annotate bamFingerprint.xml @ 31:7889d260cc37 draft default tip

planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 3bc1d1c6f4e28ac7ff8df79fe4e3f00a195938e6-dirty
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date Wed, 21 Oct 2015 02:50:24 -0400
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f7712a057440 new bugfix release
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1 <tool id="deeptools_bamFingerprint" name="bamFingerprint" version="@WRAPPER_VERSION@.0">
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2 <description>plots profiles of BAM files; useful for assesing ChIP signal strength</description>
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3 <macros>
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4 <token name="@BINARY@">bamFingerprint</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 @multiple_input_bams@
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12 bamFingerprint
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14 @THREADS@
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16 --bamfiles #echo " ".join($files)
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17 --labels #echo " ".join($labels)
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19 --fragmentLength $fragmentLength
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21 --plotFile $outFileName
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23 #if $output.showOutputSettings == "yes"
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24 --plotFileFormat $output.outFileFormat
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25 #if $output.saveRawCounts:
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26 --outRawCounts '$outFileRawCounts'
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27 #end if
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28 #else
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29 --plotFileFormat 'png'
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30 #end if
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32 #if str($region).strip() != '':
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33 --region '$region'
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34 #end if
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36 #if $advancedOpt.showAdvancedOpt == "yes":
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37 --binSize '$advancedOpt.binSize'
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38 --numberOfSamples '$advancedOpt.numberOfSamples'
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39
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40 $advancedOpt.doNotExtendPairedEnds
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41 $advancedOpt.ignoreDuplicates
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42 $advancedOpt.skipZeros
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44 #if $advancedOpt.minMappingQuality:
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45 --minMappingQuality '$advancedOpt.minMappingQuality'
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46 #end if
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47
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48 #if $advancedOpt.plotTitle and str($advancedOpt.plotTitle.value) != "":
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49 --plotTitle '$advancedOpt.plotTitle'
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50 #end if
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52 #end if
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53 ]]>
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54 </command>
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55
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56 <inputs>
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57 <expand macro="multiple_input_bams" />
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58 <expand macro="fragmentLength" />
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59 <expand macro="region_limit_operation" />
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61 <conditional name="advancedOpt">
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62 <param name="showAdvancedOpt" type="select" label="Show advanced options" >
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63 <option value="no" selected="true">no</option>
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64 <option value="yes">yes</option>
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65 </param>
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66 <when value="no" />
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67 <when value="yes">
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68 <param name="binSize" type="integer" value="500" min="1"
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69 label="Bin size in bp"
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70 help="Length in base pairs for a window used to sample the genome."/>
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71 <param name="numberOfSamples" type="integer" value="100000" min="1"
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72 label="Number of samples"
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73 help="Number of samples taken from the genome to compute the scaling factors. (--numberOfSamples)"/>
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74 <expand macro="doNotExtendPairedEnds" />
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75 <expand macro="ignoreDuplicates" />
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76 <expand macro="minMappingQuality" />
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77 <expand macro="skipZeros" />
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78 <expand macro="plotTitle" />
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79 </when>
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80 </conditional>
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81 <conditional name="output">
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82 <param name="showOutputSettings" type="select" label="Show advanced output settings">
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83 <option value="no" selected="true">no</option>
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84 <option value="yes">yes</option>
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85 </param>
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86 <when value="no" />
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87 <when value="yes">
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88 <expand macro="input_image_file_format" />
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89 <param name="saveRawCounts" type="boolean" label="Save the bin counts" help="(--outRawCounts)"/>
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90 </when>
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91 </conditional>
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92 </inputs>
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93 <outputs>
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94 <expand macro="output_image_file_format" />
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95 <data format="tabular" name="outFileRawCounts" label="${tool.name} on ${on_string}: bin counts">
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96 <filter>
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97 ((
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98 output['showOutputSettings'] == 'yes' and
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99 output['saveRawCounts'] is True
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100 ))
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101 </filter>
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102 </data>
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103 </outputs>
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104 <tests>
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105 <test>
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106 <repeat name="input_files">
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107 <param name="bamfile" value="bowtie2-test1.bam" ftype="bam" />
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108 </repeat>
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109 <repeat name="input_files">
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110 <param name="bamfile" value="bowtie2-test1.bam" ftype="bam" />
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111 </repeat>
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112 <param name="fragmentLength" value="200" />
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113 <param name="showAdvancedOpt" value="no" />
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114 <param name="showOutputSettings" value="no" />
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115 <output name="outFileName" file="bamFingerprint_result1.png" ftype="png" compare="sim_size" />
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116 </test>
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117 </tests>
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118 <help>
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119 <![CDATA[
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120 **What it does**
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121
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122 This tool is useful to assess the strength of a ChIP (i.e. how clearly the enrichment signal can be separated from the background signal)
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123 and it is based on a method developed by Diaz et al. (2012) Stat Appl Genet Mol Biol 11(3).
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124
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125 The tool first samples indexed BAM files and counts all reads overlapping a window (bin) of specified length.
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126 These counts are then sorted according to their rank (the bin with the highest number of reads has the highest rank)
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127 and the cumulative sum of read counts are plotted. An ideal input (control sample) with perfect uniform distribution of reads
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128 along the genome (i.e. without enrichments in open chromatin etc.) should
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129 generate a straight diagonal line. A very specific and strong ChIP enrichment will be indicated by a prominent and steep
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130 rise of the cumulative sum towards the highest rank. This means that a big chunk of reads from the ChIP sample is located in
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131 few bins which corresponds to high, narrow enrichments seen for transcription factors.
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132
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133
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134 .. image:: $PATH_TO_IMAGES/QC_fingerprint.png
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135
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136
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137 You can find more details on the bamFingerprint wiki page: https://github.com/fidelram/deepTools/wiki/QC#wiki-bamFingerprint
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138
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139
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140 **Output files**:
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141
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142 - Diagnostic plot
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143 - Data matrix of raw counts
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144
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145 -----
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146
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147 @REFERENCES@
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148 ]]>
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149 </help>
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150 <expand macro="citations" />
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151 </tool>