample in $input
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22 '$sample.name'
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23 #end for
0
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24 --output '$output_tab' &&
3
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25 #if $R_method=='lattice':
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26 Rscript '$__tool_directory__'/lattice_small_rna_map.r --output_tab '$output_tab' --output_pdf '$output_pdf'
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27 #else:
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28 Rscript '$__tool_directory__'/small_rna_map.r --output_tab '$output_tab' --output_pdf '$output_pdf'
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29 #end if
0
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30 ]]></command>
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31 <inputs>
3
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32 <param name="input" type="data" format="bam" label="Select multiple alignments to parse" multiple="True"/>
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33 <param help="Select the R package to produce graphics" label="lattice or ggplot" name="R_method" type="select">
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34 <option selected="True" value="lattice">lattice</option>
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35 <option value="ggplot">ggplot</option>
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36 </param>
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37
0
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38 </inputs>
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39
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40 <outputs>
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41 <data format="tabular" name="output_tab" label="tabular file" />
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42 <data format="pdf" name="output_pdf" label="PDF file" />
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43 </outputs>
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44
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45 <tests>
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46 <test>
3
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47 <param name="input" value="input1.bam,input2.bam" ftype="bam"/>
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48 <param name="R_method" value="lattice" />
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49 <output file="output.tab" name="output_tab" />
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50 <output file="output_lattice.pdf" name="output_pdf" />
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51 </test>
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52 <test>
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53 <param name="input" value="input1.bam,input1.bam" ftype="bam"/>
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54 <param name="R_method" value="lattice" />
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55 <output file="output_doubled.tab" name="output_tab" />
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56 <output file="output_lattice_doubled.pdf" name="output_pdf" />
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57 </test>
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58 <test>
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59 <param name="input" value="input1.bam,input2.bam" ftype="bam"/>
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60 <param name="R_method" value="ggplot" />
0
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61 <output file="output.tab" name="output_tab" />
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62 <output file="output.pdf" name="output_pdf" />
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63 </test>
3
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64 <test>
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65 <param name="input" value="input1.bam,input1.bam" ftype="bam"/>
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66 <param name="R_method" value="ggplot" />
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67 <output file="output_doubled.tab" name="output_tab" />
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68 <output file="output_doubled.pdf" name="output_pdf" />
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69 </test>
0
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70 </tests>
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71
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73 <help>
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74
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75 **What it does**
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76
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77 Generate read count maps from alignment BAM files, using pysam and ggplot.
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78 In addition to the read counts (bars), median size and mean size of reads mapping at a given position are plotted in the graphs.
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79
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80 **Inputs**
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81 Bam alignment files. Be carreful to select Bam corresponding to alignments to the same reference
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82
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83 **Output**
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84 A pdf file generated by the R package ggplot2
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85
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86 </help>
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87
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88 <citations>
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89 <citation type="doi">10.1093/bioinformatics/btp352</citation>
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90 <citation type="bibtex">@Book{,
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91 author = {Hadley Wickham},
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92 title = {ggplot2: Elegant Graphics for Data Analysis},
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93 publisher = {Springer-Verlag New York},
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94 year = {2009},
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95 isbn = {978-0-387-98140-6},
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96 url = {http://ggplot2.org},
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97 }</citation>
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98 </citations>
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99 </tool>
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100