annotate utils_filter-by-energy.xml @ 4:63df1e23f4ff draft

planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/segmentation_fold_galaxy_wrapper commit 00690c63c51a7f7563f2428c313d7fa75f2657e5-dirty

<tool id="smf_utils_filter-by-energy" name="filter-by-energy" version="@VERSION@-1">
    <description>Split entries over two files based on the estimated energy</description>
    
    <macros>
        <import>macros.xml</import>
    </macros>
    
    <requirements>
        <requirement type="package" version="2.7.10">python</requirement>
        <requirement type="package" version="1.9">numpy</requirement>
        <requirement type="package" version="0.8.2.1">pysam</requirement>
        <requirement type="package" version="0.6.1">htseq</requirement>
        <requirement type="package" version="2.0.1">segmentation-fold-utils</requirement>
    </requirements>
    <expand macro="stdio" />
    
    <version_command>@VERSION_COMMAND_UTILS@</version_command>
    
    <command><![CDATA[
        segmentation-fold-utils
            filter-by-energy
                --energy ${energy}
                '$dbn_input_file'
                '$dbn_output_file_larger_or_equal'
                '$dbn_output_file_smaller'
    ]]></command>

    <inputs>
        <param name="dbn_input_file"
               type="data"
               format="dbn,txt"
               label="Input DBN file"
               help="The 'fasta'-headers should contain the genomic position being used to find overlapping reads in the BAM file"/>
        <param name="energy"
               type="float"
               value="0.0"
               argument="--energy"
               label="Energy value"
               help="Entries with transitions with energy smaller than energy (&lt; e) or without transitions will be put into DBN_OUTPUT_FILE_LARGER_OR_EQUAL and those larger or equal (&gt;= e) to DBN_OUTPUT_FILE_SMALLER" />
    </inputs>

    <outputs>
        <data name="dbn_output_file_larger_or_equal"
              format="dbn"
              label="${tool.name} on ${dbn_input_file.hid}: ${dbn_input_file.name} - energy larger/equal than selected"/>
        <data name="dbn_output_file_smaller"
              format="dbn"
              label="${tool.name} on ${dbn_input_file.hid}: ${dbn_input_file.name} - energy smaller than selected"/>
    </outputs>
    
    <tests>
        <test>
            <param name="dbn_input_file" value="DBNFile.test_03.in.dbn" ftype="dbn"/>
            <param name="energy" value='0.0'/>

            <output name="dbn_output_file_larger_or_equal" file="DBNFile.test_03.out.l.dbn" />
            <output name="dbn_output_file_smaller" file="DBNFile.test_03.out.s.dbn" />
        </test>
    </tests>
    
    <help><![CDATA[
Filter based on whether the entries in the DBN file are already annotated or not
    ]]></help>
    
    <expand macro="citations" />
</tool>