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annotate peakachu.xml @ 0:28c319539b42 draft default tip

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planemo upload for repository https://github.com/tbischler/PEAKachu commit 21413560ba7ac260a92531c08899c4a342d1660d
author bgruening
date Thu, 15 Feb 2018 11:09:43 -0500
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28c319539b42 planemo upload for repository https://github.com/tbischler/PEAKachu commit 21413560ba7ac260a92531c08899c4a342d1660d
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1 <tool id="peakachu" name="PEAKachu" version="0.1.0.0">
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2 <description>Calls Peaks in CLIP data</description>
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3 <requirements>
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4 <requirement type="package" version="3.6">python</requirement>
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5 <requirement type="package" version="0.1.0">peakachu</requirement>
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6 </requirements>
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7 <version_command>
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8 <![CDATA[
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9 peakachu --version
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10 ]]>
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11 </version_command>
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12 <command detect_errors="aggressive">
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13 <![CDATA[
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14 #for $i, $clib in enumerate($controlLibs):
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15 #if $clib:
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16 ln -s -f '$clib' ${i}.c.bam &&
28c319539b42 planemo upload for repository https://github.com/tbischler/PEAKachu commit 21413560ba7ac260a92531c08899c4a342d1660d
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17 ln -s -f '$clib.metadata.bam_index' ${i}.c.bam.bai &&
28c319539b42 planemo upload for repository https://github.com/tbischler/PEAKachu commit 21413560ba7ac260a92531c08899c4a342d1660d
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18 #end if
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19 #end for
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20 #for $j, $elib in enumerate($experimentLibs):
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21 ln -s -f '$elib' ${j}.e.bam &&
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22 ln -s -f '$elib.metadata.bam_index' ${j}.e.bam.bai &&
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23 #end for
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24
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25 pwd &&
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26 mkdir ./tmp_output &&
28c319539b42 planemo upload for repository https://github.com/tbischler/PEAKachu commit 21413560ba7ac260a92531c08899c4a342d1660d
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27 peakachu
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28 ${mode.mode_selector}
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29 --exp_libs
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30 #for $i, $elib in enumerate($experimentLibs):
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31 '${i}.e.bam'
28c319539b42 planemo upload for repository https://github.com/tbischler/PEAKachu commit 21413560ba7ac260a92531c08899c4a342d1660d
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32 #end for
28c319539b42 planemo upload for repository https://github.com/tbischler/PEAKachu commit 21413560ba7ac260a92531c08899c4a342d1660d
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33 #for $i, $clib in enumerate($controlLibs):
28c319539b42 planemo upload for repository https://github.com/tbischler/PEAKachu commit 21413560ba7ac260a92531c08899c4a342d1660d
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34 #if $clib and $i == 0:
28c319539b42 planemo upload for repository https://github.com/tbischler/PEAKachu commit 21413560ba7ac260a92531c08899c4a342d1660d
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35 --ctr_libs
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36 #end if
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37 #if $clib:
28c319539b42 planemo upload for repository https://github.com/tbischler/PEAKachu commit 21413560ba7ac260a92531c08899c4a342d1660d
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38 '${i}.c.bam'
28c319539b42 planemo upload for repository https://github.com/tbischler/PEAKachu commit 21413560ba7ac260a92531c08899c4a342d1660d
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39 #end if
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40 #end for
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41 $pairwise_replicates
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42 $paired_end
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43 --max_insert_size $max_insert_size
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44 --features '$features'
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45 --sub_features '$sub_features'
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46 --max_proc "\${GALAXY_SLOTS:-1}"
28c319539b42 planemo upload for repository https://github.com/tbischler/PEAKachu commit 21413560ba7ac260a92531c08899c4a342d1660d
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47 --output_folder ./tmp_output
28c319539b42 planemo upload for repository https://github.com/tbischler/PEAKachu commit 21413560ba7ac260a92531c08899c4a342d1660d
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48 #if str($mode.mode_selector) == 'adaptive':
28c319539b42 planemo upload for repository https://github.com/tbischler/PEAKachu commit 21413560ba7ac260a92531c08899c4a342d1660d
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49 --min_cluster_expr_frac $mode.min_cluster_expr_frac
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50 --min_block_overlap $mode.min_block_overlap
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51 --min_max_block_expr $mode.min_max_block_expr
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52 #elif str($mode.mode_selector) == 'window':
28c319539b42 planemo upload for repository https://github.com/tbischler/PEAKachu commit 21413560ba7ac260a92531c08899c4a342d1660d
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53 --window_size $mode.window_size
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54 --step_size $mode.step_size
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55 --stat_test $mode.stat_test
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56 --het_p_val_threshold $mode.het_p_val_threshold
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57 --rep_pair_p_val_threshold $mode.rep_pair_p_val_threshold
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58 #end if
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59 --norm_method $mode.norm_method.norm_method_selector
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60 #if str($mode.norm_method.norm_method_selector) == 'manual':
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61 --size_factors $size_factors
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62 #end if
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63 --mad_multiplier $mad_multiplier
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64 --fc_cutoff $fc_cutoff
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65 --padj_threshold $padj_threshold
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66
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67 &&
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68 head -n 1 -q ./tmp_output/peak_tables/*.csv | head -n 1 > peaks.tsv &&
28c319539b42 planemo upload for repository https://github.com/tbischler/PEAKachu commit 21413560ba7ac260a92531c08899c4a342d1660d
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69 tail -n +2 -q ./tmp_output/peak_tables/*.csv >> peaks.tsv &&
28c319539b42 planemo upload for repository https://github.com/tbischler/PEAKachu commit 21413560ba7ac260a92531c08899c4a342d1660d
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70 mv peaks.tsv '$peak_tables' &&
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71 mv ./tmp_output/plots/Initial*.png '$MA_plot'
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72
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73 ]]>
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74 </command>
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75 <inputs>
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76 <param name="experimentLibs" type="data" format="bam" label="Experiment Libraries" multiple="True"/>
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77 <param name="controlLibs" type="data" format="bam" label="Control Libraries" multiple="True" optional="True"/>
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78 <param argument="--pairwise_replicates" type="boolean" truevalue="--pairwise_replicates" falsevalue="" checked="False" label="Pairwise Replicates" />
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79 <param argument="--paired_end" type="boolean" truevalue="--paired_end" falsevalue="" checked="False" label="Paired End" />
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80 <param argument="--max_insert_size" type="integer" value="50" label="Maximum Insert Size"/>
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81 <!-- The gff feature is not implemented, because the function can easily be accomplished with featureCount or other tools
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82 <param name="gffs" type="data" format="gff" label="Annotation" optional="True" multiple="True"/-->
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83 <param argument="--features" type="text" label="Features">
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84 <sanitizer>
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85 <valid initial="default"/>
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86 </sanitizer>
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87 </param>
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88 <param argument="--sub_features" type="text" label="Sub-Features">
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89 <sanitizer>
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90 <valid initial="default"/>
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91 </sanitizer>
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92 </param>
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93
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94 <conditional name="mode">
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95 <param name="mode_selector" type="select" label="Select Mode" help="These modes work differently.">
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96 <option value="adaptive" selected="True">Adaptive</option>
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97 <option value="window">Window</option>
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98 <!-- The following options are not implemented because they are vastly different and should be implemented as their own tool, if need be.
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99 <option value="coverage">Coverage</option>
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100 <option value="consensus_peak">Consensus Peak</option-->
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101 </param>
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102 <when value="adaptive">
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103 <param argument="--min_cluster_expr_frac" label="Minimum cluster Expression Fraction" help="Minimum fraction of a block in a cluster for further consideration." type="float" value="0.01"/>
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104 <param argument="--min_block_overlap" label="Minimum Block Overlap" help="Minimum fraction of the width of blocks for merging." type="float" value="0.5"/>
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105 <param argument="--min_max_block_expr" label="Minimum Block Expression" help="Minimum fraction of expression of blocks for merging." type="float" value="0.1"/>
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106 <conditional name="norm_method">
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107 <param name="norm_method_selector" type="select" label="Normalisation Method.">
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108 <option value="deseq" selected="True">DESeq2</option>
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109 <option value="manual">Manual</option>
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110 <option value="none">None</option>
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111 </param>
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112 <when value="deseq"/>
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113 <when value="none"/>
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114 <when value="manual">
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115 <param argument="--size_factors" label="Size Factors" type="text" help="Size factors have to be seperated by SPACE">
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116 <sanitizer>
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117 <valid initial="default"/>
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118 </sanitizer>
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119 </param>
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120 </when>
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121 </conditional>
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122 </when>
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123 <when value="window">
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124 <param argument="--window_size" label="Window Size" type="integer" value="25"/>
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125 <param argument="--step_size" label="Step Size" type="integer" value="5"/>
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126 <param name="stat_test" type="select" label="Statistical Test">
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127 <option value="gtest" selected="True">gtest</option>
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128 <option value="deseq">DESeq2</option>
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129 </param>
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130 <conditional name="norm_method">
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131 <param name="norm_method_selector" type="select" label="Normalisation Method.">
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132 <option value="tmm" selected="True">TMM</option>
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133 <option value="deseq">DESeq2</option>
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134 <option value="count">Count</option>
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135 <option value="manual">Manual</option>
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136 <option value="none">None</option>
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137 </param>
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138 <when value="deseq"/>
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139 <when value="tmm"/>
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140 <when value="count"/>
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141 <when value="none"/>
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142 <when value="manual">
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143 <param argument="--size_factors" label="Size Factors" type="text" help="Size factors have to be seperated by SPACE">
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144 <sanitizer>
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145 <valid initial="default"/>
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146 </sanitizer>
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147 </param>
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148 </when>
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149 </conditional>
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150 <param argument="--het_p_val_threshold" label="Heterogeneous p-value Threshold" type="float" value="0.01"/>
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151 <param argument="--rep_pair_p_val_threshold" label="Paired p-value Threshold" type="float" value="0.05"/>
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152 </when>
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153 </conditional>
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154 <param argument="--mad_multiplier" label="Mad Multiplier" type="float" value="2.0"/>
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155 <param argument="--fc_cutoff" label="Fold Change Threshold" type="float" value="2.0"/>
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156 <param argument="--padj_threshold" type="float" label="Adjusted p-value Threshold" value="0.05"/>
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157 </inputs>
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158 <outputs>
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159 <data format="tabular" name="peak_tables" label="${tool.name} ${mode.mode_selector} on ${on_string}: peaks"/>
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160 <data format="png" name="MA_plot" label="${tool.name} ${mode.mode_selector} on ${on_string}: MA plot"/>
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161 </outputs>
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162 <tests>
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163 <test>
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164 <param name="experimentLibs" value="test1_+xl.bam"/>
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165 <param name="controlLibs" value="test1_-xl.bam"/>
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166 <output name="peak_tables" ftype="tabular" file="test1_peaks.tsv"/>
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167 <output name="MA_plot" ftype="png" file="test1_MA.png"/>
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168 </test>
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169 </tests>
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170 <help>
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171 <![CDATA[
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172 **PEAKachu**
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173
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174 PEAKachu is a tool for the accurate mapping of RBP binding sites based on CLIP-seq and RIP-seq data.
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175 PEAKachu uses signal and control libraries (ideally more than three each) to detect binding sites.
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176 It implements two peak calling approaches
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177
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178 **adaptive**
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179
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180 The adaptive approach applies a three-step procedure to detect regions that are significantly enriched over controls.
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181
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182 - blockbuster is applied to the pooled libraries to combine similar sets of reads into blocks
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183 - blocks are decomposed into peaks by iteratively applying a block merging heuristic
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184 - peaks with significant enrichment of signal over control libraries are determined using DESeq2
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185
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186 **windowed**
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187
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188 The windowed approach subdivides the genome into overlapping regions.
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189 After filtering of lowly expressed regions and library normalization (either using manual size factors, TMM, or DESeq2), this approach determines significantly enriched windows using eiterh DESeq2 or repeated G-tests of goodness-of-fit.
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190
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191 ]]>
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192 </help>
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193 <citations>
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194 </citations>
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195 </tool>