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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_map commit 339b809565195d32271f5d17c689dee15063e477
author artbio
date Wed, 12 Jul 2017 13:40:36 -0400
parents 2299eb1e7c93
children 2e0dc6032a98
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7feee0446c5c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_map commit 339b809565195d32271f5d17c689dee15063e477
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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="2.2.1=r3.3.1_0">r-gridextra</requirement>
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9 </requirements>
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10 <stdio>
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11 <exit_code range="1:" level="fatal" description="Tool exception" />
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12 </stdio>
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13 <command detect_errors="exit_code"><![CDATA[
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14 python '$__tool_directory__'/small_rna_map.py
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15 --input
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16 #for $file in $input
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17 '$file'
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18 #end for
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19 --output '$output_tab' &&
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20 Rscript '$__tool_directory__'/small_rna_map.r --output_tab '$output_tab' --output_pdf '$output_pdf'
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21 ]]></command>
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22 <inputs>
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23 <param name="input" type="data" format="bam" label="Select multiple alignments to parse" multiple="True"/>
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24 </inputs>
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26 <outputs>
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27 <data format="tabular" name="output_tab" label="tabular file" />
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28 <data format="pdf" name="output_pdf" label="PDF file" />
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29 </outputs>
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31 <tests>
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32 <test>
1
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33 <param name="input" value="input1.bam,input2.bam,input3.bam,input4.bam" ftype="bam"/>
0
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34 <output file="output.tab" name="output_tab" />
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35 <output file="output.pdf" name="output_pdf" />
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36 </test>
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37 </tests>
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1ad5d040f85f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_map commit fa452d860cf550c7524df59e77b36fd39e3e2a45
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40 <help>
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42 **What it does**
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43
1ad5d040f85f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_map commit fa452d860cf550c7524df59e77b36fd39e3e2a45
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44 Generate read count maps from alignment BAM files, using pysam and ggplot.
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45 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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46
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47 **Inputs**
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48 Bam alignment files. Be carreful to select Bam corresponding to alignments to the same reference
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49
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50 **Output**
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51 A pdf file generated by the R package ggplot2
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52
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53 </help>
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55 <citations>
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56 <citation type="doi">10.1093/bioinformatics/btp352</citation>
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57 <citation type="bibtex">@Book{,
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58 author = {Hadley Wickham},
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59 title = {ggplot2: Elegant Graphics for Data Analysis},
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60 publisher = {Springer-Verlag New York},
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61 year = {2009},
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62 isbn = {978-0-387-98140-6},
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63 url = {http://ggplot2.org},
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64 }</citation>
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65 </citations>
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66 </tool>
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