comparison diff.xml @ 4:10ef1bf99074 draft

planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diff commit 1a6c4a793ef68a43de93316523c1cd9196d80b73

3:156d0908e232

<tool id="diff" name="diff" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@">
    <description>analyzes two files and generates an unidiff text file with information about the differences and an optional Html report</description>
    <macros>
        <token name="@TOOL_VERSION@">3.7</token>
        <token name="@GALAXY_VERSION@">0</token>
    </macros>
    <requirements>
        <requirement type="package" version="@TOOL_VERSION@">diffutils</requirement>
        <requirement type="package" version="4.8">sed</requirement>

    <stdio>
        <exit_code range="2:" level="fatal" description="Something went wrong trying to check differences in files. Please check output log for more details."/>
        <regex match="diff: memory exhausted" source="stdout" level="fatal_oom" description="Out of memory error occurred"/>
    </stdio>
    <command><![CDATA[
        diff -u '$input1' '$input2' > '$diff_file';
        #if $generate_report:
            sed -e 's/@@title@@/Diff report for "$input1.element_identifier" and "$input2.element_identifier"/g'
                -e 's/@@outputformat@@/'$output_format'/g'
                -e '/@@diffoutput@@/{r'$diff_file'' -e ';d}'
                '$__tool_directory__/template.html' > '$html_file'
        #end if
    ]]>
    </command>
    <inputs>
        <param name="input1" type="data" format="txt" label="First input file"/>
        <param name="input2" type="data" format="txt" label="Second input file"/>
        <param name="generate_report" type="boolean" checked="true" truevalue="true" falsevalue="false" label="Generate HTML report" help="Generates an HTML report to visualize the differences"/>
        <param name="output_format" type="select" label="Choose report output format" help="Displays the differences in the report using the selected format. Either line by line or side by side.">
            <option value="side-by-side">Side by side</option>
            <option value="line-by-line">Line by line</option>
        </param>
    </inputs>
    <outputs>
        <data format="txt" name="diff_file" from_work_dir="output.txt" label="${tool.name} on ${on_string}: Raw Output"/>
        <data format="html" name="html_file" from_work_dir="output.html" label="${tool.name} on ${on_string}: Html Report">
            <filter>generate_report is True</filter>
        </data>
    </outputs>
    <tests>
        <test expect_exit_code="0" expect_failure="false" expect_num_outputs="1">
            <param name="input1" value="file1.txt"/>
            <param name="input2" value="file1.txt"/>
            <param name="generate_report" value="false"/>
            <output name="diff_file">
                <assert_contents>
                    <has_n_lines n="0"/>
                </assert_contents>
            </output>
        </test>
        <test expect_exit_code="1" expect_failure="false" expect_num_outputs="1">
            <param name="input1" value="file1.txt"/>
            <param name="input2" value="file2.txt"/>
            <param name="generate_report" value="false"/>
            <output name="diff_file">
                <assert_contents>
                    <has_n_lines n="5"/>
                    <has_line line=" a"/>
                    <has_line line="+b"/>

            </output>
        </test>
        <test expect_exit_code="0" expect_failure="false" expect_num_outputs="2">
            <param name="input1" value="file1.txt"/>
            <param name="input2" value="file2.txt"/>
            <param name="generate_report" value="true"/>
            <output name="html_file">
                <assert_contents>
                    <has_text text="!DOCTYPE html"/>
                </assert_contents>
            </output>
        </test>
        <test expect_exit_code="0" expect_failure="false" expect_num_outputs="2">
            <param name="input1" value="file1.txt"/>
            <param name="input2" value="file2.txt"/>
            <param name="generate_report" value="true"/>
            <param name="output_format" value="side-by-side"/>
            <output name="html_file">
                <assert_contents>
                    <has_text text="!DOCTYPE html"/>
                    <has_text text="side-by-side"/>
                </assert_contents>
            </output>
        </test>
        <test expect_exit_code="0" expect_failure="false" expect_num_outputs="2">
            <param name="input1" value="file1.txt"/>
            <param name="input2" value="file2.txt"/>
            <param name="generate_report" value="true"/>
            <param name="output_format" value="line-by-line"/>
            <output name="html_file">
                <assert_contents>
                    <has_text text="!DOCTYPE html"/>
                    <has_text text="line-by-line"/>
                </assert_contents>
            </output>
        </test>
        <test expect_exit_code="0" expect_failure="false" expect_num_outputs="2">
            <param name="input1" value="file 3.txt"/>
            <param name="input2" value="file 3.txt"/>
            <param name="generate_report" value="true"/>
            <output name="diff_file">
                <assert_contents>
                    <has_n_lines n="0"/>
                </assert_contents>
            </output>

4:10ef1bf99074

<tool id="diff" name="diff" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="23.0">
    <description>analyzes two files and generates an unidiff text file with information about the differences and an optional Html report</description>
    <macros>
        <token name="@TOOL_VERSION@">3.10</token>
        <token name="@GALAXY_VERSION@">0</token>
    </macros>
    <requirements>
        <requirement type="package" version="@TOOL_VERSION@">diffutils</requirement>
        <requirement type="package" version="4.8">sed</requirement>

    <stdio>
        <exit_code range="2:" level="fatal" description="Something went wrong trying to check differences in files. Please check output log for more details."/>
        <regex match="diff: memory exhausted" source="stdout" level="fatal_oom" description="Out of memory error occurred"/>
    </stdio>
    <command><![CDATA[
        diff
        #if $report_format.report_format_select == 'txt_lines' or $report_format.report_format_select == 'html'
            ## the -u option is needed to convert the output later to HTML
            --unified=$report_format.unified
        #else if $report_format.report_format_select == 'txt_columns'
            -y
        #end if
        ## If the compared input files differ the diff command returns exit-code 1
        '$input1' '$input2' > '$diff_file' || [ \$? -eq 1 ];
        #if $report_format.report_format_select == 'html'
            sed -e 's/@@title@@/Diff report for "$input1.element_identifier" and "$input2.element_identifier"/g'
                -e 's/@@outputformat@@/'$report_format.output_format'/g'
                -e '/@@diffoutput@@/{r'$diff_file'' -e ';d}'
                '$__tool_directory__/template.html' > '$html_file'
        #end if
    ]]>
    </command>
    <inputs>
        <param name="input1" type="data" format="txt" label="First input file"/>
        <param name="input2" type="data" format="txt" label="Second input file"/>
        <conditional name="report_format">
            <param name="report_format_select" type="select" label="Choose a report format">
                <option value="txt_lines">Text file, line-by-line (-u)</option>
                <option value="txt_columns">Text file, side-by-side (-y)</option>
                <option value="html">Generates an HTML report to visualize the differences</option>
            </param>
            <when value="txt_lines">
                <param argument="--unified" type="integer" min="0" value="3" label="Output this amount of lines of unified context"/>
            </when>
            <when value="txt_columns"/>
            <when value="html">
                <param argument="--unified" type="integer" min="0" value="3" label="Output this amount of lines of unified context"/>
                <param name="output_format" type="select" label="Choose report output format" help="Displays the differences in the report using the selected format. Either line by line or side by side.">
                    <option value="side-by-side">Side by side</option>
                    <option value="line-by-line">Line by line</option>
                </param>
            </when>
        </conditional>
    </inputs>
    <outputs>
        <data format="txt" name="diff_file" from_work_dir="output.txt" label="${tool.name} on ${on_string}: Raw Output"/>
        <data format="html" name="html_file" from_work_dir="output.html" label="${tool.name} on ${on_string}: Html Report">
            <filter>report_format['report_format_select'] == 'html'</filter>
        </data>
    </outputs>
    <tests>
        <test expect_exit_code="0" expect_failure="false" expect_num_outputs="1">
            <param name="input1" value="file1.txt"/>
            <param name="input2" value="file1.txt"/>
            <conditional name="report_format">
                <param name="report_format_select" value="txt_lines"/>
            </conditional>
            <output name="diff_file">
                <assert_contents>
                    <has_n_lines n="0"/>
                </assert_contents>
            </output>
        </test>
        <test expect_exit_code="0" expect_failure="false" expect_num_outputs="1">
            <param name="input1" value="file1.txt"/>
            <param name="input2" value="file2.txt"/>
            <conditional name="report_format">
                <param name="report_format_select" value="txt_lines"/>
            </conditional>
            <output name="diff_file">
                <assert_contents>
                    <has_n_lines n="5"/>
                    <has_line line=" a"/>
                    <has_line line="+b"/>

            </output>
        </test>
        <test expect_exit_code="0" expect_failure="false" expect_num_outputs="2">
            <param name="input1" value="file1.txt"/>
            <param name="input2" value="file2.txt"/>
            <conditional name="report_format">
                <param name="report_format_select" value="html"/>
            </conditional>
            <output name="html_file">
                <assert_contents>
                    <has_text text="!DOCTYPE html"/>
                </assert_contents>
            </output>
        </test>
        <test expect_exit_code="0" expect_failure="false" expect_num_outputs="2">
            <param name="input1" value="file1.txt"/>
            <param name="input2" value="file2.txt"/>
            <conditional name="report_format">
                <param name="report_format_select" value="html"/>
                <param name="output_format" value="side-by-side"/>
            </conditional>
            <output name="html_file">
                <assert_contents>
                    <has_text text="!DOCTYPE html"/>
                    <has_text text="side-by-side"/>
                </assert_contents>
            </output>
        </test>
        <test expect_exit_code="0" expect_failure="false" expect_num_outputs="2">
            <param name="input1" value="file1.txt"/>
            <param name="input2" value="file2.txt"/>
            <conditional name="report_format">
                <param name="report_format_select" value="html"/>
                <param name="output_format" value="line-by-line"/>
            </conditional>
            <output name="html_file">
                <assert_contents>
                    <has_text text="!DOCTYPE html"/>
                    <has_text text="line-by-line"/>
                </assert_contents>
            </output>
        </test>
        <test expect_exit_code="0" expect_failure="false" expect_num_outputs="2">
            <param name="input1" value="file3.txt"/>
            <param name="input2" value="file3.txt"/>
            <conditional name="report_format">
                <param name="report_format_select" value="html"/>
                <param name="output_format" value="side-by-side"/>
            </conditional>
            <output name="diff_file">
                <assert_contents>
                    <has_n_lines n="0"/>
                </assert_contents>
            </output>