Mercurial > repos > bgruening > diff

annotate diff.xml @ 3:156d0908e232 draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diff commit 978d7977e5f59f99e3d20a0df70f31ce577d0372"
author bgruening
date Fri, 12 Mar 2021 16:22:44 +0000
parents 95a9dc82fc9a
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
2
95a9dc82fc9a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diff commit 04afacfdfc505fb74219d0e6124afdce61e2ad8f"
bgruening
parents: 1
diff changeset
1 <tool id="diff" name="diff" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@">
1
02dfbbf869d8 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diff commit d1ef0f3da4118bf352c5acf720f277fc5ef07665"
bgruening
parents: 0
diff changeset
2 <description>analyzes two files and generates an unidiff text file with information about the differences and an optional Html report</description>
2
95a9dc82fc9a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diff commit 04afacfdfc505fb74219d0e6124afdce61e2ad8f"
bgruening
parents: 1
diff changeset
3 <macros>
3
156d0908e232 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diff commit 978d7977e5f59f99e3d20a0df70f31ce577d0372"
bgruening
parents: 2
diff changeset
4 <token name="@TOOL_VERSION@">3.7</token>
156d0908e232 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diff commit 978d7977e5f59f99e3d20a0df70f31ce577d0372"
bgruening
parents: 2
diff changeset
5 <token name="@GALAXY_VERSION@">0</token>
2
95a9dc82fc9a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diff commit 04afacfdfc505fb74219d0e6124afdce61e2ad8f"
bgruening
parents: 1
diff changeset
6 </macros>
0
8a18547725cf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diff commit 9b11cc5751c0931172d00799b246fcbd63660311"
bgruening
parents:
diff changeset
7 <requirements>
2
95a9dc82fc9a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diff commit 04afacfdfc505fb74219d0e6124afdce61e2ad8f"
bgruening
parents: 1
diff changeset
8 <requirement type="package" version="@TOOL_VERSION@">diffutils</requirement>
3
156d0908e232 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diff commit 978d7977e5f59f99e3d20a0df70f31ce577d0372"
bgruening
parents: 2
diff changeset
9 <requirement type="package" version="4.8">sed</requirement>
0
8a18547725cf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diff commit 9b11cc5751c0931172d00799b246fcbd63660311"
bgruening
parents:
diff changeset
10 </requirements>
8a18547725cf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diff commit 9b11cc5751c0931172d00799b246fcbd63660311"
bgruening
parents:
diff changeset
11 <stdio>
2
95a9dc82fc9a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diff commit 04afacfdfc505fb74219d0e6124afdce61e2ad8f"
bgruening
parents: 1
diff changeset
12 <exit_code range="2:" level="fatal" description="Something went wrong trying to check differences in files. Please check output log for more details."/>
95a9dc82fc9a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diff commit 04afacfdfc505fb74219d0e6124afdce61e2ad8f"
bgruening
parents: 1
diff changeset
13 <regex match="diff: memory exhausted" source="stdout" level="fatal_oom" description="Out of memory error occurred"/>
0
8a18547725cf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diff commit 9b11cc5751c0931172d00799b246fcbd63660311"
bgruening
parents:
diff changeset
14 </stdio>
2
95a9dc82fc9a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diff commit 04afacfdfc505fb74219d0e6124afdce61e2ad8f"
bgruening
parents: 1
diff changeset
15 <command><![CDATA[
1
02dfbbf869d8 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diff commit d1ef0f3da4118bf352c5acf720f277fc5ef07665"
bgruening
parents: 0
diff changeset
16 diff -u '$input1' '$input2' > '$diff_file';
02dfbbf869d8 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diff commit d1ef0f3da4118bf352c5acf720f277fc5ef07665"
bgruening
parents: 0
diff changeset
17 #if $generate_report:
2
95a9dc82fc9a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diff commit 04afacfdfc505fb74219d0e6124afdce61e2ad8f"
bgruening
parents: 1
diff changeset
18 sed -e 's/@@title@@/Diff report for "$input1.element_identifier" and "$input2.element_identifier"/g'
1
02dfbbf869d8 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diff commit d1ef0f3da4118bf352c5acf720f277fc5ef07665"
bgruening
parents: 0
diff changeset
19 -e 's/@@outputformat@@/'$output_format'/g'
02dfbbf869d8 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diff commit d1ef0f3da4118bf352c5acf720f277fc5ef07665"
bgruening
parents: 0
diff changeset
20 -e '/@@diffoutput@@/{r'$diff_file'' -e ';d}'
02dfbbf869d8 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diff commit d1ef0f3da4118bf352c5acf720f277fc5ef07665"
bgruening
parents: 0
diff changeset
21 '$__tool_directory__/template.html' > '$html_file'
02dfbbf869d8 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diff commit d1ef0f3da4118bf352c5acf720f277fc5ef07665"
bgruening
parents: 0
diff changeset
22 #end if
0
8a18547725cf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diff commit 9b11cc5751c0931172d00799b246fcbd63660311"
bgruening
parents:
diff changeset
23 ]]>
8a18547725cf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diff commit 9b11cc5751c0931172d00799b246fcbd63660311"
bgruening
parents:
diff changeset
24 </command>
8a18547725cf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diff commit 9b11cc5751c0931172d00799b246fcbd63660311"
bgruening
parents:
diff changeset
25 <inputs>
2
95a9dc82fc9a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diff commit 04afacfdfc505fb74219d0e6124afdce61e2ad8f"
bgruening
parents: 1
diff changeset
26 <param name="input1" type="data" format="txt" label="First input file"/>
95a9dc82fc9a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diff commit 04afacfdfc505fb74219d0e6124afdce61e2ad8f"
bgruening
parents: 1
diff changeset
27 <param name="input2" type="data" format="txt" label="Second input file"/>
1
02dfbbf869d8 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diff commit d1ef0f3da4118bf352c5acf720f277fc5ef07665"
bgruening
parents: 0
diff changeset
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"/>
02dfbbf869d8 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diff commit d1ef0f3da4118bf352c5acf720f277fc5ef07665"
bgruening
parents: 0
diff changeset
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.">
02dfbbf869d8 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diff commit d1ef0f3da4118bf352c5acf720f277fc5ef07665"
bgruening
parents: 0
diff changeset
30 <option value="side-by-side">Side by side</option>
02dfbbf869d8 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diff commit d1ef0f3da4118bf352c5acf720f277fc5ef07665"
bgruening
parents: 0
diff changeset
31 <option value="line-by-line">Line by line</option>
02dfbbf869d8 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diff commit d1ef0f3da4118bf352c5acf720f277fc5ef07665"
bgruening
parents: 0
diff changeset
32 </param>
0
8a18547725cf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diff commit 9b11cc5751c0931172d00799b246fcbd63660311"
bgruening
parents:
diff changeset
33 </inputs>
8a18547725cf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diff commit 9b11cc5751c0931172d00799b246fcbd63660311"
bgruening
parents:
diff changeset
34 <outputs>
2
95a9dc82fc9a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diff commit 04afacfdfc505fb74219d0e6124afdce61e2ad8f"
bgruening
parents: 1
diff changeset
35 <data format="txt" name="diff_file" from_work_dir="output.txt" label="${tool.name} on ${on_string}: Raw Output"/>
1
02dfbbf869d8 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diff commit d1ef0f3da4118bf352c5acf720f277fc5ef07665"
bgruening
parents: 0
diff changeset
36 <data format="html" name="html_file" from_work_dir="output.html" label="${tool.name} on ${on_string}: Html Report">
02dfbbf869d8 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diff commit d1ef0f3da4118bf352c5acf720f277fc5ef07665"
bgruening
parents: 0
diff changeset
37 <filter>generate_report is True</filter>
02dfbbf869d8 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diff commit d1ef0f3da4118bf352c5acf720f277fc5ef07665"
bgruening
parents: 0
diff changeset
38 </data>
0
8a18547725cf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diff commit 9b11cc5751c0931172d00799b246fcbd63660311"
bgruening
parents:
diff changeset
39 </outputs>
8a18547725cf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diff commit 9b11cc5751c0931172d00799b246fcbd63660311"
bgruening
parents:
diff changeset
40 <tests>
1
02dfbbf869d8 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diff commit d1ef0f3da4118bf352c5acf720f277fc5ef07665"
bgruening
parents: 0
diff changeset
41 <test expect_exit_code="0" expect_failure="false" expect_num_outputs="1">
2
95a9dc82fc9a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diff commit 04afacfdfc505fb74219d0e6124afdce61e2ad8f"
bgruening
parents: 1
diff changeset
42 <param name="input1" value="file1.txt"/>
95a9dc82fc9a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diff commit 04afacfdfc505fb74219d0e6124afdce61e2ad8f"
bgruening
parents: 1
diff changeset
43 <param name="input2" value="file1.txt"/>
95a9dc82fc9a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diff commit 04afacfdfc505fb74219d0e6124afdce61e2ad8f"
bgruening
parents: 1
diff changeset
44 <param name="generate_report" value="false"/>
1
02dfbbf869d8 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diff commit d1ef0f3da4118bf352c5acf720f277fc5ef07665"
bgruening
parents: 0
diff changeset
45 <output name="diff_file">
0
8a18547725cf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diff commit 9b11cc5751c0931172d00799b246fcbd63660311"
bgruening
parents:
diff changeset
46 <assert_contents>
2
95a9dc82fc9a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diff commit 04afacfdfc505fb74219d0e6124afdce61e2ad8f"
bgruening
parents: 1
diff changeset
47 <has_n_lines n="0"/>
0
8a18547725cf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diff commit 9b11cc5751c0931172d00799b246fcbd63660311"
bgruening
parents:
diff changeset
48 </assert_contents>
8a18547725cf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diff commit 9b11cc5751c0931172d00799b246fcbd63660311"
bgruening
parents:
diff changeset
49 </output>
8a18547725cf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diff commit 9b11cc5751c0931172d00799b246fcbd63660311"
bgruening
parents:
diff changeset
50 </test>
1
02dfbbf869d8 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diff commit d1ef0f3da4118bf352c5acf720f277fc5ef07665"
bgruening
parents: 0
diff changeset
51 <test expect_exit_code="1" expect_failure="false" expect_num_outputs="1">
2
95a9dc82fc9a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diff commit 04afacfdfc505fb74219d0e6124afdce61e2ad8f"
bgruening
parents: 1
diff changeset
52 <param name="input1" value="file1.txt"/>
95a9dc82fc9a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diff commit 04afacfdfc505fb74219d0e6124afdce61e2ad8f"
bgruening
parents: 1
diff changeset
53 <param name="input2" value="file2.txt"/>
95a9dc82fc9a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diff commit 04afacfdfc505fb74219d0e6124afdce61e2ad8f"
bgruening
parents: 1
diff changeset
54 <param name="generate_report" value="false"/>
1
02dfbbf869d8 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diff commit d1ef0f3da4118bf352c5acf720f277fc5ef07665"
bgruening
parents: 0
diff changeset
55 <output name="diff_file">
0
8a18547725cf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diff commit 9b11cc5751c0931172d00799b246fcbd63660311"
bgruening
parents:
diff changeset
56 <assert_contents>
2
95a9dc82fc9a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diff commit 04afacfdfc505fb74219d0e6124afdce61e2ad8f"
bgruening
parents: 1
diff changeset
57 <has_n_lines n="5"/>
95a9dc82fc9a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diff commit 04afacfdfc505fb74219d0e6124afdce61e2ad8f"
bgruening
parents: 1
diff changeset
58 <has_line line=" a"/>
95a9dc82fc9a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diff commit 04afacfdfc505fb74219d0e6124afdce61e2ad8f"
bgruening
parents: 1
diff changeset
59 <has_line line="+b"/>
95a9dc82fc9a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diff commit 04afacfdfc505fb74219d0e6124afdce61e2ad8f"
bgruening
parents: 1
diff changeset
60 </assert_contents>
95a9dc82fc9a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diff commit 04afacfdfc505fb74219d0e6124afdce61e2ad8f"
bgruening
parents: 1
diff changeset
61 </output>
95a9dc82fc9a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diff commit 04afacfdfc505fb74219d0e6124afdce61e2ad8f"
bgruening
parents: 1
diff changeset
62 </test>
95a9dc82fc9a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diff commit 04afacfdfc505fb74219d0e6124afdce61e2ad8f"
bgruening
parents: 1
diff changeset
63 <test expect_exit_code="0" expect_failure="false" expect_num_outputs="2">
95a9dc82fc9a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diff commit 04afacfdfc505fb74219d0e6124afdce61e2ad8f"
bgruening
parents: 1
diff changeset
64 <param name="input1" value="file1.txt"/>
95a9dc82fc9a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diff commit 04afacfdfc505fb74219d0e6124afdce61e2ad8f"
bgruening
parents: 1
diff changeset
65 <param name="input2" value="file2.txt"/>
95a9dc82fc9a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diff commit 04afacfdfc505fb74219d0e6124afdce61e2ad8f"
bgruening
parents: 1
diff changeset
66 <param name="generate_report" value="true"/>
95a9dc82fc9a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diff commit 04afacfdfc505fb74219d0e6124afdce61e2ad8f"
bgruening
parents: 1
diff changeset
67 <output name="html_file">
95a9dc82fc9a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diff commit 04afacfdfc505fb74219d0e6124afdce61e2ad8f"
bgruening
parents: 1
diff changeset
68 <assert_contents>
95a9dc82fc9a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diff commit 04afacfdfc505fb74219d0e6124afdce61e2ad8f"
bgruening
parents: 1
diff changeset
69 <has_text text="!DOCTYPE html"/>
0
8a18547725cf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diff commit 9b11cc5751c0931172d00799b246fcbd63660311"
bgruening
parents:
diff changeset
70 </assert_contents>
8a18547725cf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diff commit 9b11cc5751c0931172d00799b246fcbd63660311"
bgruening
parents:
diff changeset
71 </output>
8a18547725cf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diff commit 9b11cc5751c0931172d00799b246fcbd63660311"
bgruening
parents:
diff changeset
72 </test>
1
02dfbbf869d8 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diff commit d1ef0f3da4118bf352c5acf720f277fc5ef07665"
bgruening
parents: 0
diff changeset
73 <test expect_exit_code="0" expect_failure="false" expect_num_outputs="2">
2
95a9dc82fc9a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diff commit 04afacfdfc505fb74219d0e6124afdce61e2ad8f"
bgruening
parents: 1
diff changeset
74 <param name="input1" value="file1.txt"/>
95a9dc82fc9a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diff commit 04afacfdfc505fb74219d0e6124afdce61e2ad8f"
bgruening
parents: 1
diff changeset
75 <param name="input2" value="file2.txt"/>
95a9dc82fc9a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diff commit 04afacfdfc505fb74219d0e6124afdce61e2ad8f"
bgruening
parents: 1
diff changeset
76 <param name="generate_report" value="true"/>
95a9dc82fc9a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diff commit 04afacfdfc505fb74219d0e6124afdce61e2ad8f"
bgruening
parents: 1
diff changeset
77 <param name="output_format" value="side-by-side"/>
1
02dfbbf869d8 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diff commit d1ef0f3da4118bf352c5acf720f277fc5ef07665"
bgruening
parents: 0
diff changeset
78 <output name="html_file">
02dfbbf869d8 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diff commit d1ef0f3da4118bf352c5acf720f277fc5ef07665"
bgruening
parents: 0
diff changeset
79 <assert_contents>
2
95a9dc82fc9a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diff commit 04afacfdfc505fb74219d0e6124afdce61e2ad8f"
bgruening
parents: 1
diff changeset
80 <has_text text="!DOCTYPE html"/>
95a9dc82fc9a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diff commit 04afacfdfc505fb74219d0e6124afdce61e2ad8f"
bgruening
parents: 1
diff changeset
81 <has_text text="side-by-side"/>
1
02dfbbf869d8 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diff commit d1ef0f3da4118bf352c5acf720f277fc5ef07665"
bgruening
parents: 0
diff changeset
82 </assert_contents>
02dfbbf869d8 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diff commit d1ef0f3da4118bf352c5acf720f277fc5ef07665"
bgruening
parents: 0
diff changeset
83 </output>
02dfbbf869d8 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diff commit d1ef0f3da4118bf352c5acf720f277fc5ef07665"
bgruening
parents: 0
diff changeset
84 </test>
02dfbbf869d8 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diff commit d1ef0f3da4118bf352c5acf720f277fc5ef07665"
bgruening
parents: 0
diff changeset
85 <test expect_exit_code="0" expect_failure="false" expect_num_outputs="2">
2
95a9dc82fc9a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diff commit 04afacfdfc505fb74219d0e6124afdce61e2ad8f"
bgruening
parents: 1
diff changeset
86 <param name="input1" value="file1.txt"/>
95a9dc82fc9a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diff commit 04afacfdfc505fb74219d0e6124afdce61e2ad8f"
bgruening
parents: 1
diff changeset
87 <param name="input2" value="file2.txt"/>
95a9dc82fc9a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diff commit 04afacfdfc505fb74219d0e6124afdce61e2ad8f"
bgruening
parents: 1
diff changeset
88 <param name="generate_report" value="true"/>
95a9dc82fc9a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diff commit 04afacfdfc505fb74219d0e6124afdce61e2ad8f"
bgruening
parents: 1
diff changeset
89 <param name="output_format" value="line-by-line"/>
1
02dfbbf869d8 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diff commit d1ef0f3da4118bf352c5acf720f277fc5ef07665"
bgruening
parents: 0
diff changeset
90 <output name="html_file">
02dfbbf869d8 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diff commit d1ef0f3da4118bf352c5acf720f277fc5ef07665"
bgruening
parents: 0
diff changeset
91 <assert_contents>
2
95a9dc82fc9a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diff commit 04afacfdfc505fb74219d0e6124afdce61e2ad8f"
bgruening
parents: 1
diff changeset
92 <has_text text="!DOCTYPE html"/>
95a9dc82fc9a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diff commit 04afacfdfc505fb74219d0e6124afdce61e2ad8f"
bgruening
parents: 1
diff changeset
93 <has_text text="line-by-line"/>
1
02dfbbf869d8 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diff commit d1ef0f3da4118bf352c5acf720f277fc5ef07665"
bgruening
parents: 0
diff changeset
94 </assert_contents>
02dfbbf869d8 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diff commit d1ef0f3da4118bf352c5acf720f277fc5ef07665"
bgruening
parents: 0
diff changeset
95 </output>
02dfbbf869d8 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diff commit d1ef0f3da4118bf352c5acf720f277fc5ef07665"
bgruening
parents: 0
diff changeset
96 </test>
02dfbbf869d8 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diff commit d1ef0f3da4118bf352c5acf720f277fc5ef07665"
bgruening
parents: 0
diff changeset
97 <test expect_exit_code="0" expect_failure="false" expect_num_outputs="2">
2
95a9dc82fc9a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diff commit 04afacfdfc505fb74219d0e6124afdce61e2ad8f"
bgruening
parents: 1
diff changeset
98 <param name="input1" value="file 3.txt"/>
95a9dc82fc9a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diff commit 04afacfdfc505fb74219d0e6124afdce61e2ad8f"
bgruening
parents: 1
diff changeset
99 <param name="input2" value="file 3.txt"/>
95a9dc82fc9a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diff commit 04afacfdfc505fb74219d0e6124afdce61e2ad8f"
bgruening
parents: 1
diff changeset
100 <param name="generate_report" value="true"/>
95a9dc82fc9a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diff commit 04afacfdfc505fb74219d0e6124afdce61e2ad8f"
bgruening
parents: 1
diff changeset
101 <output name="diff_file">
95a9dc82fc9a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diff commit 04afacfdfc505fb74219d0e6124afdce61e2ad8f"
bgruening
parents: 1
diff changeset
102 <assert_contents>
95a9dc82fc9a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diff commit 04afacfdfc505fb74219d0e6124afdce61e2ad8f"
bgruening
parents: 1
diff changeset
103 <has_n_lines n="0"/>
95a9dc82fc9a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diff commit 04afacfdfc505fb74219d0e6124afdce61e2ad8f"
bgruening
parents: 1
diff changeset
104 </assert_contents>
95a9dc82fc9a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diff commit 04afacfdfc505fb74219d0e6124afdce61e2ad8f"
bgruening
parents: 1
diff changeset
105 </output>
1
02dfbbf869d8 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diff commit d1ef0f3da4118bf352c5acf720f277fc5ef07665"
bgruening
parents: 0
diff changeset
106 <output name="html_file">
02dfbbf869d8 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diff commit d1ef0f3da4118bf352c5acf720f277fc5ef07665"
bgruening
parents: 0
diff changeset
107 <assert_contents>
2
95a9dc82fc9a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diff commit 04afacfdfc505fb74219d0e6124afdce61e2ad8f"
bgruening
parents: 1
diff changeset
108 <has_text text="!DOCTYPE html"/>
1
02dfbbf869d8 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diff commit d1ef0f3da4118bf352c5acf720f277fc5ef07665"
bgruening
parents: 0
diff changeset
109 </assert_contents>
02dfbbf869d8 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diff commit d1ef0f3da4118bf352c5acf720f277fc5ef07665"
bgruening
parents: 0
diff changeset
110 </output>
02dfbbf869d8 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diff commit d1ef0f3da4118bf352c5acf720f277fc5ef07665"
bgruening
parents: 0
diff changeset
111 </test>
0
8a18547725cf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diff commit 9b11cc5751c0931172d00799b246fcbd63660311"
bgruening
parents:
diff changeset
112 </tests>
8a18547725cf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diff commit 9b11cc5751c0931172d00799b246fcbd63660311"
bgruening
parents:
diff changeset
113 <help><![CDATA[
8a18547725cf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diff commit 9b11cc5751c0931172d00799b246fcbd63660311"
bgruening
parents:
diff changeset
114 .. class:: infomark
8a18547725cf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diff commit 9b11cc5751c0931172d00799b246fcbd63660311"
bgruening
parents:
diff changeset
115
8a18547725cf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diff commit 9b11cc5751c0931172d00799b246fcbd63660311"
bgruening
parents:
diff changeset
116 **Purpose**
8a18547725cf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diff commit 9b11cc5751c0931172d00799b246fcbd63660311"
bgruening
parents:
diff changeset
117
8a18547725cf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diff commit 9b11cc5751c0931172d00799b246fcbd63660311"
bgruening
parents:
diff changeset
118 The **diff** utility is a data comparison tool that calculates and displays the differences between two files.
8a18547725cf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diff commit 9b11cc5751c0931172d00799b246fcbd63660311"
bgruening
parents:
diff changeset
119
8a18547725cf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diff commit 9b11cc5751c0931172d00799b246fcbd63660311"
bgruening
parents:
diff changeset
120 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.
8a18547725cf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diff commit 9b11cc5751c0931172d00799b246fcbd63660311"
bgruening
parents:
diff changeset
121
8a18547725cf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diff commit 9b11cc5751c0931172d00799b246fcbd63660311"
bgruening
parents:
diff changeset
122 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.
8a18547725cf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diff commit 9b11cc5751c0931172d00799b246fcbd63660311"
bgruening
parents:
diff changeset
123
8a18547725cf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diff commit 9b11cc5751c0931172d00799b246fcbd63660311"
bgruening
parents:
diff changeset
124 .. class:: infomark
8a18547725cf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diff commit 9b11cc5751c0931172d00799b246fcbd63660311"
bgruening
parents:
diff changeset
125
8a18547725cf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diff commit 9b11cc5751c0931172d00799b246fcbd63660311"
bgruening
parents:
diff changeset
126 **Input**
8a18547725cf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diff commit 9b11cc5751c0931172d00799b246fcbd63660311"
bgruening
parents:
diff changeset
127
8a18547725cf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diff commit 9b11cc5751c0931172d00799b246fcbd63660311"
bgruening
parents:
diff changeset
128 Two text files to be checked for differences line by line.
8a18547725cf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diff commit 9b11cc5751c0931172d00799b246fcbd63660311"
bgruening
parents:
diff changeset
129
8a18547725cf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diff commit 9b11cc5751c0931172d00799b246fcbd63660311"
bgruening
parents:
diff changeset
130 .. class:: infomark
8a18547725cf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diff commit 9b11cc5751c0931172d00799b246fcbd63660311"
bgruening
parents:
diff changeset
131
8a18547725cf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diff commit 9b11cc5751c0931172d00799b246fcbd63660311"
bgruening
parents:
diff changeset
132 **Output**
8a18547725cf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diff commit 9b11cc5751c0931172d00799b246fcbd63660311"
bgruening
parents:
diff changeset
133
1
02dfbbf869d8 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diff commit d1ef0f3da4118bf352c5acf720f277fc5ef07665"
bgruening
parents: 0
diff changeset
134 A *text file*, either:
0
8a18547725cf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diff commit 9b11cc5751c0931172d00799b246fcbd63660311"
bgruening
parents:
diff changeset
135
8a18547725cf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diff commit 9b11cc5751c0931172d00799b246fcbd63660311"
bgruening
parents:
diff changeset
136 - containing the lines differences in **unified format** (*unidiff*),
8a18547725cf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diff commit 9b11cc5751c0931172d00799b246fcbd63660311"
bgruening
parents:
diff changeset
137
8a18547725cf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diff commit 9b11cc5751c0931172d00799b246fcbd63660311"
bgruening
parents:
diff changeset
138 - or an **empty** file if the two input files are the same.
1
02dfbbf869d8 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diff commit d1ef0f3da4118bf352c5acf720f277fc5ef07665"
bgruening
parents: 0
diff changeset
139
02dfbbf869d8 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diff commit d1ef0f3da4118bf352c5acf720f277fc5ef07665"
bgruening
parents: 0
diff changeset
140 An **optional** *HTML report* with a friendlier visual representation of the differences.
0
8a18547725cf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diff commit 9b11cc5751c0931172d00799b246fcbd63660311"
bgruening
parents:
diff changeset
141 ]]>
8a18547725cf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diff commit 9b11cc5751c0931172d00799b246fcbd63660311"
bgruening
parents:
diff changeset
142 </help>
8a18547725cf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diff commit 9b11cc5751c0931172d00799b246fcbd63660311"
bgruening
parents:
diff changeset
143 <citations>
8a18547725cf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diff commit 9b11cc5751c0931172d00799b246fcbd63660311"
bgruening
parents:
diff changeset
144 <citation type="bibtex">
8a18547725cf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diff commit 9b11cc5751c0931172d00799b246fcbd63660311"
bgruening
parents:
diff changeset
145 @misc{gnudiffutils,
8a18547725cf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diff commit 9b11cc5751c0931172d00799b246fcbd63660311"
bgruening
parents:
diff changeset
146 author = {The Free Software Foundation (FSF), Inc},
8a18547725cf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diff commit 9b11cc5751c0931172d00799b246fcbd63660311"
bgruening
parents:
diff changeset
147 year = {2017},
8a18547725cf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diff commit 9b11cc5751c0931172d00799b246fcbd63660311"
bgruening
parents:
diff changeset
148 title = {diff (GNU diffutils)},
8a18547725cf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diff commit 9b11cc5751c0931172d00799b246fcbd63660311"
bgruening
parents:
diff changeset
149 publisher = {The Free Software Foundation (FSF), Inc},
8a18547725cf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diff commit 9b11cc5751c0931172d00799b246fcbd63660311"
bgruening
parents:
diff changeset
150 url = {http://www.gnu.org/software/diffutils/},
8a18547725cf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diff commit 9b11cc5751c0931172d00799b246fcbd63660311"
bgruening
parents:
diff changeset
151 }
8a18547725cf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diff commit 9b11cc5751c0931172d00799b246fcbd63660311"
bgruening
parents:
diff changeset
152 </citation>
1
02dfbbf869d8 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diff commit d1ef0f3da4118bf352c5acf720f277fc5ef07665"
bgruening
parents: 0
diff changeset
153 <citation type="bibtex">
02dfbbf869d8 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diff commit d1ef0f3da4118bf352c5acf720f277fc5ef07665"
bgruening
parents: 0
diff changeset
154 @misc{diff2html,
02dfbbf869d8 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diff commit d1ef0f3da4118bf352c5acf720f277fc5ef07665"
bgruening
parents: 0
diff changeset
155 author = {Rodrigo Fernandes},
02dfbbf869d8 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diff commit d1ef0f3da4118bf352c5acf720f277fc5ef07665"
bgruening
parents: 0
diff changeset
156 year = {2014},
02dfbbf869d8 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diff commit d1ef0f3da4118bf352c5acf720f277fc5ef07665"
bgruening
parents: 0
diff changeset
157 title = {Pretty diff to html javascript library (diff2html)},
02dfbbf869d8 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diff commit d1ef0f3da4118bf352c5acf720f277fc5ef07665"
bgruening
parents: 0
diff changeset
158 publisher = {Github},
02dfbbf869d8 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diff commit d1ef0f3da4118bf352c5acf720f277fc5ef07665"
bgruening
parents: 0
diff changeset
159 url = {https://github.com/rtfpessoa/diff2html},
02dfbbf869d8 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diff commit d1ef0f3da4118bf352c5acf720f277fc5ef07665"
bgruening
parents: 0
diff changeset
160 }
02dfbbf869d8 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diff commit d1ef0f3da4118bf352c5acf720f277fc5ef07665"
bgruening
parents: 0
diff changeset
161 </citation>
02dfbbf869d8 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diff commit d1ef0f3da4118bf352c5acf720f277fc5ef07665"
bgruening
parents: 0
diff changeset
162 <citation type="bibtex">
02dfbbf869d8 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diff commit d1ef0f3da4118bf352c5acf720f277fc5ef07665"
bgruening
parents: 0
diff changeset
163 @misc{sed,
02dfbbf869d8 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diff commit d1ef0f3da4118bf352c5acf720f277fc5ef07665"
bgruening
parents: 0
diff changeset
164 author = {The Free Software Foundation (FSF), Inc},
02dfbbf869d8 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diff commit d1ef0f3da4118bf352c5acf720f277fc5ef07665"
bgruening
parents: 0
diff changeset
165 year = {2017},
02dfbbf869d8 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diff commit d1ef0f3da4118bf352c5acf720f277fc5ef07665"
bgruening
parents: 0
diff changeset
166 title = {sed (GNU sed)},
02dfbbf869d8 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diff commit d1ef0f3da4118bf352c5acf720f277fc5ef07665"
bgruening
parents: 0
diff changeset
167 publisher = {The Free Software Foundation (FSF), Inc},
02dfbbf869d8 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diff commit d1ef0f3da4118bf352c5acf720f277fc5ef07665"
bgruening
parents: 0
diff changeset
168 url = {http://www.gnu.org/software/sed/},
02dfbbf869d8 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diff commit d1ef0f3da4118bf352c5acf720f277fc5ef07665"
bgruening
parents: 0
diff changeset
169 }
02dfbbf869d8 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diff commit d1ef0f3da4118bf352c5acf720f277fc5ef07665"
bgruening
parents: 0
diff changeset
170 </citation>
0
8a18547725cf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diff commit 9b11cc5751c0931172d00799b246fcbd63660311"
bgruening
parents:
diff changeset
171 </citations>
8a18547725cf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diff commit 9b11cc5751c0931172d00799b246fcbd63660311"
bgruening
parents:
diff changeset
172 </tool>