comparison bismark_methylation_extractor.xml @ 4:243e8f9fb75b draft

Uploaded

3:91f07ff056ca

        <requirement type="package" version="0.12.8">bowtie</requirement>
        <requirement type="package" version="2.1.0">bowtie2</requirement>
    </requirements>
    <parallelism method="basic"></parallelism>
    <command interpreter="python">
        bismark_methylation_extractor.py

        --infile $input

        --bismark_path \$SCRIPT_PATH

        #if $singlePaired.sPaired == "single":
            --single-end
        #else:
            --paired-end

                --cpg_ctob $cpg_ctob
            #end if
        ## end compress
        #end if

    </command>
    <inputs>
        <!-- Input Parameters -->
        <param name="input" type="data" format="sam,bam" label="SAM/BAM file from Bismark bisulfite mapper" />
        <conditional name="singlePaired">

    <tests>
    </tests>

    <help>

**What it does**

The following is a brief description of all options to control the Bismark_
methylation extractor. The script reads in a bisulfite read alignment results file 
produced by the Bismark bisulfite mapper and extracts the methylation information
for individual cytosines. This information is found in the methylation call field
which can contain the following characters:

                           methylation call string. This can remove e.g. a restriction enzyme site
                           at the start of each read.

Output::

  --comprehensive          Specifying this option will merge all four possible strand-specific 
                           methylation info into context-dependent output files. The default 
                           contexts are:
                            - CpG context
                            - CHG context
                            - CHH context

  --report                 Prints out a short methylation summary as well as the paramaters used to run
                           this script.


  </help>
</tool>

4:243e8f9fb75b

        <requirement type="package" version="0.12.8">bowtie</requirement>
        <requirement type="package" version="2.1.0">bowtie2</requirement>
    </requirements>
    <parallelism method="basic"></parallelism>
    <command interpreter="python">
<![CDATA[
        bismark_methylation_extractor.py

        --infile $input

        #--bismark_path \$SCRIPT_PATH

        #if $singlePaired.sPaired == "single":
            --single-end
        #else:
            --paired-end

                --cpg_ctob $cpg_ctob
            #end if
        ## end compress
        #end if

]]>
    </command>
    <inputs>
        <!-- Input Parameters -->
        <param name="input" type="data" format="sam,bam" label="SAM/BAM file from Bismark bisulfite mapper" />
        <conditional name="singlePaired">

    <tests>
    </tests>

    <help>
<![CDATA[

**What it does**

The following is a brief description of all options to control the Bismark_
methylation extractor. The script reads in a bisulfite read alignment results file
produced by the Bismark bisulfite mapper and extracts the methylation information
for individual cytosines. This information is found in the methylation call field
which can contain the following characters:

                           methylation call string. This can remove e.g. a restriction enzyme site
                           at the start of each read.

Output::

  --comprehensive          Specifying this option will merge all four possible strand-specific
                           methylation info into context-dependent output files. The default
                           contexts are:
                            - CpG context
                            - CHG context
                            - CHH context

  --report                 Prints out a short methylation summary as well as the paramaters used to run
                           this script.


]]>
  </help>
</tool>