comparison macs2_callpeak.xml @ 16:495a4173006f draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 77a41905b31b6e93ff95b2c36bae865b60ab62d6

15:c33686854b19

                </conditional>
            </when>
            <when value="No" />
        </conditional>

        <param name="format" type="select" label="Format of Input Files" help="For Paired-end BAM (BAMPE) the 'Build model step' will be ignored and the real fragments will be used for each template defined by leftmost and rightmost mapping positions (--format). Default: Single-end BAM">
            <option value="BAM" selected="True">Single-end BAM</option>
            <option value="BAMPE">Paired-end BAM</option>
            <option value="BED">Single-end BED</option>
        </param>

                <option value="create_model" selected="true">Build the shifting model</option>
            </param>
            <when value="create_model">
                <param name="mfold_lower" type="integer" value="5" label="Set lower mfold bound" help="Select the lower region within MFOLD range of high confidence enrichment ratio against background to build model. Fold-enrichment in regions must be higher than lower limit (--mfold). Default: 5" />
                <param name="mfold_upper" type="integer" value="50" label="Set upper mfold bound" help="Select the upper region within MFOLD range of high confidence enrichment ratio against background to build model. Fold-enrichment in regions must be lower than the upper limit (--mfold). Default: 50"/>
                <param name="band_width" type="integer" value="300"
                label="Band width for picking regions to compute fragment size"
                help=" You can set this parameter as the medium fragment size expected from sonication or size selection (--bw). Default: 300" />
            </when>
            <when value="nomodel">
                <param name="extsize" type="integer" value="200" label="Set extension size" help="The arbitrary extension size in bp. When nomodel is true, MACS will use this value as fragment size to extend each read towards 3-prime; end, then pile them up. It is exactly twice the number of obsolete SHIFTSIZE. In previous language, each read is moved 5-prime-to-3-prime direction to middle of fragment by 0.5 d, then extended to both direction with 0.5 d. This is equivalent to say each read is extended towards 5-prime-to-3-prime into a d size fragment. --extsize (this option) and --shift (the option below) can be combined when necessary. See --shift option below. Default: 200 (--extsize)."/>
                <param name="shift" type="integer" value="0" label="Set shift size" help="(NOT the legacy --shiftsize option!) The arbitrary shift in bp. Use discretion while setting it other than default value. When NOMODEL is set, MACS will use this value to move cutting ends (5-prime) towards 5-prime-to-3-prime  direction then apply EXTSIZE to extend them to fragments. When this value is negative, ends will be moved toward 3-prime-to-5-prime  direction. Recommended to keep it as default 0 for ChIP-Seq datasets, or -1 * 0.5 of --extsize (option above) together with --extsize option for detecting enriched cutting loci such as certain DNAseI-Seq datasets. Note, you can't set values other than 0 if format is paired-end data (BAMPE). Default: 0 (--shift)."/>
            </when>
        </conditional>

        <conditional name="cutoff_options">
            <param name="cutoff_options_selector" type="select" label="Peak detection based on" help="default uses q-value">
                <option value="qvalue" selected="true">q-value</option>
                <option value="pvalue">p-value</option>
            </param>
            <when value="pvalue">
                <param name="pvalue" type="float" value="" label="p-value cutoff for peak detection" help="default: not set (--pvalue)"/>
            </when>
            <when value="qvalue">
                <param name="qvalue" type="float" value="0.05" label="Minimum FDR (q-value) cutoff for peak detection" help="The q-value (minimum FDR) cutoff to call significant regions. Default is 0.05. For broad marks, you can try 0.05 as cutoff. Q-values are calculated from p-values using Benjamini-Hochberg procedure. (--qvalue)"/>
            </when>
        </conditional>

        <param name="outputs" type="select" display="checkboxes" multiple="True" optional="True" label="Additional Outputs" help="PDF is only created when the model is built">
            <option value="peaks_tabular">Peaks as tabular file (compatible wih MultiQC)</option>

            <option value="html">Summary page (html)</option>
            <option value="pdf">Plot in PDF (only available if a model is created and if BAMPE is not used)</option>
        </param>

        <section name="advanced_options" title="Advanced Options">
                <param name="to_large" type="boolean" truevalue="--to-large" falsevalue="" checked="False" optional="True"
                    label="When set, scale the small sample up to the bigger sample"
                    help="By default, the bigger dataset will be scaled down towards the smaller dataset, which will lead to smaller p/qvalues and more specific results. Keep in mind that scaling down will bring down background noise more. (--to-large). Default: No"/>
                <param name="nolambda" type="boolean" truevalue="--nolambda" falsevalue="" checked="False" optional="True"
                    label="Use fixed background lambda as local lambda for every peak region" help="up to 9X more time consuming (--nolambda). Default: No"/>
                <param name="spmr" type="boolean" truevalue="--SPMR" falsevalue="" checked="False" optional="True"
                    label="Save signal per million reads for fragment pileup profiles"
                    help="Requires 'Scores in bedGraph files (--bdg)' output to be selected. (--SPMR). Default: No"/>
                <param name="ratio" type="float" optional="True"
                    label="When set, use a custom scaling ratio of ChIP/control (e.g. calculated using NCIS) for linear scaling"
                    help="(--ratio) Default: ignore"/>
                <param name="slocal" type="integer" optional="True" label="The small nearby region in basepairs to calculate dynamic lambda"
                    help="This is used to capture the bias near the peak summit region. Invalid if there is no control data. If you set this to 0, MACS will skip slocal lambda calculation. *Note* that MACS will always perform a d-size local lambda calculation. The final local bias should be the maximum of the lambda value from d, slocal, and llocal size windows. (--slocal). Default: 1000"/>
                <param name="llocal" type="integer" optional="True" label="The large nearby region in basepairs to calculate dynamic lambda"
                    help="This is used to capture the surround bias. If you set this to 0, MACS will skip llocal lambda calculation. *Note* that MACS will always perform a d-size local lambda calculation. The final local bias should be the maximum of the lambda value from d, slocal, and llocal size windows. (--llocal) Default: 10000"/>
                <conditional name="broad_options">
                    <param name="broad_options_selector" type="select"
                        label="Composite broad regions" help="by putting nearby highly enriched regions into a broad region with loose cutoff (--broad)">
                        <option value="nobroad" selected="true">No broad regions</option>
                        <option value="broad">broad regions</option>
                    </param>
                    <when value="broad">
                        <param name="broad_cutoff" type="float" label="Cutoff for broad region" value="0.1"
                            help="value is either p-value or q-value as specified above (--broad-cutoff)"/>
                    </when>
                    <when value="nobroad">
                        <param name="call_summits" type="boolean" truevalue="--call-summits" falsevalue="" checked="False"
                            label="Use a more sophisticated signal processing approach to find subpeak summits in each enriched peak region"
                            help="(--call-summits)"/>
                    </when>
                </conditional>
                <expand macro="keep_duplicates" />
        </section>
    </inputs>

            <param name="outputs" value="pdf"/>
            <output name="output_narrowpeaks" file="callpeak_bampe_narrow.bed"/>
        </test>
    </tests>
    <help><![CDATA[

.. class:: infomark

**What it does**

**callpeak** is the main function of the MACS2_ package. MACS identifies enriched binding sites in ChIP-seq experiments. It captures the influence of genome complexity to evaluate the significance of enriched ChIP regions, and improves the spatial resolution of binding sites through combining the information of both sequencing tag position and orientation.

The default output is the narrowPeak BED file (BED6+4 format). This contains the peak locations, together with peak summit, pvalue and qvalue. You can load it to UCSC genome browser.

    Example:

    ======= ========= ======= ============ ==== === ======= ======== ======= =======
    1          2        3          4        5    6     7       8         9   **10**
    ======= ========= ======= ============ ==== === ======= ======== ======= =======
    chr1    840081    840400  treat1_peak_1  69   .  4.89872 10.50944 6.91052 158
    chr1    919419    919785  treat1_peak_2  87   .  5.85158 12.44148 8.70936 130
    chr1    937220    937483  treat1_peak_3  66   .  4.87632 10.06728 6.61759 154
    ======= ========= ======= ============ ==== === ======= ======== ======= =======

    Columns contain the following data:

* **1st**: chromosome name
* **2nd**: start position of peak

A BED file which contains the peak summits locations for every peaks. The 5th column in this file is -log10qvalue, the same as in the Peaks BED file. If you want to find the motifs at the binding sites, this file is recommended. The file can be loaded directly to UCSC genome browser. Remove the beginning track line if you want to analyze it by other tools.

    Example:

    ======= ========= ======= ============ =======
    1          2        3          4        **5**
    ======= ========= ======= ============ =======
    chr1    840239    840240  treat1_peak_1 6.91052
    chr1    919549    919550  treat1_peak_2 8.70936
    chr1    937374    937375  treat1_peak_3 6.61759
    ======= ========= ======= ============ =======

    Columns contain the following data:

* **1st**: chromosome name
* **2nd**: start position of peak

If the broad option (--broad) is selected unded Advanced Options above, MACS2 will output a broadPeaks file. When this flag is on, MACS will try to composite broad regions in BED12 ( a gene-model-like format ) by putting nearby highly enriched regions into a broad region with loose cutoff. The broad region is controlled by another cutoff through --broad-cutoff. The maximum length of broad region length is 4 times of d from MACS. The broad peaks file is in BED6+3 format which is similar to the narrowPeak file, except for missing the 10th column for annotating peak summits.

    Example:

    ======= ========= ======= ============ ==== === ======= ======= =======
    1        2         3       4            5    6   7       8       9
    ======= ========= ======= ============ ==== === ======= ======= =======
    chr1    840081    840400  treat1_peak_1  52   .  4.08790 8.57605 5.21506
    chr1    919419    919785  treat1_peak_2  56   .  4.37270 8.90436 5.60462
    chr1    937220    937483  treat1_peak_3  48   .  4.02343 8.06676 4.86861
    ======= ========= ======= ============ ==== === ======= ======= =======


Columns contain the following data:

* **1st**: chromosome name
* **2nd**: start position of peak

If the broad option (--broad) is selected unded Advanced Options above, MACS2 will also output a gappedPeaks file. The gappedPeak file is in BED12+3 format and contains both the broad region and narrow peaks. The file can be loaded directly to UCSC genome browser.

    Example:

    ======= ========= ======= ============ ==== === ======= ======= === === === === ======= ======= =======
    1       2         3       4            5    6    7       8       9   10  11  12  13      14     15
    ======= ========= ======= ============ ==== === ======= ======= === === === === ======= ======= =======
    chr1    840081    840400  treat1_peak_1  52   .  840081  840400   0   1  319  0  4.08790 8.57605 5.21506
    chr1    919419    919785  treat1_peak_2  56   .  919419  919785   0   1  366  0  4.37270 8.90436 5.60462
    chr1    937220    937483  treat1_peak_3  48   .  937220  937483   0   1  263  0  4.02343 8.06676 4.86861
    ======= ========= ======= ============ ==== === ======= ======= === === === === ======= ======= =======

Columns contain the following data:

* **1st**: chromosome name
* **2nd**: start position of peak

16:495a4173006f

                </conditional>
            </when>
            <when value="No" />
        </conditional>

        <param argument="--format" type="select" label="Format of Input Files" help="For Paired-end BAM (BAMPE) the 'Build model step' will be ignored and the real fragments will be used for each template defined by leftmost and rightmost mapping positions. Default: Single-end BAM">
            <option value="BAM" selected="True">Single-end BAM</option>
            <option value="BAMPE">Paired-end BAM</option>
            <option value="BED">Single-end BED</option>
        </param>

                <option value="create_model" selected="true">Build the shifting model</option>
            </param>
            <when value="create_model">
                <param name="mfold_lower" type="integer" value="5" label="Set lower mfold bound" help="Select the lower region within MFOLD range of high confidence enrichment ratio against background to build model. Fold-enrichment in regions must be higher than lower limit (--mfold). Default: 5" />
                <param name="mfold_upper" type="integer" value="50" label="Set upper mfold bound" help="Select the upper region within MFOLD range of high confidence enrichment ratio against background to build model. Fold-enrichment in regions must be lower than the upper limit (--mfold). Default: 50"/>
                <param name="band_width" argument="--bw" type="integer" value="300"
                label="Band width for picking regions to compute fragment size"
                help=" You can set this parameter as the medium fragment size expected from sonication or size selection. Default: 300" />
            </when>
            <when value="nomodel">
                <param argument="--extsize" type="integer" value="200" label="Set extension size" help="The arbitrary extension size in bp. When nomodel is true, MACS will use this value as fragment size to extend each read towards 3-prime; end, then pile them up. It is exactly twice the number of obsolete SHIFTSIZE. In previous language, each read is moved 5-prime-to-3-prime direction to middle of fragment by 0.5 d, then extended to both direction with 0.5 d. This is equivalent to say each read is extended towards 5-prime-to-3-prime into a d size fragment. --extsize (this option) and --shift (the option below) can be combined when necessary. See --shift option below. Default: 200."/>
                <param argument="--shift" type="integer" value="0" label="Set shift size" help="(NOT the legacy --shiftsize option!) The arbitrary shift in bp. Use discretion while setting it other than default value. When NOMODEL is set, MACS will use this value to move cutting ends (5-prime) towards 5-prime-to-3-prime  direction then apply EXTSIZE to extend them to fragments. When this value is negative, ends will be moved toward 3-prime-to-5-prime  direction. Recommended to keep it as default 0 for ChIP-Seq datasets, or -1 * 0.5 of --extsize (option above) together with --extsize option for detecting enriched cutting loci such as certain DNAseI-Seq datasets. Note, you can't set values other than 0 if format is paired-end data (BAMPE). Default: 0"/>
            </when>
        </conditional>

        <conditional name="cutoff_options">
            <param name="cutoff_options_selector" type="select" label="Peak detection based on" help="default uses q-value">
                <option value="qvalue" selected="true">q-value</option>
                <option value="pvalue">p-value</option>
            </param>
            <when value="pvalue">
                <param argument="--pvalue" type="float" value="" label="p-value cutoff for peak detection" help="Default: not set"/>
            </when>
            <when value="qvalue">
                <param argument="--qvalue" type="float" value="0.05" label="Minimum FDR (q-value) cutoff for peak detection" help="The q-value (minimum FDR) cutoff to call significant regions. Default is 0.05. For broad marks, you can try 0.05 as cutoff. Q-values are calculated from p-values using Benjamini-Hochberg procedure"/>
            </when>
        </conditional>

        <param name="outputs" type="select" display="checkboxes" multiple="True" optional="True" label="Additional Outputs" help="PDF is only created when the model is built">
            <option value="peaks_tabular">Peaks as tabular file (compatible wih MultiQC)</option>

            <option value="html">Summary page (html)</option>
            <option value="pdf">Plot in PDF (only available if a model is created and if BAMPE is not used)</option>
        </param>

        <section name="advanced_options" title="Advanced Options">
                <param name="to_large" argument="--to-large" type="boolean" truevalue="--to-large" falsevalue="" checked="false"
                    label="When set, scale the small sample up to the bigger sample"
                    help="By default, the bigger dataset will be scaled down towards the smaller dataset, which will lead to smaller p/qvalues and more specific results. Keep in mind that scaling down will bring down background noise more. Default: No"/>
                <param argument="--nolambda" type="boolean" truevalue="--nolambda" falsevalue="" checked="false"
                    label="Use fixed background lambda as local lambda for every peak region" help="up to 9X more time consuming. Default: No"/>
                <param name="spmr" argument="--SPMR" type="boolean" truevalue="--SPMR" falsevalue="" checked="false"
                    label="Save signal per million reads for fragment pileup profiles"
                    help="Requires 'Scores in bedGraph files (--bdg)' output to be selected. Default: No"/>
                <param argument="--ratio" type="float" optional="true"
                    label="When set, use a custom scaling ratio of ChIP/control (e.g. calculated using NCIS) for linear scaling"
                    help="Default: ignore"/>
                <param name="slocal" type="integer" optional="True" label="The small nearby region in basepairs to calculate dynamic lambda"
                    help="This is used to capture the bias near the peak summit region. Invalid if there is no control data. If you set this to 0, MACS will skip slocal lambda calculation. *Note* that MACS will always perform a d-size local lambda calculation. The final local bias should be the maximum of the lambda value from d, slocal, and llocal size windows. (--slocal). Default: 1000"/>
                <param argument="--llocal" type="integer" optional="True" label="The large nearby region in basepairs to calculate dynamic lambda"
                    help="This is used to capture the surround bias. If you set this to 0, MACS will skip llocal lambda calculation. *Note* that MACS will always perform a d-size local lambda calculation. The final local bias should be the maximum of the lambda value from d, slocal, and llocal size windows. Default: 10000"/>
                <conditional name="broad_options">
                    <param name="broad_options_selector" argument="--broad" type="select"
                        label="Composite broad regions" help="by putting nearby highly enriched regions into a broad region with loose cutoff">
                        <option value="nobroad" selected="true">No broad regions</option>
                        <option value="broad">broad regions</option>
                    </param>
                    <when value="broad">
                        <param name="broad_cutoff" type="float" label="Cutoff for broad region" value="0.1"
                            help="value is either p-value or q-value as specified above (--broad-cutoff)"/>
                    </when>
                    <when value="nobroad">
                        <param name="call_summits" argument="--call-summits" type="boolean" truevalue="--call-summits" falsevalue="" checked="false"
                            label="Use a more sophisticated signal processing approach to find subpeak summits in each enriched peak region"/>
                    </when>
                </conditional>
                <expand macro="keep_duplicates" />
        </section>
    </inputs>

            <param name="outputs" value="pdf"/>
            <output name="output_narrowpeaks" file="callpeak_bampe_narrow.bed"/>
        </test>
    </tests>
    <help><![CDATA[
.. class:: infomark

**What it does**

**callpeak** is the main function of the MACS2_ package. MACS identifies enriched binding sites in ChIP-seq experiments. It captures the influence of genome complexity to evaluate the significance of enriched ChIP regions, and improves the spatial resolution of binding sites through combining the information of both sequencing tag position and orientation.

The default output is the narrowPeak BED file (BED6+4 format). This contains the peak locations, together with peak summit, pvalue and qvalue. You can load it to UCSC genome browser.

    Example:

    ======= ========= ======= ============= ==== === ======= ======== ======= =======
    1          2        3          4         5    6     7       8         9   **10**
    ======= ========= ======= ============= ==== === ======= ======== ======= =======
    chr1    840081    840400  treat1_peak_1  69   .  4.89872 10.50944 6.91052 158
    chr1    919419    919785  treat1_peak_2  87   .  5.85158 12.44148 8.70936 130
    chr1    937220    937483  treat1_peak_3  66   .  4.87632 10.06728 6.61759 154
    ======= ========= ======= ============= ==== === ======= ======== ======= =======

    Columns contain the following data:

* **1st**: chromosome name
* **2nd**: start position of peak

A BED file which contains the peak summits locations for every peaks. The 5th column in this file is -log10qvalue, the same as in the Peaks BED file. If you want to find the motifs at the binding sites, this file is recommended. The file can be loaded directly to UCSC genome browser. Remove the beginning track line if you want to analyze it by other tools.

    Example:

    ======= ========= ======= ============= =======
    1          2        3          4         **5**
    ======= ========= ======= ============= =======
    chr1    840239    840240  treat1_peak_1 6.91052
    chr1    919549    919550  treat1_peak_2 8.70936
    chr1    937374    937375  treat1_peak_3 6.61759
    ======= ========= ======= ============= =======

    Columns contain the following data:

* **1st**: chromosome name
* **2nd**: start position of peak

If the broad option (--broad) is selected unded Advanced Options above, MACS2 will output a broadPeaks file. When this flag is on, MACS will try to composite broad regions in BED12 ( a gene-model-like format ) by putting nearby highly enriched regions into a broad region with loose cutoff. The broad region is controlled by another cutoff through --broad-cutoff. The maximum length of broad region length is 4 times of d from MACS. The broad peaks file is in BED6+3 format which is similar to the narrowPeak file, except for missing the 10th column for annotating peak summits.

    Example:

    ======= ====== ====== ============= ==== === ======= ======= =======
    1        2      3      4             5    6   7       8       9
    ======= ====== ====== ============= ==== === ======= ======= =======
    chr1    840081 840400 treat1_peak_1   52   . 4.08790 8.57605 5.21506
    chr1    919419 919785 treat1_peak_2   56   . 4.37270 8.90436 5.60462
    chr1    937220 937483 treat1_peak_3   48   . 4.02343 8.06676 4.86861
    ======= ====== ====== ============= ==== === ======= ======= =======

Columns contain the following data:

* **1st**: chromosome name
* **2nd**: start position of peak

If the broad option (--broad) is selected unded Advanced Options above, MACS2 will also output a gappedPeaks file. The gappedPeak file is in BED12+3 format and contains both the broad region and narrow peaks. The file can be loaded directly to UCSC genome browser.

    Example:

    ======= ========= ======= ============= === === ======= ======= === === === === ======= ======= =======
    1       2         3       4              5   6     7       8     9   10  11  12  13      14     15
    ======= ========= ======= ============= === === ======= ======= === === === === ======= ======= =======
    chr1    840081    840400  treat1_peak_1  52   .  840081  840400   0   1 319   0 4.08790 8.57605 5.21506
    chr1    919419    919785  treat1_peak_2  56   .  919419  919785   0   1 366   0 4.37270 8.90436 5.60462
    chr1    937220    937483  treat1_peak_3  48   .  937220  937483   0   1 263   0 4.02343 8.06676 4.86861
    ======= ========= ======= ============= === === ======= ======= === === === === ======= ======= =======

Columns contain the following data:

* **1st**: chromosome name
* **2nd**: start position of peak