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author | jbrayet |
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date | Thu, 21 Jan 2016 09:43:32 -0500 |
parents | e55d0b7dbfab |
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<tool id="peakcalling_ccat" name="CCAT" version="0.0.1"> <description>Control-based ChIP-seq Analysis Tool</description> <requirements> <container type="docker">institutcuriengsintegration/ccat:1.0</container> </requirements> <command interpreter="python">ccat_wrapper.py '$input_tag_file' '$input_control_file' '$genome' #if str( $options_type[ 'options_type_selector' ] ) == 'advanced': '$input_advanced_config_file' #else: '$options_type.input_config_file' #end if 'CCAT' '$output_peak_file' '$output_region_file' '$output_top_file' '$output_log_file' '${__root_dir__}'</command> <inputs> <param name="input_tag_file" type="data" format="bed" label="ChIP-Seq Tag File" /> <param name="input_control_file" type="data" format="bed" label="ChIP-Seq Control File" /> <param name="genome" type="select" label="Genome" > <option value="hg19" selected="True">Human (hg19)</option> <option value="mm10" >Mouse (mm10)</option> <option value="hg18" >Human (hg18)</option> <option value="mm9" >Mouse (mm9)</option> </param> <conditional name="options_type"> <param name="options_type_selector" type="select" label="Advanced Options"> <option value="basic" selected="True">Hide Advanced Options and select configuration file</option> <option value="advanced">Show Advanced Options</option> </param> <when value="basic"> <param name="input_config_file" type="data" format="txt" label="Select a pre-defined configuration file" /> </when> <when value="advanced"> <param name="fragment_size" type="integer" label="Length of DNA fragment" value="200"/> <param name="sliding_window_size" type="integer" label="Sliding window size" value="500" help="transcription factor binding default: 300; histone modifications default: 500"/> <param name="moving_step" type="integer" label="Step of sliding window" value="50" help="transcription factor binding default: 10; histone modifications default: 50"/> <param name="is_strand_sensitive_mode" type="select" label="isStrandSensitiveMode" > <option value="1">Transition from sense strand to anti-sense strand</option> <option value="0" selected="True">Local maximum of read-enrichment profile</option> </param> <param name="min_count" type="integer" label="Minimum number of read counts at the peak" value="4"/> <param name="output_num" type="integer" label="Number of peaks reported in top peak file" value="100000"/> <param name="random_seed" type="integer" label="Random Seed" value="123456"/> <param name="min_score" type="float" label="Minimum score of normalized difference" value="3.0"/> <param name="bootstrap_pass" type="integer" label="Number of passes in the bootstrapping process" value="50"/> </when> </conditional> </inputs> <outputs> <data name="output_peak_file" format="interval" label="${tool.name} on ${on_string} (peaks)"> <actions> <action type="metadata" name="chromCol" default="1"/> <action type="metadata" name="startCol" default="3"/> <action type="metadata" name="endCol" default="4"/> </actions> </data> <data name="output_region_file" format="interval" label="${tool.name} on ${on_string} (regions)"> <actions> <action type="metadata" name="chromCol" default="1"/> <action type="metadata" name="startCol" default="3"/> <action type="metadata" name="endCol" default="4"/> </actions> </data> <data name="output_top_file" format="interval" label="${tool.name} on ${on_string} (top peaks)"> <actions> <action type="metadata" name="chromCol" default="1"/> <action type="metadata" name="startCol" default="3"/> <action type="metadata" name="endCol" default="4"/> </actions> </data> <data name="output_log_file" format="txt" label="${tool.name} on ${on_string} (log)"/> </outputs> <configfiles> <configfile name="input_advanced_config_file">#if str( $options_type['options_type_selector' ] ) == 'advanced': fragmentSize ${options_type[ 'fragment_size' ]} slidingWinSize ${options_type[ 'sliding_window_size' ]} movingStep ${options_type[ 'moving_step' ]} isStrandSensitiveMode ${options_type[ 'is_strand_sensitive_mode' ]} minCount ${options_type[ 'min_count' ]} outputNum ${options_type[ 'output_num' ]} randomSeed ${options_type[ 'random_seed' ]} minScore ${options_type[ 'min_score' ]} bootstrapPass ${options_type[ 'bootstrap_pass' ]} #end if</configfile> </configfiles> <tests> <test> <param name="input_tag_file" value="chipseq_enriched.bed.gz" ftype="bed" dbkey="hg18" /> <param name="input_control_file" value="chipseq_input.bed.gz" ftype="bed" dbkey="hg18" /> <param name="options_type_selector" value="advanced" /> <param name="fragment_size" value="200" /> <param name="sliding_window_size" value="500" /> <param name="moving_step" value="50" /> <param name="is_strand_sensitive_mode" value="0" /> <param name="min_count" value="4" /> <param name="output_num" value="100000" /> <param name="random_seed" value="123456" /> <param name="min_score" value="5.0" /> <param name="bootstrap_pass" value="50" /> <output name="output_peak_file" file="peakcalling_ccat/3.0/ccat_test_peak_out_1.interval.re_match" compare="re_match" /> <output name="output_region_file" file="peakcalling_ccat/3.0/ccat_test_region_out_1.interval.re_match" compare="re_match" /> <output name="output_top_file" file="peakcalling_ccat/3.0/ccat_test_top_out_1.interval.sorted.re_match" compare="re_match" sort="True" /> <output name="output_log_file" file="peakcalling_ccat/3.0/ccat_test_log_out_1.txt" /> </test> <test> <param name="input_tag_file" value="chipseq_enriched.bed.gz" ftype="bed" dbkey="hg18" /> <param name="input_control_file" value="chipseq_input.bed.gz" ftype="bed" dbkey="hg18" /> <param name="options_type_selector" value="basic" /> <param name="input_config_file" value="ccat_3.0_histone_config" /> <output name="output_peak_file" file="peakcalling_ccat/3.0/ccat_test_peak_out_1.interval.re_match" compare="re_match" /> <output name="output_region_file" file="peakcalling_ccat/3.0/ccat_test_region_out_1.interval.re_match" compare="re_match" /> <output name="output_top_file" file="peakcalling_ccat/3.0/ccat_test_top_out_1.interval.sorted.re_match" compare="re_match" sort="true" /> <output name="output_log_file" file="peakcalling_ccat/3.0/ccat_test_log_out_1.txt" /> </test> </tests> <help> **What it does** This tool allows ChIP-seq peak/region calling using CCAT. View the original CCAT `documentation. <http://cmb.gis.a-star.edu.sg/ChIPSeq/paperCCAT.html>`_ ------ **Citation** 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>`_ If you use this tool in Galaxy, please cite Blankenberg D, et al. *In preparation.* </help> </tool>