/tools/peak_calling/ccat_wrapper.xml
XML | 148 lines | 125 code | 7 blank | 16 comment | 0 complexity | 3f4417401f31adab4d20a53f58de6ce9 MD5 | raw file
1<tool id="peakcalling_ccat" name="CCAT" version="0.0.1"> 2 <description>Control-based ChIP-seq Analysis Tool</description> 3 <command interpreter="python">ccat_wrapper.py '$input_tag_file' '$input_control_file' '$chromInfo' 4 #if str( $options_type[ 'options_type_selector' ] ) == 'advanced': 5 '$input_advanced_config_file' 6 #else: 7 '${ options_type.input_config_file.fields.path }' 8 #end if 9 'CCAT in Galaxy' 10 '$output_peak_file' '$output_region_file' '$output_top_file' '$output_log_file'</command> 11 <requirements> 12 <requirement type="binary" version="3.0">CCAT</requirement> 13 </requirements> 14 <inputs> 15 <param name="input_tag_file" type="data" format="bed" label="ChIP-Seq Tag File" > 16 <validator type="unspecified_build" /> 17 </param> 18 <param name="input_control_file" type="data" format="bed" label="ChIP-Seq Control File" > 19 <validator type="unspecified_build" /> 20 </param> 21 <conditional name="options_type"> 22 <param name="options_type_selector" type="select" label="Advanced Options"> 23 <option value="basic" selected="True">Hide Advanced Options</option> 24 <option value="advanced">Show Advanced Options</option> 25 </param> 26 <when value="basic"> 27 <param name="input_config_file" type="select" label="Select a pre-defined configuration file"> 28 <options from_data_table="ccat_configurations"> 29 <validator type="no_options" message="No configurations are available"/> 30 </options> 31 </param> 32 </when> 33 <when value="advanced"> 34 <param name="fragment_size" type="integer" label="Length of DNA fragment" value="200"/> 35 <param name="sliding_window_size" type="integer" label="Sliding window size" value="500" help="transcription factor binding default: 300; histone modifications default: 500"/> 36 <param name="moving_step" type="integer" label="Step of sliding window" value="50" help="transcription factor binding default: 10; histone modifications default: 50"/> 37 <param name="is_strand_sensitive_mode" type="select" label="isStrandSensitiveMode" > 38 <option value="1">Transition from sense strand to anti-sense strand</option> 39 <option value="0" selected="True">Local maximum of read-enrichment profile</option> 40 </param> 41 <param name="min_count" type="integer" label="Minimum number of read counts at the peak" value="4"/> 42 <param name="output_num" type="integer" label="Number of peaks reported in top peak file" value="100000"/> 43 <param name="random_seed" type="integer" label="Random Seed" value="123456"/> 44 <param name="min_score" type="float" label="Minimum score of normalized difference" value="3.0"/> 45 <param name="bootstrap_pass" type="integer" label="Number of passes in the bootstrapping process" value="50"/> 46 </when> 47 </conditional> 48 </inputs> 49 <outputs> 50 <data name="output_peak_file" format="interval" label="${tool.name} on ${on_string} (peaks)"> 51 <actions> 52 <action type="metadata" name="chromCol" default="1"/> 53 <action type="metadata" name="startCol" default="3"/> 54 <action type="metadata" name="endCol" default="4"/> 55 </actions> 56 </data> 57 <data name="output_region_file" format="interval" label="${tool.name} on ${on_string} (regions)"> 58 <actions> 59 <action type="metadata" name="chromCol" default="1"/> 60 <action type="metadata" name="startCol" default="3"/> 61 <action type="metadata" name="endCol" default="4"/> 62 </actions> 63 </data> 64 <data name="output_top_file" format="interval" label="${tool.name} on ${on_string} (top peaks)"> 65 <actions> 66 <action type="metadata" name="chromCol" default="1"/> 67 <action type="metadata" name="startCol" default="3"/> 68 <action type="metadata" name="endCol" default="4"/> 69 </actions> 70 </data> 71 <data name="output_log_file" format="txt" label="${tool.name} on ${on_string} (log)"/> 72 </outputs> 73 <configfiles> 74 <configfile name="input_advanced_config_file">#if str( $options_type['options_type_selector' ] ) == 'advanced': 75fragmentSize ${options_type[ 'fragment_size' ]} 76slidingWinSize ${options_type[ 'sliding_window_size' ]} 77movingStep ${options_type[ 'moving_step' ]} 78isStrandSensitiveMode ${options_type[ 'is_strand_sensitive_mode' ]} 79minCount ${options_type[ 'min_count' ]} 80outputNum ${options_type[ 'output_num' ]} 81randomSeed ${options_type[ 'random_seed' ]} 82minScore ${options_type[ 'min_score' ]} 83bootstrapPass ${options_type[ 'bootstrap_pass' ]} 84#end if</configfile> 85 </configfiles> 86 <tests> 87 <test> 88 <param name="input_tag_file" value="chipseq_enriched.bed.gz" ftype="bed" dbkey="hg18" /> 89 <param name="input_control_file" value="chipseq_input.bed.gz" ftype="bed" dbkey="hg18" /> 90 <param name="options_type_selector" value="advanced" /> 91 <param name="fragment_size" value="200" /> 92 <param name="sliding_window_size" value="500" /> 93 <param name="moving_step" value="50" /> 94 <param name="is_strand_sensitive_mode" value="0" /> 95 <param name="min_count" value="4" /> 96 <param name="output_num" value="100000" /> 97 <param name="random_seed" value="123456" /> 98 <param name="min_score" value="5.0" /> 99 <param name="bootstrap_pass" value="50" /> 100 <output name="output_peak_file" file="peakcalling_ccat/3.0/ccat_test_peak_out_1.interval.re_match" compare="re_match" /> 101 <output name="output_region_file" file="peakcalling_ccat/3.0/ccat_test_region_out_1.interval.re_match" compare="re_match" /> 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" /> 103 <output name="output_log_file" file="peakcalling_ccat/3.0/ccat_test_log_out_1.txt" /> 104 </test> 105 <test> 106 <param name="input_tag_file" value="chipseq_enriched.bed.gz" ftype="bed" dbkey="hg18" /> 107 <param name="input_control_file" value="chipseq_input.bed.gz" ftype="bed" dbkey="hg18" /> 108 <param name="options_type_selector" value="basic" /> 109 <param name="input_config_file" value="ccat_3.0_histone_config" /> 110 <output name="output_peak_file" file="peakcalling_ccat/3.0/ccat_test_peak_out_1.interval.re_match" compare="re_match" /> 111 <output name="output_region_file" file="peakcalling_ccat/3.0/ccat_test_region_out_1.interval.re_match" compare="re_match" /> 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" /> 113 <output name="output_log_file" file="peakcalling_ccat/3.0/ccat_test_log_out_1.txt" /> 114 </test> 115 <!-- Test below gives different answers on different architectures, 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 117 slidingWinSize was fixed to be 1000, default as per readme.txt 118 --> 119 <!-- 120 <test> 121 <param name="input_tag_file" value="chipseq_enriched.bed.gz" ftype="bed" dbkey="hg18" /> 122 <param name="input_control_file" value="chipseq_input.bed.gz" ftype="bed" dbkey="hg18" /> 123 <param name="options_type_selector" value="basic" /> 124 <param name="input_config_file" value="ccat_3.0_histone_config_readme" /> 125 <output name="output_peak_file" file="peakcalling_ccat/3.0/ccat_test_peak_out_2.interval.re_match" compare="re_match" /> 126 <output name="output_region_file" file="peakcalling_ccat/3.0/ccat_test_region_out_2.interval.re_match" compare="re_match" /> 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" /> 128 <output name="output_log_file" file="peakcalling_ccat/3.0/ccat_test_log_out_2.txt" /> 129 </test> 130 --> 131 </tests> 132 <help> 133**What it does** 134 135This tool allows ChIP-seq peak/region calling using CCAT. 136 137View the original CCAT documentation: http://cmb.gis.a-star.edu.sg/ChIPSeq/paperCCAT.htm. 138 139------ 140 141**Citation** 142 143For 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>`_ 144 145If you use this tool in Galaxy, please cite Blankenberg D, et al. *In preparation.* 146 147 </help> 148</tool>