comparison flaimapper.xml @ 41:3cf217373ae2 draft default tip

planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/flaimapper commit bc077ab7d773c0764642ae8a439d6077ff64fd3c

40:af0ee8dc5471

<?xml version="1.0" encoding="UTF-8"?>
<tool id="flaimapper" name="FlaiMapper" version="2.5.0-0">
    <description>detects small ncRNA derived fragments in small RNA-Seq data</description>
    <requirements>
        <requirement type="package" version="2.5.0">flaimapper</requirement>
    </requirements>

    <version_command><![CDATA[ flaimapper --version 2>&1 | head -n 1 ]]></version_command>

    <command detect_errors="exit_code"><![CDATA[

            <param name="output_format" value="2" />
            <param name="parameters" value="filter-parameters.duck.15.txt"/>

            <output name="output" file="snord81.flaimapper.duck-15.gtf" />
        </test>
    </tests>

    <help><![CDATA[
FlaiMapper wrapper for Galaxy
=============================

41:3cf217373ae2

<?xml version="1.0" encoding="UTF-8"?>
<tool id="flaimapper" name="FlaiMapper" version="3.0.0-0">
    <description>detects small ncRNA derived fragments in small RNA-Seq data</description>
    <requirements>
        <requirement type="package" version="3.0.0">flaimapper</requirement>
    </requirements>

    <version_command><![CDATA[ flaimapper --version 2>&1 | head -n 1 ]]></version_command>

    <command detect_errors="exit_code"><![CDATA[

            <param name="output_format" value="2" />
            <param name="parameters" value="filter-parameters.duck.15.txt"/>

            <output name="output" file="snord81.flaimapper.duck-15.gtf" />
        </test>
        
        <!-- Tests a new feature that allows multiple fragments of different size, starting at one identical positions -->
        <test>
            <param name="alignment" value="multilength_fragments_per_position_001.bam" ftype="bam" />
            <param name="output_format" value="1" />

            <output name="output" file="multilength_fragments_per_position_001.txt" />
        </test>
    </tests>

    <help><![CDATA[
FlaiMapper wrapper for Galaxy
=============================