<tool id="peakcalling_sicer" name="SICER" version="@TOOL_VERSION@">
    <description>Statistical approach for the Identification of ChIP-Enriched Regions</description>
    <macros>
        <token name="@TOOL_VERSION@">1.1</token>
    </macros>
    <requirements>
        <requirement type="package" version="@TOOL_VERSION@">SICER</requirement>
    </requirements>
    <command detect_errors="exit_code"><![CDATA[
python '$__tool_directory__/sicer_wrapper.py'
--bed_file '${input_bed_file}' 
#if str($input_control_file) != 'None':
    --control_file '${input_control_file}'
    --significant_islands_output_file "${significant_islands_output_file}"
    --islands_summary_output_file "${islands_summary_output_file}"
    --significant_islands_summary_output_file "${significant_islands_summary_output_file}"
#end if
${fix_off_by_one_errors}
--dbkey '${input_bed_file.dbkey}'
--redundancy_threshold '${redundancy_threshold}'
--window_size '${window_size}'
--fragment_size '${fragment_size}'
--effective_genome_fraction '${effective_genome_fraction}'
--gap_size '${gap_size}'
--error_cut_off '${error_cut_off}'
##output files
--stdout "${output_log_file}"
--redundancy_removed_test_bed_output_file "${redundancy_removed_test_bed_output_file}"
--redundancy_removed_control_bed_output_file "${redundancy_removed_control_bed_output_file}"
--score_island_output_file "${score_island_output_file}"
--summary_graph_output_file "${summary_graph_output_file}"
--test_normalized_wig_output_file "${test_normalized_wig_output_file}"
--island_filtered_output_file "${island_filtered_output_file}"
--island_filtered_normalized_wig_output_file "${island_filtered_normalized_wig_output_file}"
    ]]></command>
    <inputs>
        <param name="input_bed_file" type="data" format="bed" label="ChIP-Seq Tag File" >
            <validator type="expression" message="SICER is not available for the genome.">value is not None and value.dbkey in ['mm8', 'mm9', 'hg18', 'hg19', 'dm2', 'dm3', 'sacCer1', 'pombe', 'rn4', 'tair8']</validator>
        </param>
        <param name="input_control_file" type="data" format="bed" label="ChIP-Seq Control File" optional="true"> <!-- fix me, add filter to match dbkeys -->
            <options>
                <filter type="data_meta" ref="input_bed_file" key="dbkey" />
            </options>
        </param>
        <param name="fix_off_by_one_errors" type="boolean" truevalue="--fix_off_by_one_errors" falsevalue="" checked="true" label="Fix off-by-one errors in output files" help="SICER creates non-standard output files, this option will fix these coordinates"/> 
        <param name="redundancy_threshold" type="integer" label="Redundancy Threshold" value="1" help="The number of copies of identical reads allowed in a library" />
        <param name="window_size" type="integer" value="200" label="Window size" help="Resolution of SICER algorithm. For histone modifications, one can use 200 bp" />
        <param name="fragment_size" type="integer" value="150" label="Fragment size" help="for determination of the amount of shift from the beginning of a read to the center of the DNA fragment represented by the read. FRAGMENT_SIZE=150 means the shift is 75." />
        <param name="effective_genome_fraction" type="float" value="0.74" label="Effective genome fraction" help="Effective Genome as fraction of the genome size. It depends on read length." />
        <param name="gap_size" type="integer" value="600" label="Gap size" help="Needs to be multiples of window size. Namely if the window size is 200, the gap size should be 0, 200, 400, 600, ..." />
        <param name="error_cut_off" type="float" value="0.01" label="Statistic threshold value" help="FDR (with control) or E-value (without control)" />
    </inputs>
    <outputs>
        <data name="redundancy_removed_test_bed_output_file" format="bed" label="${tool.name} on ${on_string} (test-${redundancy_threshold}-removed.bed)"/>
        <data name="redundancy_removed_control_bed_output_file" format="bed" label="${tool.name} on ${on_string} (control-${redundancy_threshold}-removed.bed)">
            <filter>input_control_file is not None</filter>
        </data>
        <data name="summary_graph_output_file" format="bedgraph" label="${tool.name} on ${on_string} (test-W${window_size}.graph)"/>
        <data name="test_normalized_wig_output_file" format="wig" label="${tool.name} on ${on_string} (test-W${window_size}-normalized.wig)"/>
        <data name="significant_islands_output_file" format="interval" label="${tool.name} on ${on_string} (test-W${window_size}-G${gap_size}-FDR${error_cut_off}-island.bed)">
            <filter>input_control_file is not None</filter>
        </data>
        <data name="island_filtered_output_file" format="bed" label="${tool.name} on ${on_string} (#if str( $input_control_file ) != 'None' then ''.join( map( str, [ 'test-W', $window_size, '-G',$gap_size, '-FDR', $error_cut_off, '-islandfiltered.bed' ] ) ) else ''.join( map( str, [ 'test-W', $window_size, '-G', $gap_size, '-E', $error_cut_off, '-islandfiltered.bed' ] ) ) #)"/>
        <data name="island_filtered_normalized_wig_output_file" format="wig" label="${tool.name} on ${on_string} (#if str( $input_control_file ) != 'None' then ''.join( map( str, [ 'test-W', $window_size, '-G',$gap_size, '-FDR', $error_cut_off, '-islandfiltered-normalized.wig' ] ) ) else ''.join( map( str, [ 'test-W', $window_size, '-G', $gap_size, '-E', $error_cut_off, '-islandfiltered-normalized.wig' ] ) ) #)"/>
        <data name="score_island_output_file" format="interval" label="${tool.name} on ${on_string} (#if str( $input_control_file ) != 'None' then ''.join( map( str, [ 'test-W', $window_size, '-G',$gap_size, '.scoreisland' ] ) ) else ''.join( map( str, [ 'test-W', $window_size, '-G', $gap_size, '-E', $error_cut_off, '.scoreisland' ] ) ) #)"/>
        <data name="islands_summary_output_file" format="interval" label="${tool.name} on ${on_string} (test-W${window_size}-G${gap_size}-islands-summary)">
            <filter>input_control_file is not None</filter>
        </data>
        <data name="significant_islands_summary_output_file" format="interval" label="${tool.name} on ${on_string} (test-W${window_size}-G${gap_size}-islands-summary-FDR${error_cut_off})">
            <filter>input_control_file is not None</filter>
        </data>
        <data name="output_log_file" format="txt" label="${tool.name} on ${on_string} (log)"/>
    </outputs>
    <tests>
        <test>
            <param name="input_bed_file" value="chipseq_enriched.bed.gz" ftype="bed" dbkey="mm8" />
            <param name="input_control_file" />
            <param name="fix_off_by_one_errors" />
            <param name="redundancy_threshold" value="1" />
            <param name="window_size" value="200" />
            <param name="fragment_size" value="150" />
            <param name="effective_genome_fraction" value="0.74" />
            <param name="gap_size" value="600" />
            <param name="error_cut_off" value="0.01" />
            <output name="redundancy_removed_test_bed_output_file" file="test-1-removed.bed" />
            <output name="summary_graph_output_file" file="test_1_test-W200.graph" />
            <output name="test_normalized_wig_output_file" file="test-W200-normalized.wig" />
            <output name="island_filtered_output_file" file="test-W200-G600-E0.01-islandfiltered.bed" />
            <output name="island_filtered_normalized_wig_output_file" file="test-W200-G600-E0.01-islandfiltered-normalized.wig" />
            <output name="score_island_output_file" file="test_1_test-W200-G600-E0.01.scoreisland" />
            <output name="output_log_file" file="test_1_output_log_file.contains" compare="contains"/>
        </test>
        <test>
            <param name="input_bed_file" value="chipseq_enriched.bed.gz" ftype="bed" dbkey="mm8" />
            <param name="input_control_file" value="chipseq_input.bed.gz" ftype="bed" dbkey="mm8" />
            <param name="fix_off_by_one_errors" />
            <param name="redundancy_threshold" value="1" />
            <param name="window_size" value="200" />
            <param name="fragment_size" value="150" />
            <param name="effective_genome_fraction" value="0.74" />
            <param name="gap_size" value="600" />
            <param name="error_cut_off" value="0.01" />
            <output name="redundancy_removed_test_bed_output_file" file="test-1-removed.bed" />
            <output name="redundancy_removed_control_bed_output_file" file="control-1-removed.bed" />
            <output name="summary_graph_output_file" file="test_1_test-W200.graph" />
            <output name="test_normalized_wig_output_file" file="test-W200-normalized.wig" />
            <output name="significant_islands_output_file" file="test_2_test-W200-G600-FDR0.01-island.bed" />
            <output name="island_filtered_output_file" file="test-W200-G600-FDR0.01-islandfiltered.bed" />
            <output name="island_filtered_normalized_wig_output_file" file="test-W200-G600-FDR0.01-islandfiltered-normalized.wig" />
            <output name="score_island_output_file" file="test_2_test-W200-G600.scoreisland" />
            <output name="islands_summary_output_file" file="test_2_test-W200-G600-islands-summary" />
            <output name="significant_islands_summary_output_file" file="test_2_test-W200-G600-islands-summary-FDR0.01" />
            <output name="output_log_file" file="test_2_output_log_file.contains" compare="contains"/>
        </test>
        <test>
            <param name="input_bed_file" value="chipseq_enriched.bed.gz" ftype="bed" dbkey="mm8" />
            <param name="input_control_file" value="chipseq_input.bed.gz" ftype="bed" dbkey="mm8" />
            <param name="fix_off_by_one_errors" value="True" />
            <param name="redundancy_threshold" value="1" />
            <param name="window_size" value="200" />
            <param name="fragment_size" value="150" />
            <param name="effective_genome_fraction" value="0.74" />
            <param name="gap_size" value="600" />
            <param name="error_cut_off" value="0.01" />
            <output name="redundancy_removed_test_bed_output_file" file="test-1-removed.bed" />
            <output name="redundancy_removed_control_bed_output_file" file="control-1-removed.bed" />
            <output name="summary_graph_output_file" file="test_3_test-W200.graph" />
            <output name="test_normalized_wig_output_file" file="test-W200-normalized.wig" />
            <output name="significant_islands_output_file" file="test_3_test-W200-G600-FDR0.01-island.bed" />
            <output name="island_filtered_output_file" file="test-W200-G600-FDR0.01-islandfiltered.bed" />
            <output name="island_filtered_normalized_wig_output_file" file="test-W200-G600-FDR0.01-islandfiltered-normalized.wig" />
            <output name="score_island_output_file" file="test_3_test-W200-G600.scoreisland" />
            <output name="islands_summary_output_file" file="test_3_test-W200-G600-islands-summary" />
            <output name="significant_islands_summary_output_file" file="test_3_test-W200-G600-islands-summary-FDR0.01" />
            <output name="output_log_file" file="test_2_output_log_file.contains" compare="contains"/>
        </test>
        <test>
            <param name="input_bed_file" value="chipseq_enriched.bed.gz" ftype="bed" dbkey="mm8" />
            <param name="input_control_file" />
            <param name="fix_off_by_one_errors" value="True" />
            <param name="redundancy_threshold" value="1" />
            <param name="window_size" value="200" />
            <param name="fragment_size" value="150" />
            <param name="effective_genome_fraction" value="0.74" />
            <param name="gap_size" value="600" />
            <param name="error_cut_off" value="0.01" />
            <output name="redundancy_removed_test_bed_output_file" file="test-1-removed.bed" />
            <output name="summary_graph_output_file" file="test_3_test-W200.graph" />
            <output name="test_normalized_wig_output_file" file="test-W200-normalized.wig" />
            <output name="island_filtered_output_file" file="test-W200-G600-E0.01-islandfiltered.bed" />
            <output name="island_filtered_normalized_wig_output_file" file="test-W200-G600-E0.01-islandfiltered-normalized.wig" />
            <output name="score_island_output_file" file="test_4_test-W200-G600-E0.01.scoreisland" />
            <output name="output_log_file" file="test_1_output_log_file.contains" compare="contains"/>
        </test>
    </tests>
    <help><![CDATA[
**What it does**

SICER first and foremost is a filtering tool. Its main functions are::
  
  1. Delineation of the significantly ChIP-enriched regions, which can be used to associate with other genomic landmarks. 
  2. Identification of reads on the ChIP-enriched regions, which can be used for profiling and other quantitative analysis.

View the original SICER documentation: http://home.gwu.edu/~wpeng/Software.htm.

------

.. class:: warningmark

  By default, SICER creates files that do not conform to standards (e.g. BED files are closed, not half-open). This could have implications for downstream analysis.
  To force the output of SICER to be formatted properly to standard file formats, check the **"Fix off-by-one errors in output files"** option.

------

**Citation**
If you use this tool in Galaxy, please cite Blankenberg D, et al. *In preparation.*
    ]]></help>
    <citations>
        <citation type="doi">10.1093/bioinformatics/btp340</citation>
    </citations>
</tool>