diff diff.xml @ 1:02dfbbf869d8 draft

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

--- a/diff.xml	Tue Mar 31 16:36:28 2020 -0400
+++ b/diff.xml	Tue Apr 14 13:56:01 2020 -0400
@@ -1,9 +1,10 @@
-<tool id="diff" name="diff" version="3.6+galaxy0">
+<tool id="diff" name="diff" version="3.6+galaxy1">
 
-    <description>analyzes two files and generates a text file with information about the lines that are different</description>
+    <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>
@@ -12,33 +13,49 @@
     </stdio>
 
     <command ><![CDATA[
-        diff -u '$input1' '$input2' > '$output1'
+        diff -u '$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 name="output1" format="txt" />
+        <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">
+        <test expect_exit_code="0" expect_failure="false" expect_num_outputs="1">
             <param name="input1" value="file1.txt" />
             <param name="input2" value="file1.txt" />
-            <output name="output1">
+            <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">
+        <test expect_exit_code="1" expect_failure="false" expect_num_outputs="1">
             <param name="input1" value="file1.txt" />
             <param name="input2" value="file2.txt" />
-            <output name="output1">
+            <param name="generate_report" value="false" />
+            <output name="diff_file">
                 <assert_contents>
                     <has_n_lines n="5" />
                     <has_line line=" a" />
@@ -46,6 +63,40 @@
                 </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[
@@ -69,11 +120,13 @@
 
 **Output**
 
-A *single text file*, either:
+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>
 
@@ -87,5 +140,23 @@
             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>