Mercurial > repos > bgruening > diff

annotate diff.xml @ 1:02dfbbf869d8 draft

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 d1ef0f3da4118bf352c5acf720f277fc5ef07665"
author bgruening
date Tue, 14 Apr 2020 13:56:01 -0400
parents 8a18547725cf
children 95a9dc82fc9a
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
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02dfbbf869d8 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diff commit d1ef0f3da4118bf352c5acf720f277fc5ef07665"
bgruening
parents: 0
diff changeset
1 <tool id="diff" name="diff" version="3.6+galaxy1">
0
8a18547725cf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diff commit 9b11cc5751c0931172d00799b246fcbd63660311"
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2
1
02dfbbf869d8 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diff commit d1ef0f3da4118bf352c5acf720f277fc5ef07665"
bgruening
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3 <description>analyzes two files and generates an unidiff text file with information about the differences and an optional Html report</description>
0
8a18547725cf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diff commit 9b11cc5751c0931172d00799b246fcbd63660311"
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4
8a18547725cf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diff commit 9b11cc5751c0931172d00799b246fcbd63660311"
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5 <requirements>
8a18547725cf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diff commit 9b11cc5751c0931172d00799b246fcbd63660311"
bgruening
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6 <requirement type="package" version="3.6">diffutils</requirement>
1
02dfbbf869d8 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diff commit d1ef0f3da4118bf352c5acf720f277fc5ef07665"
bgruening
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7 <requirement type="package" version="4.7">sed</requirement>
0
8a18547725cf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diff commit 9b11cc5751c0931172d00799b246fcbd63660311"
bgruening
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8 </requirements>
8a18547725cf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diff commit 9b11cc5751c0931172d00799b246fcbd63660311"
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9
8a18547725cf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diff commit 9b11cc5751c0931172d00799b246fcbd63660311"
bgruening
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10 <stdio>
8a18547725cf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diff commit 9b11cc5751c0931172d00799b246fcbd63660311"
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11 <exit_code range="2:" level="fatal" description="Something went wrong trying to check differences in files. Please check output log for more details." />
8a18547725cf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diff commit 9b11cc5751c0931172d00799b246fcbd63660311"
bgruening
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12 <regex match="diff: memory exhausted" source="stdout" level="fatal_oom" description="Out of memory error occurred" />
8a18547725cf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diff commit 9b11cc5751c0931172d00799b246fcbd63660311"
bgruening
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13 </stdio>
8a18547725cf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diff commit 9b11cc5751c0931172d00799b246fcbd63660311"
bgruening
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14
8a18547725cf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diff commit 9b11cc5751c0931172d00799b246fcbd63660311"
bgruening
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15 <command ><![CDATA[
1
02dfbbf869d8 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diff commit d1ef0f3da4118bf352c5acf720f277fc5ef07665"
bgruening
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16 diff -u '$input1' '$input2' > '$diff_file';
02dfbbf869d8 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diff commit d1ef0f3da4118bf352c5acf720f277fc5ef07665"
bgruening
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17 #if $generate_report:
02dfbbf869d8 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diff commit d1ef0f3da4118bf352c5acf720f277fc5ef07665"
bgruening
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18 sed -e 's/@@title@@/Diff report for '$input1.element_identifier' and '$input2.element_identifier'/g'
02dfbbf869d8 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diff commit d1ef0f3da4118bf352c5acf720f277fc5ef07665"
bgruening
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19 -e 's/@@outputformat@@/'$output_format'/g'
02dfbbf869d8 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diff commit d1ef0f3da4118bf352c5acf720f277fc5ef07665"
bgruening
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20 -e '/@@diffoutput@@/{r'$diff_file'' -e ';d}'
02dfbbf869d8 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diff commit d1ef0f3da4118bf352c5acf720f277fc5ef07665"
bgruening
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21 '$__tool_directory__/template.html' > '$html_file'
02dfbbf869d8 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diff commit d1ef0f3da4118bf352c5acf720f277fc5ef07665"
bgruening
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22 #end if
0
8a18547725cf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diff commit 9b11cc5751c0931172d00799b246fcbd63660311"
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23 ]]>
8a18547725cf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diff commit 9b11cc5751c0931172d00799b246fcbd63660311"
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24 </command>
8a18547725cf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diff commit 9b11cc5751c0931172d00799b246fcbd63660311"
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25
8a18547725cf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diff commit 9b11cc5751c0931172d00799b246fcbd63660311"
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26 <inputs>
8a18547725cf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diff commit 9b11cc5751c0931172d00799b246fcbd63660311"
bgruening
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27 <param name="input1" type="data" format="txt" label="First input file" />
8a18547725cf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diff commit 9b11cc5751c0931172d00799b246fcbd63660311"
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28 <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
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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"/>
02dfbbf869d8 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diff commit d1ef0f3da4118bf352c5acf720f277fc5ef07665"
bgruening
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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.">
02dfbbf869d8 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diff commit d1ef0f3da4118bf352c5acf720f277fc5ef07665"
bgruening
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31 <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
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32 <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"
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33 </param>
0
8a18547725cf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diff commit 9b11cc5751c0931172d00799b246fcbd63660311"
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34 </inputs>
8a18547725cf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diff commit 9b11cc5751c0931172d00799b246fcbd63660311"
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35
8a18547725cf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diff commit 9b11cc5751c0931172d00799b246fcbd63660311"
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36 <outputs>
1
02dfbbf869d8 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diff commit d1ef0f3da4118bf352c5acf720f277fc5ef07665"
bgruening
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37 <data format="txt" name="diff_file" from_work_dir="output.txt" label="${tool.name} on ${on_string}: Raw Output" />
02dfbbf869d8 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diff commit d1ef0f3da4118bf352c5acf720f277fc5ef07665"
bgruening
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38 <data format="html" name="html_file" from_work_dir="output.html" label="${tool.name} on ${on_string}: Html Report">
02dfbbf869d8 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diff commit d1ef0f3da4118bf352c5acf720f277fc5ef07665"
bgruening
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39 <filter>generate_report is True</filter>
02dfbbf869d8 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diff commit d1ef0f3da4118bf352c5acf720f277fc5ef07665"
bgruening
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40 </data>
0
8a18547725cf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diff commit 9b11cc5751c0931172d00799b246fcbd63660311"
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41 </outputs>
8a18547725cf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diff commit 9b11cc5751c0931172d00799b246fcbd63660311"
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42
8a18547725cf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diff commit 9b11cc5751c0931172d00799b246fcbd63660311"
bgruening
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43 <tests>
1
02dfbbf869d8 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diff commit d1ef0f3da4118bf352c5acf720f277fc5ef07665"
bgruening
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44 <test expect_exit_code="0" expect_failure="false" expect_num_outputs="1">
0
8a18547725cf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diff commit 9b11cc5751c0931172d00799b246fcbd63660311"
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45 <param name="input1" value="file1.txt" />
8a18547725cf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diff commit 9b11cc5751c0931172d00799b246fcbd63660311"
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46 <param name="input2" value="file1.txt" />
1
02dfbbf869d8 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diff commit d1ef0f3da4118bf352c5acf720f277fc5ef07665"
bgruening
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47 <param name="generate_report" value="false" />
02dfbbf869d8 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diff commit d1ef0f3da4118bf352c5acf720f277fc5ef07665"
bgruening
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48 <output name="diff_file">
0
8a18547725cf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diff commit 9b11cc5751c0931172d00799b246fcbd63660311"
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49 <assert_contents>
8a18547725cf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diff commit 9b11cc5751c0931172d00799b246fcbd63660311"
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50 <has_n_lines n="0" />
8a18547725cf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diff commit 9b11cc5751c0931172d00799b246fcbd63660311"
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51 </assert_contents>
8a18547725cf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diff commit 9b11cc5751c0931172d00799b246fcbd63660311"
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52 </output>
8a18547725cf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diff commit 9b11cc5751c0931172d00799b246fcbd63660311"
bgruening
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53 </test>
1
02dfbbf869d8 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diff commit d1ef0f3da4118bf352c5acf720f277fc5ef07665"
bgruening
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54 <test expect_exit_code="1" expect_failure="false" expect_num_outputs="1">
0
8a18547725cf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diff commit 9b11cc5751c0931172d00799b246fcbd63660311"
bgruening
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55 <param name="input1" value="file1.txt" />
8a18547725cf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diff commit 9b11cc5751c0931172d00799b246fcbd63660311"
bgruening
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56 <param name="input2" value="file2.txt" />
1
02dfbbf869d8 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diff commit d1ef0f3da4118bf352c5acf720f277fc5ef07665"
bgruening
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57 <param name="generate_report" value="false" />
02dfbbf869d8 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diff commit d1ef0f3da4118bf352c5acf720f277fc5ef07665"
bgruening
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58 <output name="diff_file">
0
8a18547725cf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diff commit 9b11cc5751c0931172d00799b246fcbd63660311"
bgruening
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59 <assert_contents>
8a18547725cf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diff commit 9b11cc5751c0931172d00799b246fcbd63660311"
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60 <has_n_lines n="5" />
8a18547725cf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diff commit 9b11cc5751c0931172d00799b246fcbd63660311"
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61 <has_line line=" a" />
8a18547725cf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diff commit 9b11cc5751c0931172d00799b246fcbd63660311"
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62 <has_line line="+b" />
8a18547725cf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diff commit 9b11cc5751c0931172d00799b246fcbd63660311"
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63 </assert_contents>
8a18547725cf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diff commit 9b11cc5751c0931172d00799b246fcbd63660311"
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64 </output>
8a18547725cf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diff commit 9b11cc5751c0931172d00799b246fcbd63660311"
bgruening
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65 </test>
1
02dfbbf869d8 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diff commit d1ef0f3da4118bf352c5acf720f277fc5ef07665"
bgruening
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66 <test expect_exit_code="0" expect_failure="false" expect_num_outputs="2">
02dfbbf869d8 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diff commit d1ef0f3da4118bf352c5acf720f277fc5ef07665"
bgruening
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67 <param name="input1" value="file1.txt" />
02dfbbf869d8 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diff commit d1ef0f3da4118bf352c5acf720f277fc5ef07665"
bgruening
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68 <param name="input2" value="file2.txt" />
02dfbbf869d8 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diff commit d1ef0f3da4118bf352c5acf720f277fc5ef07665"
bgruening
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69 <param name="generate_report" value="true" />
02dfbbf869d8 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diff commit d1ef0f3da4118bf352c5acf720f277fc5ef07665"
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70 <output name="html_file">
02dfbbf869d8 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diff commit d1ef0f3da4118bf352c5acf720f277fc5ef07665"
bgruening
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71 <assert_contents>
02dfbbf869d8 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diff commit d1ef0f3da4118bf352c5acf720f277fc5ef07665"
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72 <has_text text="!DOCTYPE html" />
02dfbbf869d8 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diff commit d1ef0f3da4118bf352c5acf720f277fc5ef07665"
bgruening
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73 </assert_contents>
02dfbbf869d8 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diff commit d1ef0f3da4118bf352c5acf720f277fc5ef07665"
bgruening
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74 </output>
02dfbbf869d8 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diff commit d1ef0f3da4118bf352c5acf720f277fc5ef07665"
bgruening
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75 </test>
02dfbbf869d8 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diff commit d1ef0f3da4118bf352c5acf720f277fc5ef07665"
bgruening
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76 <test expect_exit_code="0" expect_failure="false" expect_num_outputs="2">
02dfbbf869d8 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diff commit d1ef0f3da4118bf352c5acf720f277fc5ef07665"
bgruening
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77 <param name="input1" value="file1.txt" />
02dfbbf869d8 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diff commit d1ef0f3da4118bf352c5acf720f277fc5ef07665"
bgruening
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78 <param name="input2" value="file2.txt" />
02dfbbf869d8 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diff commit d1ef0f3da4118bf352c5acf720f277fc5ef07665"
bgruening
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79 <param name="generate_report" value="true" />
02dfbbf869d8 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diff commit d1ef0f3da4118bf352c5acf720f277fc5ef07665"
bgruening
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80 <param name="output_format" value="side-by-side" />
02dfbbf869d8 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diff commit d1ef0f3da4118bf352c5acf720f277fc5ef07665"
bgruening
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81 <output name="html_file">
02dfbbf869d8 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diff commit d1ef0f3da4118bf352c5acf720f277fc5ef07665"
bgruening
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82 <assert_contents>
02dfbbf869d8 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diff commit d1ef0f3da4118bf352c5acf720f277fc5ef07665"
bgruening
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83 <has_text text="!DOCTYPE html" />
02dfbbf869d8 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diff commit d1ef0f3da4118bf352c5acf720f277fc5ef07665"
bgruening
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84 <has_text text="side-by-side" />
02dfbbf869d8 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diff commit d1ef0f3da4118bf352c5acf720f277fc5ef07665"
bgruening
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85 </assert_contents>
02dfbbf869d8 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diff commit d1ef0f3da4118bf352c5acf720f277fc5ef07665"
bgruening
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86 </output>
02dfbbf869d8 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diff commit d1ef0f3da4118bf352c5acf720f277fc5ef07665"
bgruening
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87 </test>
02dfbbf869d8 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diff commit d1ef0f3da4118bf352c5acf720f277fc5ef07665"
bgruening
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88 <test expect_exit_code="0" expect_failure="false" expect_num_outputs="2">
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89 <param name="input1" value="file1.txt" />
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90 <param name="input2" value="file2.txt" />
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91 <param name="generate_report" value="true" />
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92 <param name="output_format" value="line-by-line" />
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93 <output name="html_file">
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94 <assert_contents>
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95 <has_text text="!DOCTYPE html" />
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96 <has_text text="line-by-line" />
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97 </assert_contents>
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98 </output>
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99 </test>
0
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100 </tests>
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101
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102 <help><![CDATA[
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103 .. class:: infomark
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104
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105 **Purpose**
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106
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107 The **diff** utility is a data comparison tool that calculates and displays the differences between two files.
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108
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109 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.
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110
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111 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.
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112
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113 .. class:: infomark
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114
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115 **Input**
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116
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117 Two text files to be checked for differences line by line.
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118
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119 .. class:: infomark
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120
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121 **Output**
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122
1
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123 A *text file*, either:
0
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124
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125 - containing the lines differences in **unified format** (*unidiff*),
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126
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127 - or an **empty** file if the two input files are the same.
1
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128
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129 An **optional** *HTML report* with a friendlier visual representation of the differences.
0
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130 ]]>
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131 </help>
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132
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133 <citations>
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134 <citation type="bibtex">
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135 @misc{gnudiffutils,
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136 author = {The Free Software Foundation (FSF), Inc},
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137 year = {2017},
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138 title = {diff (GNU diffutils)},
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139 publisher = {The Free Software Foundation (FSF), Inc},
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140 url = {http://www.gnu.org/software/diffutils/},
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141 }
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142 </citation>
1
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143 <citation type="bibtex">
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144 @misc{diff2html,
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145 author = {Rodrigo Fernandes},
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146 year = {2014},
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147 title = {Pretty diff to html javascript library (diff2html)},
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148 publisher = {Github},
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149 url = {https://github.com/rtfpessoa/diff2html},
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150 }
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151 </citation>
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152 <citation type="bibtex">
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153 @misc{sed,
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154 author = {The Free Software Foundation (FSF), Inc},
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155 year = {2017},
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156 title = {sed (GNU sed)},
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157 publisher = {The Free Software Foundation (FSF), Inc},
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158 url = {http://www.gnu.org/software/sed/},
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159 }
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160 </citation>
0
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161 </citations>
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162 </tool>