comparison macros.xml @ 4:5d5b14dbd092 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"

3:d55e29ac02e3

<macros>
    <token name="@GET_VERSION@"><![CDATA[ 2>&1 | head -1 | cut -d' ' -f 2 ]]></token>
    <token name="@STRING2VECTOR@">
string2numericvector = function(string){
    #' Converts a string to a valid vector
    #'
    #' e.g. "-1,2:5,2"  evaluates to c(-1,2,3,4,5,2)

    #'   e.g. "red,yellow,white" evaluates to c("red","yellow","white")
    return(unlist(strsplit(string,",")))
}
    </token>
    <token name="@VERSION_RACEID@">3</token>
    <token name="@VERSION_PACKAGE@">0.2</token>
    <macro name="requirements" >
        <requirements>
            <requirement type="package" version="0.1.1">r-raceid</requirement>
            <requirement type="package" version="1.6.2">bioconductor-scran</requirement>
        </requirements>

    <macro name="citations" >
        <citations>
            <citation type="doi">10.1038/nature14966</citation>
            <citation type="doi">10.1038/nmeth.4662</citation>
        </citations>
    </macro>
    <macro name="select_cells" token_sectionname="@SECTIONNAME@" token_sectiontitle="@SECTIONTITLE@" >
        <section name="@SECTIONNAME@" title="@SECTIONTITLE@" expanded="true" >
            <param name="name_set" type="text" optional="true" label="Name of Set" >
                <!-- Aname, Bname -->
                <expand macro="sanitize_title" />
            </param>
            <conditional name="meth" >
                <param name="type" type="select" label="Selection method" >
                    <option value="cln" selected="true">Cluster Numbers</option>
                    <option value="regex" >Regular Expression</option>
                    <option value="manual" >Manual Selection</option>
                </param>
                <when value="cln" >
                    <param name="selector" type="text" value="" label="List of clusters" >
                        <expand macro="sanitize_numeric_vector" />
                    </param>
                </when>
                <when value="regex" >
                    <param name="selector" type="text" value="" label="Regular Expression to select gene names" >
                        <expand macro="sanitize_regex" />
                    </param>
                </when>
                <when value="manual" >
                    <param name="selector" type="text" value="" label="List of genes" >
                        <expand macro="sanitize_string_vector" />
                    </param>
                </when>
            </conditional>
        </section>
    </macro>
    <!-- Sanitizers -->
    <macro name="sanitize_title">
        <sanitizer invalid_char="">
            <valid initial="string.letters,string.digits" >

4:5d5b14dbd092

<macros>
    <token name="@STRING2VECTOR@">
string2numericvector = function(string){
    #' Converts a string to a valid vector
    #'
    #' e.g. "-1,2:5,2"  evaluates to c(-1,2,3,4,5,2)

    #'   e.g. "red,yellow,white" evaluates to c("red","yellow","white")
    return(unlist(strsplit(string,",")))
}
    </token>
    <token name="@VERSION_RACEID@">3</token>
    <token name="@VERSION_WRAPPER@">1</token>

    <macro name="version_command_config" token_prog="temp" token_cheetah="temp2" token_out="2&#62; '$outlog'">
        <version_command><![CDATA[
Rscript '$__tool_directory__/scripts/@PROG@' 2>&1 | head -1 | cut -d' ' -f 2
        ]]></version_command>
        <command detect_errors="exit_code"><![CDATA[
Rscript '$__tool_directory__/scripts/@PROG@' '$userconf' @OUT@
]]>
        </command>
        <configfiles>
            <configfile name="userconf" ><![CDATA[
@STRING2VECTOR@

@@CHEETAH@@
]]></configfile>
        </configfiles>
    </macro>

    <macro name="requirements" >
        <requirements>
            <requirement type="package" version="0.1.1">r-raceid</requirement>
            <requirement type="package" version="1.6.2">bioconductor-scran</requirement>
        </requirements>

    <macro name="citations" >
        <citations>
            <citation type="doi">10.1038/nature14966</citation>
            <citation type="doi">10.1038/nmeth.4662</citation>
        </citations>
    </macro>
    <!-- Sanitizers -->
    <macro name="sanitize_title">
        <sanitizer invalid_char="">
            <valid initial="string.letters,string.digits" >