comparison ChipSeqRatioDef.xml @ 6:f224513123a1 draft

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5:378565f5a875

    <description></description>
    <requirements>
      <requirement type="package">r-base64enc</requirement>
      <requirement type="package">r-r2html</requirement>
      <requirement type="package">blast</requirement>
    </requirements>
    <command interpreter="python3">
	ChipSeqRatioAnalysis.py 
	--ChipSeq=${ChipFile}
	--InputSeq=${InputFile}

        <param name="ChipFile" label="Chip Sequences" type="data" format="fasta" help="NGS data in fasta format"/> 
	<param name="InputFile" label="Input Sequences" type="data" format="fasta" help="NGS data in fasta format"/>
	<param name="ContigFile" label="Reference - Contig Sequences" type="data" format="fasta"
	       help="Contigs obtained from RepeatExplorer clustering pipeline in fasta file"/> 
	<param name="MaxCl" label="Number of clusters to be shown in graph" type="integer" value="200"/>   
	<param name="bitscore" label="Minimum bit score threshold" type="integer" value="30" help="All similarity hits with lower bit score will not be considered for ChIP/Input ratio calculation"/>   
    </inputs>
    <outputs>
    	<data name="OutputFile" format="tabular"/>
	<data name="ReportFile" format="html"/> 
    </outputs>

6:f224513123a1

    <description></description>
    <requirements>
      <requirement type="package">r-base64enc</requirement>
      <requirement type="package">r-r2html</requirement>
      <requirement type="package">blast</requirement>
      <!-- <requirement type="package">chip_seq_ration</requirement> -->
    </requirements>
    <command interpreter="python3">
	ChipSeqRatioAnalysis.py 
	--ChipSeq=${ChipFile}
	--InputSeq=${InputFile}

        <param name="ChipFile" label="Chip Sequences" type="data" format="fasta" help="NGS data in fasta format"/> 
	<param name="InputFile" label="Input Sequences" type="data" format="fasta" help="NGS data in fasta format"/>
	<param name="ContigFile" label="Reference - Contig Sequences" type="data" format="fasta"
	       help="Contigs obtained from RepeatExplorer clustering pipeline in fasta file"/> 
	<param name="MaxCl" label="Number of clusters to be shown in graph" type="integer" value="200"/>   
	<param name="bitscore" label="Minimum bit score threshold" type="integer" value="50" help="All similarity hits with lower bit score will not be considered for ChIP/Input ratio calculation"/>   
    </inputs>
    <outputs>
    	<data name="OutputFile" format="tabular"/>
	<data name="ReportFile" format="html"/> 
    </outputs>