comparison macs_wrapper.xml @ 1:7f4aca133f73 draft

planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734

0:512c6b2dba00

  <requirements>
    <requirement type="package" version="1.3.7.1">macs</requirement>
    <requirement type="package" version="2.15.0">R</requirement>
  </requirements>
  <inputs>
    <param name="experiment_name" type="text" value="MACS in Galaxy" size="50" label="Experiment Name"/>
    <conditional name="input_type">
      <param name="input_type_selector" type="select" label="Paired End Sequencing">
        <option value="paired_end">Paired End (requires elandmulti format)</option>
        <option value="single_end" selected="true">Single End</option>
      </param>

      <when value="no_wig">
        <!-- do nothing here -->
      </when>
    </conditional>
    <param name="nolambda" label="Use fixed background lambda as local lambda for every peak region" type="boolean" truevalue="--nolambda" falsevalue="" checked="False" help="up to 9X more time consuming"/>
    <param name="lambdaset" type="text" label="3 levels of regions around the peak region to calculate the maximum lambda as local lambda" value="1000,5000,10000" size="50"/>
    <conditional name="nomodel_type">
      <param name="nomodel_type_selector" type="select" label="Build Model">
        <option value="nomodel">Do not build the shifting model</option>
        <option value="create_model" selected="true">Build the shifting model</option>
      </param>

For the underlying tool, please cite `Zhang Y, Liu T, Meyer CA, Eeckhoute J, Johnson DS, Bernstein BE, Nusbaum C, Myers RM, Brown M, Li W, Liu XS. Model-based analysis of ChIP-Seq (MACS). Genome Biol. 2008;9(9):R137. <http://www.ncbi.nlm.nih.gov/pubmed/18798982>`_

If you use this tool in Galaxy, please cite Blankenberg D, et al. *In preparation.*

  </help>
</tool>

1:7f4aca133f73

  <requirements>
    <requirement type="package" version="1.3.7.1">macs</requirement>
    <requirement type="package" version="2.15.0">R</requirement>
  </requirements>
  <inputs>
    <param name="experiment_name" type="text" value="MACS in Galaxy" label="Experiment Name"/>
    <conditional name="input_type">
      <param name="input_type_selector" type="select" label="Paired End Sequencing">
        <option value="paired_end">Paired End (requires elandmulti format)</option>
        <option value="single_end" selected="true">Single End</option>
      </param>

      <when value="no_wig">
        <!-- do nothing here -->
      </when>
    </conditional>
    <param name="nolambda" label="Use fixed background lambda as local lambda for every peak region" type="boolean" truevalue="--nolambda" falsevalue="" checked="False" help="up to 9X more time consuming"/>
    <param name="lambdaset" type="text" label="3 levels of regions around the peak region to calculate the maximum lambda as local lambda" value="1000,5000,10000"/>
    <conditional name="nomodel_type">
      <param name="nomodel_type_selector" type="select" label="Build Model">
        <option value="nomodel">Do not build the shifting model</option>
        <option value="create_model" selected="true">Build the shifting model</option>
      </param>

For the underlying tool, please cite `Zhang Y, Liu T, Meyer CA, Eeckhoute J, Johnson DS, Bernstein BE, Nusbaum C, Myers RM, Brown M, Li W, Liu XS. Model-based analysis of ChIP-Seq (MACS). Genome Biol. 2008;9(9):R137. <http://www.ncbi.nlm.nih.gov/pubmed/18798982>`_

If you use this tool in Galaxy, please cite Blankenberg D, et al. *In preparation.*

    </help>
    <citations>
        <citation type="doi">10.1186/gb-2008-9-9-r137</citation>
    </citations>
</tool>