comparison diff.xml @ 1:02dfbbf869d8 draft

"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diff commit d1ef0f3da4118bf352c5acf720f277fc5ef07665"

0:8a18547725cf

<tool id="diff" name="diff" version="3.6+galaxy0">

    <description>analyzes two files and generates a text file with information about the lines that are different</description>

    <requirements>
        <requirement type="package" version="3.6">diffutils</requirement>
    </requirements>

    <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' > '$output1'
    ]]>
    </command>

    <inputs>
        <param name="input1" type="data" format="txt" label="First input file" />
        <param name="input2" type="data" format="txt" label="Second input file" />
    </inputs>

    <outputs>
        <data name="output1" format="txt" />
    </outputs>

    <tests>
        <test expect_exit_code="0" expect_failure="false">
            <param name="input1" value="file1.txt" />
            <param name="input2" value="file1.txt" />
            <output name="output1">
                <assert_contents>
                    <has_n_lines n="0" />
                </assert_contents>
            </output>
        </test>
        <test expect_exit_code="1" expect_failure="false">
            <param name="input1" value="file1.txt" />
            <param name="input2" value="file2.txt" />
            <output name="output1">
                <assert_contents>
                    <has_n_lines n="5" />
                    <has_line line=" a" />
                    <has_line line="+b" />
                </assert_contents>
            </output>
        </test>
    </tests>

.. class:: infomark

**Output**

A *single text file*, either:

- containing the lines differences in **unified format** (*unidiff*),

- or an **empty** file if the two input files are the same.
    ]]>
    </help>

    <citations>
        <citation type="bibtex">

            title = {diff (GNU diffutils)},
            publisher = {The Free Software Foundation (FSF), Inc},
            url = {http://www.gnu.org/software/diffutils/},
            }
        </citation>
    </citations>
</tool>

1:02dfbbf869d8

<tool id="diff" name="diff" version="3.6+galaxy1">

    <description>analyzes two files and generates an unidiff text file with information about the differences and an optional Html report</description>

    <requirements>
        <requirement type="package" version="3.6">diffutils</requirement>
        <requirement type="package" version="4.7">sed</requirement>
    </requirements>

    <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" />
                </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" />
            <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>
    </tests>

.. class:: infomark

**Output**

A *text file*, either:

- containing the lines differences in **unified format** (*unidiff*),

- or an **empty** file if the two input files are the same.

An **optional** *HTML report* with a friendlier visual representation of the differences.
    ]]>
    </help>

    <citations>
        <citation type="bibtex">

            title = {diff (GNU diffutils)},
            publisher = {The Free Software Foundation (FSF), Inc},
            url = {http://www.gnu.org/software/diffutils/},
            }
        </citation>
        <citation type="bibtex">
            @misc{diff2html,
            author = {Rodrigo Fernandes},
            year = {2014},
            title = {Pretty diff to html javascript library (diff2html)},
            publisher = {Github},
            url = {https://github.com/rtfpessoa/diff2html},
            }
        </citation>
        <citation type="bibtex">
            @misc{sed,
            author = {The Free Software Foundation (FSF), Inc},
            year = {2017},
            title = {sed (GNU sed)},
            publisher = {The Free Software Foundation (FSF), Inc},
            url = {http://www.gnu.org/software/sed/},
            }
        </citation>
    </citations>
</tool>