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comparison diff.xml @ 2:95a9dc82fc9a draft

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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diff commit 04afacfdfc505fb74219d0e6124afdce61e2ad8f"
author bgruening
date Wed, 03 Feb 2021 20:49:42 +0000
parents 02dfbbf869d8
children 156d0908e232
comparison
equal deleted inserted replaced
1:02dfbbf869d8 2:95a9dc82fc9a
1 <tool id="diff" name="diff" version="3.6+galaxy1"> 1 <tool id="diff" name="diff" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@">
2
3 <description>analyzes two files and generates an unidiff text file with information about the differences and an optional Html report</description> 2 <description>analyzes two files and generates an unidiff text file with information about the differences and an optional Html report</description>
4 3 <macros>
4 <token name="@TOOL_VERSION@">3.6</token>
5 <token name="@GALAXY_VERSION@">2</token>
6 </macros>
5 <requirements> 7 <requirements>
6 <requirement type="package" version="3.6">diffutils</requirement> 8 <requirement type="package" version="@TOOL_VERSION@">diffutils</requirement>
7 <requirement type="package" version="4.7">sed</requirement> 9 <requirement type="package" version="4.7">sed</requirement>
8 </requirements> 10 </requirements>
9
10 <stdio> 11 <stdio>
11 <exit_code range="2:" level="fatal" description="Something went wrong trying to check differences in files. Please check output log for more details." /> 12 <exit_code range="2:" level="fatal" description="Something went wrong trying to check differences in files. Please check output log for more details."/>
12 <regex match="diff: memory exhausted" source="stdout" level="fatal_oom" description="Out of memory error occurred" /> 13 <regex match="diff: memory exhausted" source="stdout" level="fatal_oom" description="Out of memory error occurred"/>
13 </stdio> 14 </stdio>
14 15 <command><![CDATA[
15 <command ><![CDATA[
16 diff -u '$input1' '$input2' > '$diff_file'; 16 diff -u '$input1' '$input2' > '$diff_file';
17 #if $generate_report: 17 #if $generate_report:
18 sed -e 's/@@title@@/Diff report for '$input1.element_identifier' and '$input2.element_identifier'/g' 18 sed -e 's/@@title@@/Diff report for "$input1.element_identifier" and "$input2.element_identifier"/g'
19 -e 's/@@outputformat@@/'$output_format'/g' 19 -e 's/@@outputformat@@/'$output_format'/g'
20 -e '/@@diffoutput@@/{r'$diff_file'' -e ';d}' 20 -e '/@@diffoutput@@/{r'$diff_file'' -e ';d}'
21 '$__tool_directory__/template.html' > '$html_file' 21 '$__tool_directory__/template.html' > '$html_file'
22 #end if 22 #end if
23 ]]> 23 ]]>
24 </command> 24 </command>
25
26 <inputs> 25 <inputs>
27 <param name="input1" type="data" format="txt" label="First input file" /> 26 <param name="input1" type="data" format="txt" label="First input file"/>
28 <param name="input2" type="data" format="txt" label="Second input file" /> 27 <param name="input2" type="data" format="txt" label="Second input file"/>
29 <param name="generate_report" type="boolean" checked="true" truevalue="true" falsevalue="false" label="Generate HTML report" help="Generates an HTML report to visualize the differences"/> 28 <param name="generate_report" type="boolean" checked="true" truevalue="true" falsevalue="false" label="Generate HTML report" help="Generates an HTML report to visualize the differences"/>
30 <param name="output_format" type="select" label="Choose report output format" help="Displays the differences in the report using the selected format. Either line by line or side by side."> 29 <param name="output_format" type="select" label="Choose report output format" help="Displays the differences in the report using the selected format. Either line by line or side by side.">
31 <option value="side-by-side">Side by side</option> 30 <option value="side-by-side">Side by side</option>
32 <option value="line-by-line">Line by line</option> 31 <option value="line-by-line">Line by line</option>
33 </param> 32 </param>
34 </inputs> 33 </inputs>
35
36 <outputs> 34 <outputs>
37 <data format="txt" name="diff_file" from_work_dir="output.txt" label="${tool.name} on ${on_string}: Raw Output" /> 35 <data format="txt" name="diff_file" from_work_dir="output.txt" label="${tool.name} on ${on_string}: Raw Output"/>
38 <data format="html" name="html_file" from_work_dir="output.html" label="${tool.name} on ${on_string}: Html Report"> 36 <data format="html" name="html_file" from_work_dir="output.html" label="${tool.name} on ${on_string}: Html Report">
39 <filter>generate_report is True</filter> 37 <filter>generate_report is True</filter>
40 </data> 38 </data>
41 </outputs> 39 </outputs>
42
43 <tests> 40 <tests>
44 <test expect_exit_code="0" expect_failure="false" expect_num_outputs="1"> 41 <test expect_exit_code="0" expect_failure="false" expect_num_outputs="1">
45 <param name="input1" value="file1.txt" /> 42 <param name="input1" value="file1.txt"/>
46 <param name="input2" value="file1.txt" /> 43 <param name="input2" value="file1.txt"/>
47 <param name="generate_report" value="false" /> 44 <param name="generate_report" value="false"/>
48 <output name="diff_file"> 45 <output name="diff_file">
49 <assert_contents> 46 <assert_contents>
50 <has_n_lines n="0" /> 47 <has_n_lines n="0"/>
51 </assert_contents> 48 </assert_contents>
52 </output> 49 </output>
53 </test> 50 </test>
54 <test expect_exit_code="1" expect_failure="false" expect_num_outputs="1"> 51 <test expect_exit_code="1" expect_failure="false" expect_num_outputs="1">
55 <param name="input1" value="file1.txt" /> 52 <param name="input1" value="file1.txt"/>
56 <param name="input2" value="file2.txt" /> 53 <param name="input2" value="file2.txt"/>
57 <param name="generate_report" value="false" /> 54 <param name="generate_report" value="false"/>
58 <output name="diff_file"> 55 <output name="diff_file">
59 <assert_contents> 56 <assert_contents>
60 <has_n_lines n="5" /> 57 <has_n_lines n="5"/>
61 <has_line line=" a" /> 58 <has_line line=" a"/>
62 <has_line line="+b" /> 59 <has_line line="+b"/>
63 </assert_contents> 60 </assert_contents>
64 </output> 61 </output>
65 </test> 62 </test>
66 <test expect_exit_code="0" expect_failure="false" expect_num_outputs="2"> 63 <test expect_exit_code="0" expect_failure="false" expect_num_outputs="2">
67 <param name="input1" value="file1.txt" /> 64 <param name="input1" value="file1.txt"/>
68 <param name="input2" value="file2.txt" /> 65 <param name="input2" value="file2.txt"/>
69 <param name="generate_report" value="true" /> 66 <param name="generate_report" value="true"/>
70 <output name="html_file"> 67 <output name="html_file">
71 <assert_contents> 68 <assert_contents>
72 <has_text text="!DOCTYPE html" /> 69 <has_text text="!DOCTYPE html"/>
73 </assert_contents> 70 </assert_contents>
74 </output> 71 </output>
75 </test> 72 </test>
76 <test expect_exit_code="0" expect_failure="false" expect_num_outputs="2"> 73 <test expect_exit_code="0" expect_failure="false" expect_num_outputs="2">
77 <param name="input1" value="file1.txt" /> 74 <param name="input1" value="file1.txt"/>
78 <param name="input2" value="file2.txt" /> 75 <param name="input2" value="file2.txt"/>
79 <param name="generate_report" value="true" /> 76 <param name="generate_report" value="true"/>
80 <param name="output_format" value="side-by-side" /> 77 <param name="output_format" value="side-by-side"/>
81 <output name="html_file"> 78 <output name="html_file">
82 <assert_contents> 79 <assert_contents>
83 <has_text text="!DOCTYPE html" /> 80 <has_text text="!DOCTYPE html"/>
84 <has_text text="side-by-side" /> 81 <has_text text="side-by-side"/>
85 </assert_contents> 82 </assert_contents>
86 </output> 83 </output>
87 </test> 84 </test>
88 <test expect_exit_code="0" expect_failure="false" expect_num_outputs="2"> 85 <test expect_exit_code="0" expect_failure="false" expect_num_outputs="2">
89 <param name="input1" value="file1.txt" /> 86 <param name="input1" value="file1.txt"/>
90 <param name="input2" value="file2.txt" /> 87 <param name="input2" value="file2.txt"/>
91 <param name="generate_report" value="true" /> 88 <param name="generate_report" value="true"/>
92 <param name="output_format" value="line-by-line" /> 89 <param name="output_format" value="line-by-line"/>
93 <output name="html_file"> 90 <output name="html_file">
94 <assert_contents> 91 <assert_contents>
95 <has_text text="!DOCTYPE html" /> 92 <has_text text="!DOCTYPE html"/>
96 <has_text text="line-by-line" /> 93 <has_text text="line-by-line"/>
94 </assert_contents>
95 </output>
96 </test>
97 <test expect_exit_code="0" expect_failure="false" expect_num_outputs="2">
98 <param name="input1" value="file 3.txt"/>
99 <param name="input2" value="file 3.txt"/>
100 <param name="generate_report" value="true"/>
101 <output name="diff_file">
102 <assert_contents>
103 <has_n_lines n="0"/>
104 </assert_contents>
105 </output>
106 <output name="html_file">
107 <assert_contents>
108 <has_text text="!DOCTYPE html"/>
97 </assert_contents> 109 </assert_contents>
98 </output> 110 </output>
99 </test> 111 </test>
100 </tests> 112 </tests>
101
102 <help><![CDATA[ 113 <help><![CDATA[
103 .. class:: infomark 114 .. class:: infomark
104 115
105 **Purpose** 116 **Purpose**
106 117
127 - or an **empty** file if the two input files are the same. 138 - or an **empty** file if the two input files are the same.
128 139
129 An **optional** *HTML report* with a friendlier visual representation of the differences. 140 An **optional** *HTML report* with a friendlier visual representation of the differences.
130 ]]> 141 ]]>
131 </help> 142 </help>
132
133 <citations> 143 <citations>
134 <citation type="bibtex"> 144 <citation type="bibtex">
135 @misc{gnudiffutils, 145 @misc{gnudiffutils,
136 author = {The Free Software Foundation (FSF), Inc}, 146 author = {The Free Software Foundation (FSF), Inc},
137 year = {2017}, 147 year = {2017},