Mercurial > repos > bgruening > deeptools_plot_coverage

annotate plotCoverage.xml @ 0:fd4a79e7e5f0 draft

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planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2bc06301d647fca37a822431d14ffab7a8f9fb67-dirty
author bgruening
date Mon, 21 Dec 2015 19:06:15 -0500
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children 9f2b016177e7
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1 <tool id="deeptools_plot_coverage" name="plotCoverage" version="@WRAPPER_VERSION@.0">
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2 <description>creates a heatmap of correlation scores between different samples </description>
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3 <macros>
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4 <token name="@BINARY@">plotCoverage</token>
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5 <import>deepTools_macros.xml</import>
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6 </macros>
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7 <expand macro="requirements"/>
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8 <command>
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9 <![CDATA[
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10 #set files=[]
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11 #set labels=[]
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12
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13 @multiple_input_bams@
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14
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15 @BINARY@
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17 @THREADS@
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18
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19 --plotFile '$outFileName'
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20 --bamfiles '#echo "' '".join($files)#'
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21 --labels '#echo "' '".join($labels)#'
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22 --plotFileFormat "$outFileFormat"
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23
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24 #if $outRawCounts:
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25 --outRawCounts '$outFileRawCounts'
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26 #end if
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28 #if $advancedOpt.showAdvancedOpt == "yes":
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29 --numberOfSamples '$advancedOpt.numberOfSamples'
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30 $advancedOpt.skipZeros
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31
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32 #if str($advancedOpt.region).strip() != '':
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33 --region '$advancedOpt.region'
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34 #end if
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35 --numberOfSamples $advancedOpt.numberOfSamples
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36
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37 #if $advancedOpt.plotTitle and str($advancedOpt.plotTitle.value) != "":
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38 --plotTitle '$advancedOpt.plotTitle'
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39 #end if
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40 @ADVANCED_OPTS_READ_PROCESSING@
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41 #end if
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42
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43 ]]>
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44 </command>
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45 <inputs>
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46
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47 <expand macro="multiple_input_bams" />
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48
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49 <conditional name="advancedOpt">
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50 <param name="showAdvancedOpt" type="select" label="Show advanced options" >
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51 <option value="no" selected="true">no</option>
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52 <option value="yes">yes</option>
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53 </param>
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54 <when value="no" />
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55 <when value="yes">
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56 <param argument="--numberOfSamples" type="integer" value="100000" min="1"
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57 label="Number of samples"
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58 help="Number of samples taken from the genome to compute the scaling factors."/>
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59 <expand macro="region_limit_operation" />
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60 <expand macro="read_processing_options" />
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61 <expand macro="skipZeros" />
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62 <expand macro="plotTitle" />
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63 </when>
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64 </conditional>
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65
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66 <expand macro="input_image_file_format" />
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67 <param argument="--outRawCounts" type="boolean" label="Save raw counts (coverages) to file" help=""/>
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68
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69
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70 </inputs>
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71 <outputs>
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72 <expand macro="output_image_file_format_not_nested" />
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73 <data format="tabular" name="outFileRawCounts" label="${tool.name} on ${on_string}: bin counts">
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74 <filter>outRawCounts is True</filter>
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75 </data>
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76 </outputs>
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77 <tests>
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78 <test>
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79 <param name="bamfiles" value="bowtie2-test1.bam,bowtie2-test1.bam" ftype="bam" />
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80 <!--param name="outFileFormat" value="png" /-->
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81 <param name="showAdvancedOpt" value="yes" />
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82 <param name="plotTitle" value="Test Title from Galaxy" />
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83 <param name="outRawCounts" value="True" />
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84 <output name="outFileRawCounts" file="plotCoverage_result1.tabular" ftype="tabular" />
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85 <output name="outFileName" file="plotCoverage_result1.png" ftype="png" compare="sim_size" delta="100" />
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86 </test>
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87 </tests>
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88 <help>
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89 <![CDATA[
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90 **What it does**
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91
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92 This tools samples 1 million positions of the genome to build
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93 a coverage histogram. Multiple bam files are accepted but all should
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94 correspond to the same genome assembly.
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95
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96
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97 @REFERENCES@
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98 ]]>
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99 </help>
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100 <expand macro="citations" />
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101 </tool>