comparison macs2_callpeak.xml @ 12:38769345062e draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 09ef7ee96fadeef22273029ea23d1e140ce96737

11:cb785e26207c

<tool id="macs2_callpeak" name="MACS2 callpeak" version="@VERSION_STRING@.3">
    <description>Call peaks from alignment results</description>
    <macros>
        <import>macs2_macros.xml</import>
    </macros>
    <expand macro="requirements">

                <expand macro="keep_duplicates" />
        </section>
    </inputs>
    <outputs>
        <!--callpeaks output-->
        <data name="output_tabular" format="tabular" label="${tool.name} on ${on_string} (Peaks in tabular format)">
            <filter> outputs and 'peaks_tabular' in outputs</filter>
        </data>
        <data name="output_broadpeaks" format="bed" from_work_dir="MACS2_peaks.broadPeak" label="${tool.name} on ${on_string} (broad Peaks)">
            <filter>
            ((
              advanced_options['broad_options']['broad_options_selector'] == "broad"
            ))
            </filter>
        </data>
        <data name="output_gappedpeaks" format="bed" from_work_dir="MACS2_peaks.gappedPeak" label="${tool.name} on ${on_string} (gapped Peaks)">
            <filter>
            ((
              advanced_options['broad_options']['broad_options_selector'] == "broad"
            ))
            </filter>
        </data>
        <data name="output_narrowpeaks" format="bed" from_work_dir="MACS2_peaks.narrowPeak" label="${tool.name} on ${on_string} (narrow Peaks)">
            <filter>
            ((
              advanced_options['broad_options']['broad_options_selector'] == "nobroad"
            ))
            </filter>
        </data>
        <data name="output_summits" format="bed" from_work_dir="MACS2_summits.bed" label="${tool.name} on ${on_string} (summits in BED)">
            <filter>outputs and 'summits' in outputs</filter>
        </data>
        <data name="output_plot" format="pdf" from_work_dir="MACS2_model.pdf" label="${tool.name} on ${on_string} (plot)">
            <filter>
            ((
              outputs and 'pdf' in outputs and
              nomodel_type['nomodel_type_selector'] == "create_model" and
              format != "BAMPE"
            ))
            </filter>
        </data>
        <data name="output_treat_pileup" format="bedgraph" from_work_dir="MACS2_treat_pileup.bdg" label="${tool.name} on ${on_string} (Bedgraph Treatment)">
            <filter>outputs and 'bdg' in outputs</filter>
        </data>
        <data name="output_control_lambda" format="bedgraph" from_work_dir="MACS2_control_lambda.bdg" label="${tool.name} on ${on_string} (Bedgraph Control)">
            <filter>outputs and 'bdg' in outputs</filter>
        </data>
        <data name="output_extra_files" format="html" label="${tool.name} on ${on_string} (html report)">
            <filter>outputs and 'html' in outputs</filter>
        </data>
    </outputs>
    <tests>
        <test expect_num_outputs="5">

**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.

.. _MACS2: https://github.com/taoliu/MACS

-----

**Inputs**

MACS can be used for ChIP-Seq data (Treatment) alone, or with a Control sample with the increase of specificity (recommended).

 hs: 2.7e9
 mm: 1.87e9
 ce: 9e7
 dm: 1.2e8

-----

**Outputs**

.. class:: warningmark

If MACS2 fails, it is usually because it cannot build the model for peaks. You may want to extend **mfold** range by increasing the upper bound or play with **Build model** options. For more information, see the MACS2_ website.

.. _`UCSC website here`: https://genome.ucsc.edu/goldenPath/help/bedgraph.html

@citation@
]]></help>
  <expand macro="citations" />

12:38769345062e

<tool id="macs2_callpeak" name="MACS2 callpeak" version="@VERSION_STRING@.3" profile="17.09">
    <description>Call peaks from alignment results</description>
    <macros>
        <import>macs2_macros.xml</import>
    </macros>
    <expand macro="requirements">

                <expand macro="keep_duplicates" />
        </section>
    </inputs>
    <outputs>
        <!--callpeaks output-->
        <data name="output_tabular" format="tabular" default_identifier_source="input_treatment_file" label="${tool.name} on ${on_string} (Peaks in tabular format)">
            <filter> outputs and 'peaks_tabular' in outputs</filter>
        </data>
        <data name="output_broadpeaks" format="bed" from_work_dir="MACS2_peaks.broadPeak" default_identifier_source="input_treatment_file" label="${tool.name} on ${on_string} (broad Peaks)">
            <filter>
            ((
              advanced_options['broad_options']['broad_options_selector'] == "broad"
            ))
            </filter>
        </data>
        <data name="output_gappedpeaks" format="bed" from_work_dir="MACS2_peaks.gappedPeak" default_identifier_source="input_treatment_file" label="${tool.name} on ${on_string} (gapped Peaks)">
            <filter>
            ((
              advanced_options['broad_options']['broad_options_selector'] == "broad"
            ))
            </filter>
        </data>
        <data name="output_narrowpeaks" format="bed" from_work_dir="MACS2_peaks.narrowPeak" default_identifier_source="input_treatment_file" label="${tool.name} on ${on_string} (narrow Peaks)">
            <filter>
            ((
              advanced_options['broad_options']['broad_options_selector'] == "nobroad"
            ))
            </filter>
        </data>
        <data name="output_summits" format="bed" from_work_dir="MACS2_summits.bed" default_identifier_source="input_treatment_file" label="${tool.name} on ${on_string} (summits in BED)">
            <filter>outputs and 'summits' in outputs</filter>
        </data>
        <data name="output_plot" format="pdf" from_work_dir="MACS2_model.pdf" default_identifier_source="input_treatment_file" label="${tool.name} on ${on_string} (plot)">
            <filter>
            ((
              outputs and 'pdf' in outputs and
              nomodel_type['nomodel_type_selector'] == "create_model" and
              format != "BAMPE"
            ))
            </filter>
        </data>
        <data name="output_treat_pileup" format="bedgraph" from_work_dir="MACS2_treat_pileup.bdg" default_identifier_source="input_treatment_file" label="${tool.name} on ${on_string} (Bedgraph Treatment)">
            <filter>outputs and 'bdg' in outputs</filter>
        </data>
        <data name="output_control_lambda" format="bedgraph" from_work_dir="MACS2_control_lambda.bdg" default_identifier_source="input_treatment_file" label="${tool.name} on ${on_string} (Bedgraph Control)">
            <filter>outputs and 'bdg' in outputs</filter>
        </data>
        <data name="output_extra_files" format="html" default_identifier_source="input_treatment_file" label="${tool.name} on ${on_string} (html report)">
            <filter>outputs and 'html' in outputs</filter>
        </data>
    </outputs>
    <tests>
        <test expect_num_outputs="5">

**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.

-----

**Inputs**

MACS can be used for ChIP-Seq data (Treatment) alone, or with a Control sample with the increase of specificity (recommended).

 hs: 2.7e9
 mm: 1.87e9
 ce: 9e7
 dm: 1.2e8

Or see the **deepTools** website for updated information on calculating `Effective Genome Size`_.

-----

**Outputs**

.. class:: warningmark

If MACS2 fails, it is usually because it cannot build the model for peaks. You may want to extend **mfold** range by increasing the upper bound or play with **Build model** options. For more information, see the MACS2_ website.

.. _MACS2: https://github.com/taoliu/MACS
.. _`Effective Genome Size`: http://deeptools.readthedocs.io/en/latest/content/feature/effectiveGenomeSize.html
.. _`UCSC website here`: https://genome.ucsc.edu/goldenPath/help/bedgraph.html

@citation@
]]></help>
  <expand macro="citations" />