comparison diffbind.xml @ 15:aefe2a771a95 draft

planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit 10052765d6b712cf7d38356af4251fcc38a339b6-dirty

14:4de6355eca00

        <requirement type="binary">Rscript</requirement>
        <requirement type="R-module">DESeq2</requirement>
        <requirement type="package" version="3.0.3">R</requirement>
        <requirement type="package" version="1.2.10">deseq2</requirement>
        <requirement type="package" version="1.8.3">diffbind</requirement>
        <requirement type="set_environment">DIFFBIND_SCRIPT_PATH</requirement>
    </requirements>
    <command>
        ## seems that diffbind also needs file extensions to work properly
        #set $counter = 1
        #for $sample in $samples:
            ln -s $sample.bamreads #echo str($counter) + "_bamreads.bam"# &amp;&amp;
            ln -s ${sample.bamreads.metadata.bam_index} #echo str($counter) + "_bamreads.bai"# &amp;&amp;
            ln -s $sample.bamcontrol #echo str($counter) + "_bamcontrol.bam"# &amp;&amp;
            ln -s ${sample.bamcontrol.metadata.bam_index} #echo str($counter) + "_bamcontrol.bai"# &amp;&amp;
            #set $counter = $counter + 1
        #end for

        Rscript \$DIFFBIND_SCRIPT_PATH/diffbind.R
            -i $infile
            -o $outfile
            -p $plots
            -f $format
    </command>
    <stdio>
        <regex match="Execution halted" 
           source="both" 
           level="fatal" 
           description="Execution halted." />
        <regex match="Input-Error 01" 
           source="both" 
           level="fatal" 
           description="Error in your input parameters: Make sure you only apply factors to selected samples." />
        <regex match="Error in" 
           source="both" 
           level="fatal" 
           description="An undefined error occured, please check your intput carefully and contact your administrator." />
    </stdio>
    <inputs>
        <repeat name="samples" title="Samples" min="2">
            <param name="sample_id" type="text" value="Sample ID" label="Specify a sample id" help="e.g. BT474.1-" />

            <param name="replicate" type="integer" value="1" label="Specify the replicate number" help="e.g. 1" />
            <param format="bam" name="bamreads" type="data" label="Read BAM file" help="Specify the Read BAM file, used for Peak calling."/>
            <param format="bam" name="bamcontrol" type="data" label="Control BAM file" help="Specify the Control BAM file, used for Peak calling."/>
            <param format="bed" name="peaks" type="data" label="Peak file" help="Result of your Peak calling experiment."/>
        </repeat>
        <param name="pdf" type="boolean" truevalue="" falsevalue="" checked="true" 
            label="Visualising the analysis results"
            help="output an additional PDF files" />
        <param name="format" type="select" label="Output Format">
            <option value="bed">BED</option>
            <option value="gff">GFF</option>

            <filter>pdf == True</filter>
        </data>
    </outputs>

    <help>

.. class:: infomark

**What it does** 


------

**References** 

DiffBind_ Authors:  Rory Stark, Gordon Brown

.. _DiffBind: http://www.bioconductor.org/packages/release/bioc/html/DiffBind.html

Wrapper authors: Bjoern Gruening, Pavankumar Videm

    </help>
</tool>

15:aefe2a771a95

        <requirement type="binary">Rscript</requirement>
        <requirement type="R-module">DESeq2</requirement>
        <requirement type="package" version="3.0.3">R</requirement>
        <requirement type="package" version="1.2.10">deseq2</requirement>
        <requirement type="package" version="1.8.3">diffbind</requirement>
    </requirements>
    <command>
<![CDATA[
        ## seems that diffbind also needs file extensions to work properly
        #set $counter = 1
        #for $sample in $samples:
            ln -s $sample.bamreads #echo str($counter) + "_bamreads.bam"# &&
            ln -s ${sample.bamreads.metadata.bam_index} #echo str($counter) + "_bamreads.bai"# &&
            ln -s $sample.bamcontrol #echo str($counter) + "_bamcontrol.bam"# &&
            ln -s ${sample.bamcontrol.metadata.bam_index} #echo str($counter) + "_bamcontrol.bai"# &&
            #set $counter = $counter + 1
        #end for

        Rscript $__tool_directory__/diffbind.R
            -i $infile
            -o $outfile
            -p $plots
            -f $format
]]>
    </command>
    <stdio>
        <regex match="Execution halted"
           source="both"
           level="fatal"
           description="Execution halted." />
        <regex match="Input-Error 01"
           source="both"
           level="fatal"
           description="Error in your input parameters: Make sure you only apply factors to selected samples." />
        <regex match="Error in"
           source="both"
           level="fatal"
           description="An undefined error occured, please check your intput carefully and contact your administrator." />
    </stdio>
    <inputs>
        <repeat name="samples" title="Samples" min="2">
            <param name="sample_id" type="text" value="Sample ID" label="Specify a sample id" help="e.g. BT474.1-" />

            <param name="replicate" type="integer" value="1" label="Specify the replicate number" help="e.g. 1" />
            <param format="bam" name="bamreads" type="data" label="Read BAM file" help="Specify the Read BAM file, used for Peak calling."/>
            <param format="bam" name="bamcontrol" type="data" label="Control BAM file" help="Specify the Control BAM file, used for Peak calling."/>
            <param format="bed" name="peaks" type="data" label="Peak file" help="Result of your Peak calling experiment."/>
        </repeat>
        <param name="pdf" type="boolean" truevalue="" falsevalue="" checked="true"
            label="Visualising the analysis results"
            help="output an additional PDF files" />
        <param name="format" type="select" label="Output Format">
            <option value="bed">BED</option>
            <option value="gff">GFF</option>

            <filter>pdf == True</filter>
        </data>
    </outputs>

    <help>
<![CDATA[


**What it does**

Diffbind provides functions for  processing  ChIP-Seq  data  enriched  for  genomic  loci  where  specific  protein/DNA  binding  occurs,  including  peak sets  identified  by  ChIP-Seq  peak  callers  and  aligned  sequence  read  datasets. 

**Input**

- You have to specify your samples. Here is one example:

ID      Tissue  Factor  Condition   Treatment   Replicate   Caller  Intervals
BT4741  BT474   ER      Resistant   Full-Media  1           raw     1084

- BAM file which contains the mapped sequencing reads can be associated with each
peakset 

- Control BAM file represents a control dataset

- Peak file: Result of your Peak calling experiment


**Output**

As output format you can choose BED, GFF, WIG.


**References**

DiffBind_ Authors:  Rory Stark, Gordon Brown (2011)

.. _DiffBind: http://www.bioconductor.org/packages/release/bioc/html/DiffBind.html

Wrapper authors: Bjoern Gruening, Pavankumar Videm

]]>
    </help>
</tool>