view endorspy.xml @ 0:c165db467de0 draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/endorspy commit ac2a8c3523acfe6dd7299bbb4805233976f9d7d2

<tool id="endorspy" name="EndorSpy" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
    <description>Calculate endogenous DNA percentage, clonality, and duplicates from flagstats</description>
    <macros>
        <token name="@TOOL_VERSION@">1.3</token>
        <token name="@VERSION_SUFFIX@">0</token>
        <token name="@PROFILE@">25.1</token>
    </macros>

    <requirements>
        <requirement type="package" version="3.12">python</requirement>
    </requirements>
    <required_files>
        <include path="endorS.py"/>
    </required_files>
    <command detect_errors="exit_code"><![CDATA[
        ## 1. Links
        ln -s '$pre_flagstat' raw.stats &&
        #if $post_flagstat
            ln -s '$post_flagstat' filtered.stats &&
        #end if
        #if $dedup_flagstat
            ln -s '$dedup_flagstat' dedup.stats &&
        #end if

        ## 2. Run EndorS.py 
        python '$__tool_directory__/endorS.py' 
            -r raw.stats
            #if $post_flagstat
                -q filtered.stats 
            #end if
            #if $dedup_flagstat
                -d dedup.stats 
            #end if
            -o json &&
        
        ## 3. Output
        mv *.json '$output_json'
    ]]></command>

    <inputs>
        <param argument="-r" name="pre_flagstat" type="data" format="txt" label="Raw Flagstat" help="Output of samtools flagstat before any filtering or deduplication." />        
        <param argument="-q" name="post_flagstat" type="data" format="txt" optional="true" label="Quality-Filtered Flagstat" help="Output of samtools flagstat after quality filtering." /> 
        <param argument="-d" name="dedup_flagstat" type="data" format="txt" optional="true" label="Deduplicated Flagstat" help="Output of samtools flagstat after duplicate removal." />
    </inputs>

    <outputs>
        <data name="output_json" format="json" label="${tool.name} on ${on_string}: JSON Report" />
    </outputs>
    
    <tests>
        <test expect_num_outputs="1">
            <param name="pre_flagstat" value="raw_flagstat.txt" ftype="txt" />
            <param name="post_flagstat" value="filtered_flagstat.txt" ftype="txt" />
            <output name="output_json">
                <assert_contents>
                    <has_text text="percent_on_target" />
                    <has_text text="percent_on_target_quality_filtered" />
                </assert_contents>
            </output>
        </test>
    </tests>

    <help><![CDATA[
**EndorSpy: Endogenous DNA, Clonality, and Duplication Calculator**

This tool calculates the percent on target (Endogenous DNA), cluster factor, and percent of duplicates in a sample from `samtools flagstat` outputs.

**Inputs:**
You can provide a combination of samtools flagstat files:
* **Raw Flagstat**: Assumes no quality filtering nor duplicate removal performed.
* **Quality-Filtered Flagstat**: Assumes some form of quality filtering has been performed.
* **Deduplicated Flagstat**: Whereby duplicate removal has been performed on the input reads.

*Note: You must provide at least the Raw flagstat, OR both the Quality-filtered and Deduplicated flagstats.*

**Outputs:**
A JSON file containing the calculated statistics.
    ]]></help>

    <citations>
        <citation type="bibtex">
@misc{githubendorspy,
  author = {Andrades Valtuena, Aida},
  title = {EndorSpy},
  publisher = {GitHub},
  journal = {GitHub repository},
  url = {https://github.com/aidaanva/endorS.py}
}
        </citation>
    </citations>
    <creator>
        <person givenName="Ali Mert" familyName="Aydin" url="https://github.com/mertydn"/>
        <organization name="Galaxy Europe" url="https://galaxyproject.eu/" />
    </creator>
</tool>