comparison column_maker.xml @ 4:3335c0d583d8 draft

"planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/column_maker commit 2b17bdfc47ca4d7f1a584216c4bd61a7050df7ea"

3:35937a6b04fb

<tool id="Add_a_column1" name="Compute" version="1.2.0">
    <description>an expression on every row</description>
    <requirements>
        <requirement type="package" version="2.7.13">python</requirement>
        <requirement type="package" version="4.4">sed</requirement>
    </requirements>
    <command detect_errors="aggressive"><![CDATA[
        #if $header_lines_conditional.header_lines_select == "yes":
            (sed -n '1,1p' '$input' | sed  "s|$|%${header_lines_conditional.header_new_column_name}|" | tr "%" "\t") > header &&
            sed '1,1d' '$input' > data &&

        python '$__tool_directory__/column_maker.py'
            data column_maker_output
            "$cond"
            $round
            ${input.metadata.columns}
            "${input.metadata.column_types}" &&
        cat header column_maker_output > '$out_file1'
    ]]></command>
    <inputs>
        <param name="cond" type="text" value="c3-c2" label="Add expression"/>
        <param format="tabular" name="input" type="data" label="as a new column to" help="Dataset missing? See TIP below"/>

            </when>
            <when value="yes">
                <param name="header_new_column_name" type="text" value="New Column" label="The new column name" />
            </when>
        </conditional>
    </inputs>
    <outputs>
        <data format_source="input" name="out_file1" metadata_source="input"/>
    </outputs>
    <tests>

        <test>
            <param name="cond" value="c4*1"/>
            <param name="input" value="1.interval"/>
            <param name="round" value="yes"/>
            <output name="out_file1" file="column_maker_out3.interval"/>
        </test>
    </tests>
    <help>

 .. class:: infomark

4:3335c0d583d8

<tool id="Add_a_column1" name="Compute" version="1.3.0">
    <description>an expression on every row</description>
    <requirements>
        <requirement type="package" version="2.7.13">python</requirement>
        <requirement type="package" version="4.4">sed</requirement>
        <requirement type="package" version="1.14">numpy</requirement>
    </requirements>
    <command detect_errors="aggressive"><![CDATA[
        #if $header_lines_conditional.header_lines_select == "yes":
            (sed -n '1,1p' '$input' | sed  "s|$|%${header_lines_conditional.header_new_column_name}|" | tr "%" "\t") > header &&
            sed '1,1d' '$input' > data &&

        python '$__tool_directory__/column_maker.py'
            data column_maker_output
            "$cond"
            $round
            ${input.metadata.columns}
            "${input.metadata.column_types}"
            $avoid_scientific_notation &&
        cat header column_maker_output > '$out_file1'
    ]]></command>
    <inputs>
        <param name="cond" type="text" value="c3-c2" label="Add expression"/>
        <param format="tabular" name="input" type="data" label="as a new column to" help="Dataset missing? See TIP below"/>

            </when>
            <when value="yes">
                <param name="header_new_column_name" type="text" value="New Column" label="The new column name" />
            </when>
        </conditional>
        <param name="avoid_scientific_notation" type="select" label="Avoid scientific notation" help="If yes, use fully expanded decimal representation when writing new columns (use only if expression produces decimal numbers).">
            <option value="no">no</option>
            <option value="yes">yes</option>
        </param>
    </inputs>
    <outputs>
        <data format_source="input" name="out_file1" metadata_source="input"/>
    </outputs>
    <tests>

        <test>
            <param name="cond" value="c4*1"/>
            <param name="input" value="1.interval"/>
            <param name="round" value="yes"/>
            <output name="out_file1" file="column_maker_out3.interval"/>
        </test>
        <test>
            <param name="cond" value="float(.0000000000001)"/>
            <param name="input" value="1.bed"/>
            <param name="round" value="no"/>
            <output name="out_file1">
                <assert_contents>
                    <has_text text="CCDS10397" />
                    <has_text text="1e-13" />
                </assert_contents>
            </output>
        </test>
        <test>
            <param name="cond" value="float(.0000000000001)"/>
            <param name="input" value="1.bed"/>
            <param name="round" value="no"/>
            <param name="avoid_scientific_notation" value="yes"/>
            <output name="out_file1">
                <assert_contents>
                    <has_text text="CCDS10397" />
                    <has_text text=".0000000000001" />
                    <not_has_text text="1e-13" />
                </assert_contents>
            </output>
        </test>
    </tests>
    <help>

 .. class:: infomark