annotate zerone.xml @ 0:75962a01d8ab draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/zerone commit 537bbf2e3ae9e7dcc619354911caf774338d7a0e

<tool id="zerone" name="zerone" version="1.0">
    <requirements>
        <requirement type="package" version="1.0">zerone</requirement>
    </requirements>
    <version_command>zerone --version</version_command>
    <command detect_errors="exit_code"><![CDATA[
#set $mock_args = []
#set $chip_args = []
#for i,mock_input in enumerate($mock):
    #silent mock_args.append("'mock_%i.%s'" % ($i, $mock_input.ext))
    ln -s '$mock_input' 'mock_${i}.${mock_input.ext}' &&
#end for
#for i,chip_input in enumerate($chip):
    #silent chip_args.append("'chip_%i.%s'" % ($i, $mock_input.ext))
    ln -s '$chip_input' 'chip_${i}.${chip_input.ext}' &&
#end for

zerone
--mock #echo ",".join($mock_args)#
--chip #echo ",".join($chip_args)#
--window $window
--quality $quality
$list_output
$confidence > '$output'
    ]]></command>
    <inputs>
        <param argument="--chip" type="data" format="sam,bam" multiple="true" label="ChIP alignment file(s)"/>
        <param argument="--mock" type="data" format="sam,bam" multiple="true" label="Control alignment file(s)"/>
        <param argument="--window" type="integer" value="300" min="1" label="Window size in bp (default 300)"/>
        <param argument="--quality" type="integer" value="20" min="1" label="Minimum mapping quality (default 20)"/>
        <param argument="--list_output" type="boolean" truevalue="--list-output" falsevalue="" label="Output list of targets (default table)"/>
        <param argument="--confidence" type="boolean" truevalue="--confidence" falsevalue="" label="Print targets only with higher confidence" help="Restricts intervals accordingly in list output"/>
    </inputs>
    <outputs>
        <data name="output" format="interval" label="Zerone on $on_string"/>
    </outputs>
    <tests>
        <test>
            <param name="chip" value="ctcf1.bam,ctcf2.bam"/>
            <param name="mock" value="mock.bam"/>
            <output name="output">
                <assert_contents>
                    <has_line line="# QC score: 0.478"/>
                    <has_line line="# features: 0.025, 10.000, 0.000, 0.018, 0.924"/>
                    <has_line line="# advice: accept discretization."/>
                    <has_line_matching expression="chrX\t1\t300\t0\t0\t0\t0\t0.33332"/>
                </assert_contents>
            </output>
        </test>
        <test>
            <param name="chip" value="ctcf1.bam,ctcf2.bam"/>
            <param name="mock" value="mock.bam"/>
            <param name="list_output" value="true"/>
            <output name="output" file="list_output.tab"/>
        </test>
    </tests>
    <help><![CDATA[
**What it does**

Zerone discretizes several ChIP-seq replicates simultaneously and resolves conflicts between them. After the job is done, Zerone checks the results and tells you whether it passes the quality control.

**Results**

The first three lines contain the result of the quality control. It consists of a quality score followed by the numeric values of 5 features, and an advice to either accept or reject the discretization. The recommendation is to accept if the score is positive and reject if it is negative. If the score is higher than 1 (or lower than -1), the advice is considered extremely reliable.  

The rest of the lines contain the discretization proper. The first three columns specify the chromosome, start and end positions of each window.  
The fourth column represents the enrichment. Zerone classifies each window into one of two possible states. State 0 represents background signal and state 1 represents an enriched window.  

The fifth column contains the read counts of all the control profiles summed together per window. The following columns show the number of reads per window in the ChIP-seq files, in the order they were provided. The final column is the estimated probability that the window is a target (it is a confidence score for the call). 
 
If you select "Output list of targets" Zerone produces an alternative output in which only the targets are shown after merging consecutive windows.
The first three columns are the same as in window output i.e. chromosome or sequence name, start and end. The last column is the confidence score of the called target. It is the highest confidence of the windows merged in the same target region.
    ]]></help>
    <citations>
        <citation type="doi">10.1093/bioinformatics/btw33</citation>
    </citations>
</tool>