annotate fileinfo.xml @ 0:aa82b2e54055 draft

planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit b36048cd608ede0ec6f6559648525c9350caae34-dirty

<tool id="mimodd_info" name="MiModD File Information" version="@MIMODD_WRAPPER_VERSION@">
    <description>provides summary reports for supported sequence data formats.</description>
    <macros>
        <import>macros.xml</import>
        <xml name="test_with_formats" token_ifile="a.sam" token_oformat="text"
        token_expectformat="txt">
            <test>
                <conditional name="input_selection">
                    <param name="source" value="history" />
                    <param name="ifile" value="@IFILE@" />
                </conditional>
                <param name="oformat" value="@OFORMAT@" />
                <output name="ofile" ftype="@EXPECTFORMAT@">
                    <assert_contents>
                        <has_text text="chrI" />
                        <has_text text="chrII" />
                        <has_text text="chrIII" />
                        <has_text text="chrIV" />
                        <has_text text="chrV" />
                        <has_text text="chrX" />
                    </assert_contents>
                </output>
            </test>
        </xml>
    </macros>
    <expand macro="requirements" />
    <expand macro="stdio" />
    <expand macro="version_command" />
    <command><![CDATA[
    mimodd info -o '$ofile' --verbose --oformat $oformat
    #if str($input_selection.source) == "history":
      '$input_selection.ifile'
    #else:
      '$input_selection.ifile.fields.path'
    #end if
    ]]></command>

    <inputs>
        <conditional name="input_selection">
            <param name="source" type="select" label="Input is a">
                <option value="history">Dataset in history</option>
                <option value="cached">Genome on server</option>
            </param>
            <when value="history">
                <param name="ifile" type="data" format="bam,sam,vcf,bcf,fasta"
                label="input dataset" />
            </when>
            <when value="cached">
                <param name="ifile" type="select" label="installed genome">
                    <options from_data_table="all_fasta" />
                </param>
            </when>
        </conditional>
        <param name="oformat" type="select" display="radio"
        label="output format">
            <option value="txt">text</option>
            <option value="html">html</option>
        </param>
    </inputs>

    <outputs>
        <data name="ofile" format="txt" label="Sample Info on ${on_string}">
            <change_format>
	            <when input="oformat" value="html" format="html"/>
            </change_format>
            <actions>
                <conditional name="input_selection.source">
                    <when value="cached">
                        <action type="metadata" name="dbkey">
                            <option type="from_data_table" name="all_fasta" column="1" offset="0">
                                <filter type="param_value" ref="input_selection.ifile" column="0" />
                            </option>
                        </action>
                    </when>
                </conditional>
            </actions>
        </data>
    </outputs>

    <tests>
        <expand macro="test_with_formats" ifile="a.bam" />
        <expand macro="test_with_formats" ifile="a.sam" />
        <expand macro="test_with_formats" ifile="a.bcf" />
        <expand macro="test_with_formats" ifile="a.vcf" />
        <expand macro="test_with_formats" ifile="a.fa" />
        <expand macro="test_with_formats" ifile="a.bam" oformat="html"
        expectformat="html" />
    </tests>

    <help><![CDATA[
.. class:: infomark

   **What it does**

The tool inspects the input datasets and generates a report summarizing its contents.

It autodetects and works with most file formats produced by MiModD, i.e., **SAM / BAM, vcf / bcf and fasta**, and produces a standardized report for all of them.

@HELP_FOOTER@
    ]]></help>
    <expand macro="citations" />
</tool>