annotate tag_pileup_frequency.xml @ 3:580e8bcb6413 draft default tip

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tag_pileup_frequency commit 92a9933fda38241c033dad1f709a928f66756b6f"

<tool id="tag_pileup_frequency" name="Tag pileup frequency" version="1.0.2">
    <description></description>
    <requirements>
        <requirement type="package" version="11.0.1">openjdk</requirement>
    </requirements>
    <command detect_errors="exit_code"><![CDATA[
#import re
#set input1_identifier = re.sub('[^\s\w\-]', '_', str($input1.element_identifier))
#set input2_identifier = re.sub('[^\s\w\-]', '_', str($input2.element_identifier))
mkdir -p output &&
ln -s '${input1}' '${input1_identifier}' &&
ln -s '${input2}' '${input2_identifier}' &&
ln -s '${input1.metadata.bam_index}' '${input1_identifier}.bai' &&
java -jar '$__tool_directory__/TagPileup.jar'
-b '${input1_identifier}'
-i '${input1_identifier}.bai'
-c '$input2_identifier'
-s $tag_shift
-n $bin_size
-e $tags_equal
-r $reads
-p $proper_pe
-a $combine_strands
-t "\${GALAXY_SLOTS:-4}"
-w $composite_smoothing_window
-m true
-x '$output1'
-h $output_heatmap
#if str($output_heatmap) == "true":
    -o output
#end if
1>/dev/null
    ]]></command>
    <inputs>
        <param name="input1" type="data" format="bam" label="BAM file" />
        <param name="input2" type="data" format="bed" label="Bed file" />
        <param name="tag_shift" type="integer" value="0" min="0" label="5' to 3' Tag Shift (bp)" />
        <param name="bin_size" type="integer" value="1" min="1" label="Bin Size (bp)" />
        <param  name="tags_equal" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Set Tags to be equal?" />
        <param  name="reads" type="select" label="Reads to examine" help="Selecting combined requires paired-end BAM input">
            <option value="0" selected="true">Read1</option>
            <option value="1">Read2</option>
            <option value="2">combined</option>
        </param>
        <param  name="proper_pe" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Require proper PE?" help="Requires paired-end BAM input"/>
        <param  name="combine_strands" type="select" label="Combine strands?">
            <option value="0" selected="true">No</option>
            <option value="1">Yes</option>
        </param>
        <param name="composite_smoothing_window" type="integer" value="0" min="0" label="Composite smoothing window (bp)" />
        <param name="output_heatmap" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Output frequencies heatmap?" />
    </inputs>
    <outputs>
        <collection name="heatmaps" type="list" label="Heatmap frequencies: ${tool.name} on ${on_string}">
            <discover_datasets pattern="(?P&lt;designation&gt;.*)" directory="output" ext="tabular" visible="false" />
            <filter>output_heatmap == true</filter>
        </collection>
        <data name="output1" format="tabular"/>
    </outputs>
    <tests>
        <test>
            <param name="input1" value="input.bam" ftype="bam"/>
            <param name="input2" value="input.bed" ftype="bed"/>
            <param name="tag_shift" value="0" />
            <param name="bin_size" value="1" />
            <param name="tags_equal" value="false" />
            <param name="reads" value="0" />
            <param name="proper_pe" value="false" />
            <param name="combine_strands" value="0" />
            <param name="composite_smoothing_window" value="0" />
            <param name="output_heatmap" value="true" />
            <output name="output1" file="output1.tabular" ftype="tabular" compare="contains"/>
            <output_collection name="heatmaps" type="list">
                <element name="input_bed_input_bam_read1_anti.tabular" file="input2_input1_read1_anti.tabular" ftype="tabular" compare="contains"/>
                <element name="input_bed_input_bam_read1_sense.tabular" file="input2_input1_read1_sense.tabular" ftype="tabular" compare="contains"/>
            </output_collection>
        </test>
    </tests>
    <help>

**What it does**

Generates a frequency pileup of the 5' ends of aligned reads in a BAM file relative to reference points in a BED file.

-----

**Options**

**Global transformations**

 - **5' to 3' tag shift (bp)** - moves all tags from the 5' to the 3' direction given a specified distance in base pairs.
 - **Bin Size (bp)** - bins tags together into specified size, useful for lower resolution data or for especially wide reference windows.
 - **Set Tags to be equal** - standardizes tag count to be equal to genome size, useful for replicate comparisons.

**Read parameters**

 - **Reads to Examine** - output data for Read1, Read2, or combined (only for paired end BAM files).
 - **Require Proper PE** - require output reads to be properly paired (only for paired end BAM files).
 - **Combine Strands** - examine reads on a forward/reverse basis (strand separate) or ignoring read orientation (strand combined).

**Run parameters**

 - **Composite smoothing window (bp)** - sliding window to smooth composite frequencies.
 - **Output frequencies for heatmap** - generate an additional dataset collection containing frequencies that can be used to generate a heatmap plot.

    </help>
    <citations>
        <citation type="bibtex">
            @unpublished{None,
            author = {Lai, William},
            title = {None},
            year = {None},
            eprint = {None},
            url = {http://www.huck.psu.edu/content/research/independent-centers-excellence/center-for-eukaryotic-gene-regulation}
        }</citation>
    </citations>
</tool>