comparison macros.xml @ 1:a6ccec9faaa3 draft

planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04

0:f638ffde832e

            <regex match="Traceback" />
        </stdio>
    </xml>

    <token name="@THREADS@">--numberOfProcessors "\${GALAXY_SLOTS:-4}"</token>
    <token name="@WRAPPER_VERSION@">1.2</token>
    <xml name="requirements">
        <requirements>
            <requirement type="package" version="@WRAPPER_VERSION@">hicexplorer</requirement>
            <yield />
        </requirements>
        <expand macro="stdio" />
        <version_command>@BINARY@ --version</version_command>

    <xml name="zMax">
        <param argument="--zMax" name="zMax" type="float" optional="true" label="zMax for 3D plot"/> <!-- this should only be enabled when both or 3d is selected for param whatToShow -->
    </xml>

    <xml name="colormap">
        <param argument="--colorMap" type="select" label="Color map to use for the heatmap" help=" Available color map names can be found here: http://www.astro.lsa.umich.edu/~msshin/science/code/matplotlib_cm/">
            <option value="RdYlBu" selected="true">RdYlBu</option>
            <option value="Accent">Accent</option>
            <option value="Spectral">Spectral</option>
            <option value="Set1">Set1</option>
            <option value="Set2">Set2</option>
            <option value="Set3">Set3</option>

            <option value="RdBu_r">RdBu reversed</option>
            <option value="RdGy_r">RdGy reversed</option>
            <option value="RdPu_r">RdPu reversed</option>
            <option value="YlGn_r">YlGn reversed</option>
            <option value="PuBuGn_r">PuBuGn reversed</option>
            <option value="RdYlBu_r">RdYlBu reversed</option>
            <option value="RdYlGn_r">RdYlGn reversed</option>
            <option value="YlGnBu_r">YlGnBu reversed</option>
            <option value="YlOrBr_r">YlOrBr reversed</option>
            <option value="YlOrRd_r">YlOrRd reversed</option>
            <option value="gist_gray_r">gist_gray reversed</option>

            label="Ignore duplicates"
            help="If set, reads that have the same orientation and start position will be considered only once. If reads are paired, the mate position also has to coincide to ignore a read. (--ignoreDuplicates)" />
    </xml>

    <xml name="minMappingQuality">
        <param argument="--minMappingQuality" type="integer" optional="true" value="1" min="1"
            label="Minimum mapping quality"
            help= "If set, only reads that have a mapping quality score higher than the given value are considered.
                *Note* Bowtie's Mapping quality is related to uniqueness: the higher the score, the more unique is a read.
                A mapping quality defined by Bowtie of 10 or less indicates that there is at least a 1 in 10 chance that the read truly originated elsewhere."/>
    </xml>

1:a6ccec9faaa3

            <regex match="Traceback" />
        </stdio>
    </xml>

    <token name="@THREADS@">--numberOfProcessors "\${GALAXY_SLOTS:-4}"</token>
    <token name="@WRAPPER_VERSION@">1.7.1</token>
    <xml name="requirements">
        <requirements>
            <requirement type="package" version="2.7.13">python</requirement>
            <requirement type="package" version="@WRAPPER_VERSION@">hicexplorer</requirement>
            <yield />
        </requirements>
        <expand macro="stdio" />
        <version_command>@BINARY@ --version</version_command>

    <xml name="zMax">
        <param argument="--zMax" name="zMax" type="float" optional="true" label="zMax for 3D plot"/> <!-- this should only be enabled when both or 3d is selected for param whatToShow -->
    </xml>

    <xml name="colormap">
        <param argument="--colorMap" name="colormap" type="select" optional="True" label="Color map to use for the heatmap" help=" Available color map names can be found here: http://www.astro.lsa.umich.edu/~msshin/science/code/matplotlib_cm/">
            <option value="RdYlBu">RdYlBu</option>
            <option value="Accent">Accent</option>
            <option value="Spectral">Spectral</option>
            <option value="Set1">Set1</option>
            <option value="Set2">Set2</option>
            <option value="Set3">Set3</option>

            <option value="RdBu_r">RdBu reversed</option>
            <option value="RdGy_r">RdGy reversed</option>
            <option value="RdPu_r">RdPu reversed</option>
            <option value="YlGn_r">YlGn reversed</option>
            <option value="PuBuGn_r">PuBuGn reversed</option>
            <option value="RdYlBu_r" selected="True">RdYlBu reversed</option>
            <option value="RdYlGn_r">RdYlGn reversed</option>
            <option value="YlGnBu_r">YlGnBu reversed</option>
            <option value="YlOrBr_r">YlOrBr reversed</option>
            <option value="YlOrRd_r">YlOrRd reversed</option>
            <option value="gist_gray_r">gist_gray reversed</option>

            label="Ignore duplicates"
            help="If set, reads that have the same orientation and start position will be considered only once. If reads are paired, the mate position also has to coincide to ignore a read. (--ignoreDuplicates)" />
    </xml>

    <xml name="minMappingQuality">
        <param argument="--minMappingQuality" type="integer" optional="true" value="" min="1"
            label="Minimum mapping quality"
            help= "If set, only reads that have a mapping quality score higher than the given value are considered.
                *Note* Bowtie's Mapping quality is related to uniqueness: the higher the score, the more unique is a read.
                A mapping quality defined by Bowtie of 10 or less indicates that there is at least a 1 in 10 chance that the read truly originated elsewhere."/>
    </xml>