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1 <tool id="peakcalling_ccat" name="CCAT" version="0.0.1">
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2 <description>Control-based ChIP-seq Analysis Tool</description>
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3 <requirements>
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4 <requirement type="package" version="3.0">CCAT</requirement>
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5 </requirements>
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6 <command interpreter="python">ccat_wrapper.py '$input_tag_file' '$input_control_file' '$chromInfo'
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7 #if str( $options_type[ 'options_type_selector' ] ) == 'advanced':
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8 '$input_advanced_config_file'
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9 #else:
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10 '${ options_type.input_config_file.fields.path }'
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11 #end if
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12 'CCAT in Galaxy'
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13 '$output_peak_file' '$output_region_file' '$output_top_file' '$output_log_file'</command>
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14 <inputs>
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15 <param name="input_tag_file" type="data" format="bed" label="ChIP-Seq Tag File" >
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16 <validator type="unspecified_build" />
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17 </param>
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18 <param name="input_control_file" type="data" format="bed" label="ChIP-Seq Control File" >
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19 <validator type="unspecified_build" />
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20 </param>
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21 <conditional name="options_type">
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22 <param name="options_type_selector" type="select" label="Advanced Options">
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23 <option value="basic" selected="True">Hide Advanced Options</option>
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24 <option value="advanced">Show Advanced Options</option>
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25 </param>
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26 <when value="basic">
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27 <param name="input_config_file" type="select" label="Select a pre-defined configuration file">
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28 <options from_data_table="ccat_configurations">
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29 <validator type="no_options" message="No configurations are available"/>
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30 </options>
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31 </param>
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32 </when>
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33 <when value="advanced">
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34 <param name="fragment_size" type="integer" label="Length of DNA fragment" value="200"/>
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35 <param name="sliding_window_size" type="integer" label="Sliding window size" value="500" help="transcription factor binding default: 300; histone modifications default: 500"/>
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36 <param name="moving_step" type="integer" label="Step of sliding window" value="50" help="transcription factor binding default: 10; histone modifications default: 50"/>
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37 <param name="is_strand_sensitive_mode" type="select" label="isStrandSensitiveMode" >
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38 <option value="1">Transition from sense strand to anti-sense strand</option>
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39 <option value="0" selected="True">Local maximum of read-enrichment profile</option>
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40 </param>
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41 <param name="min_count" type="integer" label="Minimum number of read counts at the peak" value="4"/>
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42 <param name="output_num" type="integer" label="Number of peaks reported in top peak file" value="100000"/>
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43 <param name="random_seed" type="integer" label="Random Seed" value="123456"/>
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44 <param name="min_score" type="float" label="Minimum score of normalized difference" value="3.0"/>
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45 <param name="bootstrap_pass" type="integer" label="Number of passes in the bootstrapping process" value="50"/>
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46 </when>
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47 </conditional>
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48 </inputs>
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49 <outputs>
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50 <data name="output_peak_file" format="interval" label="${tool.name} on ${on_string} (peaks)">
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51 <actions>
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52 <action type="metadata" name="chromCol" default="1"/>
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53 <action type="metadata" name="startCol" default="3"/>
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54 <action type="metadata" name="endCol" default="4"/>
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55 </actions>
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56 </data>
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57 <data name="output_region_file" format="interval" label="${tool.name} on ${on_string} (regions)">
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58 <actions>
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59 <action type="metadata" name="chromCol" default="1"/>
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60 <action type="metadata" name="startCol" default="3"/>
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61 <action type="metadata" name="endCol" default="4"/>
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62 </actions>
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63 </data>
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64 <data name="output_top_file" format="interval" label="${tool.name} on ${on_string} (top peaks)">
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65 <actions>
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66 <action type="metadata" name="chromCol" default="1"/>
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67 <action type="metadata" name="startCol" default="3"/>
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68 <action type="metadata" name="endCol" default="4"/>
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69 </actions>
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70 </data>
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71 <data name="output_log_file" format="txt" label="${tool.name} on ${on_string} (log)"/>
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72 </outputs>
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73 <configfiles>
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74 <configfile name="input_advanced_config_file">#if str( $options_type['options_type_selector' ] ) == 'advanced':
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75 fragmentSize ${options_type[ 'fragment_size' ]}
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76 slidingWinSize ${options_type[ 'sliding_window_size' ]}
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77 movingStep ${options_type[ 'moving_step' ]}
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78 isStrandSensitiveMode ${options_type[ 'is_strand_sensitive_mode' ]}
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79 minCount ${options_type[ 'min_count' ]}
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80 outputNum ${options_type[ 'output_num' ]}
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81 randomSeed ${options_type[ 'random_seed' ]}
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82 minScore ${options_type[ 'min_score' ]}
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83 bootstrapPass ${options_type[ 'bootstrap_pass' ]}
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84 #end if</configfile>
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85 </configfiles>
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86 <tests>
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87 <test>
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88 <param name="input_tag_file" value="chipseq_enriched.bed.gz" ftype="bed" dbkey="hg18" />
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89 <param name="input_control_file" value="chipseq_input.bed.gz" ftype="bed" dbkey="hg18" />
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90 <param name="options_type_selector" value="advanced" />
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91 <param name="fragment_size" value="200" />
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92 <param name="sliding_window_size" value="500" />
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93 <param name="moving_step" value="50" />
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94 <param name="is_strand_sensitive_mode" value="0" />
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95 <param name="min_count" value="4" />
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96 <param name="output_num" value="100000" />
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97 <param name="random_seed" value="123456" />
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98 <param name="min_score" value="5.0" />
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99 <param name="bootstrap_pass" value="50" />
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100 <output name="output_peak_file" file="peakcalling_ccat/3.0/ccat_test_peak_out_1.interval.re_match" compare="re_match" />
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101 <output name="output_region_file" file="peakcalling_ccat/3.0/ccat_test_region_out_1.interval.re_match" compare="re_match" />
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102 <output name="output_top_file" file="peakcalling_ccat/3.0/ccat_test_top_out_1.interval.sorted.re_match" compare="re_match" sort="True" />
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103 <output name="output_log_file" file="peakcalling_ccat/3.0/ccat_test_log_out_1.txt" />
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104 </test>
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105 <test>
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106 <param name="input_tag_file" value="chipseq_enriched.bed.gz" ftype="bed" dbkey="hg18" />
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107 <param name="input_control_file" value="chipseq_input.bed.gz" ftype="bed" dbkey="hg18" />
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108 <param name="options_type_selector" value="basic" />
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109 <param name="input_config_file" value="ccat_3.0_histone_config" />
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110 <output name="output_peak_file" file="peakcalling_ccat/3.0/ccat_test_peak_out_1.interval.re_match" compare="re_match" />
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111 <output name="output_region_file" file="peakcalling_ccat/3.0/ccat_test_region_out_1.interval.re_match" compare="re_match" />
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112 <output name="output_top_file" file="peakcalling_ccat/3.0/ccat_test_top_out_1.interval.sorted.re_match" compare="re_match" sort="true" />
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113 <output name="output_log_file" file="peakcalling_ccat/3.0/ccat_test_log_out_1.txt" />
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114 </test>
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115 <!-- Test below gives different answers on different architectures,
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116 e.g.: x86_64 GNU/Linux gave an extra line (additional peak called) when compared to the version running on 10.6.0 Darwin i386
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117 slidingWinSize was fixed to be 1000, default as per readme.txt
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118 -->
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119 <!--
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120 <test>
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121 <param name="input_tag_file" value="chipseq_enriched.bed.gz" ftype="bed" dbkey="hg18" />
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122 <param name="input_control_file" value="chipseq_input.bed.gz" ftype="bed" dbkey="hg18" />
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123 <param name="options_type_selector" value="basic" />
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124 <param name="input_config_file" value="ccat_3.0_histone_config_readme" />
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125 <output name="output_peak_file" file="peakcalling_ccat/3.0/ccat_test_peak_out_2.interval.re_match" compare="re_match" />
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126 <output name="output_region_file" file="peakcalling_ccat/3.0/ccat_test_region_out_2.interval.re_match" compare="re_match" />
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127 <output name="output_top_file" file="peakcalling_ccat/3.0/ccat_test_top_out_2.interval.sorted.re_match" compare="re_match" sort="true" />
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128 <output name="output_log_file" file="peakcalling_ccat/3.0/ccat_test_log_out_2.txt" />
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129 </test>
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130 -->
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131 </tests>
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132 <help>
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133 **What it does**
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134
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135 This tool allows ChIP-seq peak/region calling using CCAT.
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136
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137 View the original CCAT documentation: http://cmb.gis.a-star.edu.sg/ChIPSeq/paperCCAT.htm.
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138
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139 ------
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140
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141 **Citation**
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142
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143 For the underlying tool, please cite `Xu H, Handoko L, Wei X, Ye C, Sheng J, Wei CL, Lin F, Sung WK. A signal-noise model for significance analysis of ChIP-seq with negative control. Bioinformatics. 2010 May 1;26(9):1199-204. <http://www.ncbi.nlm.nih.gov/pubmed/20371496>`_
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144
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145 If you use this tool in Galaxy, please cite Blankenberg D, et al. *In preparation.*
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146
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147 </help>
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148 </tool>
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