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annotate peakachu.xml @ 4:940b1d632f4d draft default tip

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"planemo upload for repository https://github.com/tbischler/PEAKachu commit 23fac1009bde8648151e533ce12c9f3d2f787a65-dirty"
author rnateam
date Mon, 13 Sep 2021 17:20:47 +0000
parents 886f5adba83d
children
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4
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1 <tool id="peakachu" name="PEAKachu" version="0.2.0+galaxy0" profile="20.01">
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="4.1.0">r-base</requirement>
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6 <requirement type="package" version="0.2.0">peakachu</requirement>
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7 </requirements>
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8 <version_command>
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9 <![CDATA[
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10 peakachu --version
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11 ]]>
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12 </version_command>
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13 <command detect_errors="aggressive">
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14 <![CDATA[
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15 #for $i, $clib in enumerate($controlLibs):
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16 #if $clib:
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17 ln -s -f '$clib' ${i}.c.bam &&
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18 ln -s -f '$clib.metadata.bam_index' ${i}.c.bam.bai &&
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19 #end if
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20 #end for
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21 #for $j, $elib in enumerate($experimentLibs):
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22 ln -s -f '$elib' ${j}.e.bam &&
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23 ln -s -f '$elib.metadata.bam_index' ${j}.e.bam.bai &&
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24 #end for
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25
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26 pwd &&
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27 mkdir ./tmp_output &&
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28 peakachu
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29 ${mode.mode_selector}
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30 --exp_libs
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31 #for $i, $elib in enumerate($experimentLibs):
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32 '${i}.e.bam'
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33 #end for
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34 #for $i, $clib in enumerate($controlLibs):
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35 #if $clib and $i == 0:
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36 --ctr_libs
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37 #end if
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38 #if $clib:
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39 '${i}.c.bam'
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40 #end if
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41 #end for
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42 $pairwise_replicates
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43 $paired_end
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44 --max_insert_size $max_insert_size
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45 --features '$features'
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46 --sub_features '$sub_features'
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47 --max_proc "\${GALAXY_SLOTS:-1}"
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48 --output_folder ./tmp_output
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49 #if str($mode.mode_selector) == 'adaptive':
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50 --min_cluster_expr_frac $mode.min_cluster_expr_frac
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51 --min_block_overlap $mode.min_block_overlap
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52 --min_max_block_expr $mode.min_max_block_expr
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53 #elif str($mode.mode_selector) == 'window':
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54 --window_size $mode.window_size
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55 --step_size $mode.step_size
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56 --stat_test $mode.stat_test
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57 --het_p_val_threshold $mode.het_p_val_threshold
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58 --rep_pair_p_val_threshold $mode.rep_pair_p_val_threshold
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59 #end if
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60 --norm_method $mode.norm_method.norm_method_selector
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61 #if str($mode.norm_method.norm_method_selector) == 'manual':
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62 --size_factors '${mode.norm_method.size_factors}'
0
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63 #end if
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64 --mad_multiplier $mad_multiplier
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65 --fc_cutoff $fc_cutoff
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66 --padj_threshold $padj_threshold
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67
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68 &&
1
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69 if ls ./tmp_output/peak_tables/*.csv > /dev/null;
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70 then
3
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71 sed -n 1p ./tmp_output/peak_tables/*.csv > peaks.tsv &&
1
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72 tail -n +2 -q ./tmp_output/peak_tables/*.csv >> peaks.tsv &&
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73 mv peaks.tsv '$peak_tables' &&
3
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74 awk '/peak/ {print $0}' ./tmp_output/peak_annotations/*.gff > peak_annotations.gff &&
1
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75 mv peak_annotations.gff '$peak_annotations' &&
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76 mv ./tmp_output/plots/Initial*.png '$MA_plot';
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77 else
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78 echo "No Peaks Found" >&2;
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79 fi
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80
0
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81
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82 ]]>
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83 </command>
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84 <inputs>
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85 <param name="experimentLibs" type="data" format="bam" label="Experiment Libraries" multiple="True"/>
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86 <param name="controlLibs" type="data" format="bam" label="Control Libraries" multiple="True" optional="True"/>
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87 <param argument="--pairwise_replicates" type="boolean" truevalue="--pairwise_replicates" falsevalue="" checked="False" label="Pairwise Replicates" />
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88 <param argument="--paired_end" type="boolean" truevalue="--paired_end" falsevalue="" checked="False" label="Paired End" />
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89 <param argument="--max_insert_size" type="integer" value="50" label="Maximum Insert Size"/>
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90 <!-- The gff feature is not implemented, because the function can easily be accomplished with featureCount or other tools
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91 <param name="gffs" type="data" format="gff" label="Annotation" optional="True" multiple="True"/-->
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92 <param argument="--features" type="text" label="Features">
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93 <sanitizer>
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94 <valid initial="default"/>
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95 </sanitizer>
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96 </param>
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97 <param argument="--sub_features" type="text" label="Sub-Features">
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98 <sanitizer>
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99 <valid initial="default"/>
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100 </sanitizer>
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101 </param>
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102
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103 <conditional name="mode">
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104 <param name="mode_selector" type="select" label="Select Mode" help="These modes work differently.">
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105 <option value="adaptive" selected="True">Adaptive</option>
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106 <option value="window">Window</option>
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107 <!-- 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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108 <option value="coverage">Coverage</option>
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109 <option value="consensus_peak">Consensus Peak</option-->
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110 </param>
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111 <when value="adaptive">
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112 <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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113 <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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114 <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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115 <conditional name="norm_method">
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116 <param name="norm_method_selector" type="select" label="Normalisation Method">
0
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117 <option value="deseq" selected="True">DESeq2</option>
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118 <option value="manual">Manual</option>
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119 <option value="none">None</option>
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120 </param>
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121 <when value="deseq"/>
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122 <when value="none"/>
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123 <when value="manual">
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124 <param argument="--size_factors" label="Size Factors" type="text" help="Size factors have to be seperated by SPACE">
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125 <sanitizer>
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126 <valid initial="default"/>
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127 </sanitizer>
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128 </param>
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129 </when>
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130 </conditional>
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131 </when>
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132 <when value="window">
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133 <param argument="--window_size" label="Window Size" type="integer" value="25"/>
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134 <param argument="--step_size" label="Step Size" type="integer" value="5"/>
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135 <param name="stat_test" type="select" label="Statistical Test">
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136 <option value="gtest" selected="True">gtest</option>
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137 <option value="deseq">DESeq2</option>
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138 </param>
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139 <conditional name="norm_method">
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140 <param name="norm_method_selector" type="select" label="Normalisation Method">
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141 <option value="tmm" selected="True">TMM</option>
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142 <option value="deseq">DESeq2</option>
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143 <option value="count">Count</option>
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144 <option value="manual">Manual</option>
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145 <option value="none">None</option>
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146 </param>
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147 <when value="deseq"/>
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148 <when value="tmm"/>
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149 <when value="count"/>
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150 <when value="none"/>
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151 <when value="manual">
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152 <param argument="--size_factors" label="Size Factors" type="text" help="Size factors have to be separated by SPACE">
0
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153 <sanitizer>
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154 <valid initial="default"/>
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155 </sanitizer>
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156 </param>
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157 </when>
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158 </conditional>
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159 <param argument="--het_p_val_threshold" label="Heterogeneous p-value Threshold" type="float" value="0.01"/>
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160 <param argument="--rep_pair_p_val_threshold" label="Paired p-value Threshold" type="float" value="0.05"/>
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161 </when>
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162 </conditional>
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163 <param argument="--mad_multiplier" label="Mad Multiplier" type="float" value="2.0"/>
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164 <param argument="--fc_cutoff" label="Fold Change Threshold" type="float" value="2.0"/>
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165 <param argument="--padj_threshold" type="float" label="Adjusted p-value Threshold" value="0.05"/>
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166 </inputs>
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167 <outputs>
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168 <data format="tabular" name="peak_tables" label="${tool.name} ${mode.mode_selector} on ${on_string}: peaks"/>
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169 <data format="gff" name="peak_annotations" label="${tool.name} ${mode.mode_selector} on ${on_string}: peak_annotations"/>
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170 <data format="png" name="MA_plot" label="${tool.name} ${mode.mode_selector} on ${on_string}: MA plot"/>
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171 </outputs>
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172 <tests>
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173 <test>
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174 <param name="experimentLibs" value="test1_plus-xl.bam"/>
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175 <param name="controlLibs" value="test1_minus-xl.bam"/>
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176 <output name="peak_tables" ftype="tabular" file="test1_peaks.tsv"/>
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177 <output name="peak_annotations" ftype="gff" file="test1_peak_annotations.gff"/>
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178 </test>
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179 </tests>
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180 <help>
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181 <![CDATA[
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182 **PEAKachu**
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183
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184 PEAKachu is a tool for the accurate mapping of RBP binding sites based on CLIP-seq and RIP-seq data.
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185 PEAKachu uses signal and control libraries (ideally more than three each) to detect binding sites.
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186 It implements two peak calling approaches
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187
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188 **adaptive**
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189
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190 The adaptive approach applies a three-step procedure to detect regions that are significantly enriched over controls.
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191
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192 - blockbuster is applied to the pooled libraries to combine similar sets of reads into blocks
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193 - blocks are decomposed into peaks by iteratively applying a block merging heuristic
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194 - peaks with significant enrichment of signal over control libraries are determined using DESeq2
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195
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196 **windowed**
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197
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198 The windowed approach subdivides the genome into overlapping regions.
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199 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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200
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201 ]]>
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202 </help>
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203 <citations>
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204 </citations>
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205 </tool>