<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>

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

**Purpose**

The **diff** utility is a data comparison tool that calculates and displays the differences between two files.

Unlike edit distance notions used for other purposes, diff is line-oriented rather than character-oriented, but it is like Levenshtein distance in that it tries to determine the smallest set of deletions and insertions to create one file from the other.

The diff command displays the changes made in a standard format, such that both humans and machines can understand the changes and apply them: given one file and the changes, the other file can be created.

.. class:: infomark

**Input**

Two text files to be checked for differences line by line.

.. 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">
            @misc{gnudiffutils,
            author = {The Free Software Foundation (FSF), Inc},
            year = {2017},
            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>