Mercurial > repos > imgteam > iscc_sum_verify

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planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/iscc-sum commit 6db86b8b65a0e05b7f3541d505fbe900633fc72a
author imgteam
date Fri, 19 Dec 2025 15:02:49 +0000
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0
9fee6d81910d planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/iscc-sum commit 6db86b8b65a0e05b7f3541d505fbe900633fc72a
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1 <tool id="iscc_sum_verify" name="Verify ISCC-CODE" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="24.1">
9fee6d81910d planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/iscc-sum commit 6db86b8b65a0e05b7f3541d505fbe900633fc72a
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2 <description>with ISCC-SUM</description>
9fee6d81910d planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/iscc-sum commit 6db86b8b65a0e05b7f3541d505fbe900633fc72a
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3 <macros>
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4 <import>macros.xml</import>
9fee6d81910d planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/iscc-sum commit 6db86b8b65a0e05b7f3541d505fbe900633fc72a
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5 <import>creators.xml</import>
9fee6d81910d planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/iscc-sum commit 6db86b8b65a0e05b7f3541d505fbe900633fc72a
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6 </macros>
9fee6d81910d planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/iscc-sum commit 6db86b8b65a0e05b7f3541d505fbe900633fc72a
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7 <expand macro="requirements" />
9fee6d81910d planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/iscc-sum commit 6db86b8b65a0e05b7f3541d505fbe900633fc72a
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8 <expand macro="version_command" />
9fee6d81910d planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/iscc-sum commit 6db86b8b65a0e05b7f3541d505fbe900633fc72a
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9 <creator>
9fee6d81910d planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/iscc-sum commit 6db86b8b65a0e05b7f3541d505fbe900633fc72a
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10 <expand macro="creators/iscc" />
9fee6d81910d planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/iscc-sum commit 6db86b8b65a0e05b7f3541d505fbe900633fc72a
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11 <expand macro="creators/lco" />
9fee6d81910d planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/iscc-sum commit 6db86b8b65a0e05b7f3541d505fbe900633fc72a
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12 <expand macro="creators/maartenpaul" />
9fee6d81910d planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/iscc-sum commit 6db86b8b65a0e05b7f3541d505fbe900633fc72a
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13 <expand macro="creators/etzm" />
9fee6d81910d planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/iscc-sum commit 6db86b8b65a0e05b7f3541d505fbe900633fc72a
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14 </creator>
9fee6d81910d planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/iscc-sum commit 6db86b8b65a0e05b7f3541d505fbe900633fc72a
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15
9fee6d81910d planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/iscc-sum commit 6db86b8b65a0e05b7f3541d505fbe900633fc72a
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16 <command detect_errors="exit_code"><![CDATA[
9fee6d81910d planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/iscc-sum commit 6db86b8b65a0e05b7f3541d505fbe900633fc72a
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17 ## Generate ISCC-CODE for input dataset
9fee6d81910d planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/iscc-sum commit 6db86b8b65a0e05b7f3541d505fbe900633fc72a
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18 GENERATED=\$(iscc-sum '${input_file}' | cut -d':' -f2 | cut -d' ' -f1) &&
9fee6d81910d planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/iscc-sum commit 6db86b8b65a0e05b7f3541d505fbe900633fc72a
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19
9fee6d81910d planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/iscc-sum commit 6db86b8b65a0e05b7f3541d505fbe900633fc72a
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20 ## Get expected ISCC-CODE
9fee6d81910d planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/iscc-sum commit 6db86b8b65a0e05b7f3541d505fbe900633fc72a
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21 EXPECTED='${expected_code}' &&
9fee6d81910d planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/iscc-sum commit 6db86b8b65a0e05b7f3541d505fbe900633fc72a
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22
9fee6d81910d planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/iscc-sum commit 6db86b8b65a0e05b7f3541d505fbe900633fc72a
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23 ## Validate expected ISCC-CODE length
9fee6d81910d planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/iscc-sum commit 6db86b8b65a0e05b7f3541d505fbe900633fc72a
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24 if [ \${#EXPECTED} -ne 55 ]; then
9fee6d81910d planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/iscc-sum commit 6db86b8b65a0e05b7f3541d505fbe900633fc72a
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25 echo "ERROR: Expected ISCC-CODE must be exactly 55 characters" >&2;
9fee6d81910d planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/iscc-sum commit 6db86b8b65a0e05b7f3541d505fbe900633fc72a
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26 echo "Found: \${#EXPECTED} characters" >&2;
9fee6d81910d planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/iscc-sum commit 6db86b8b65a0e05b7f3541d505fbe900633fc72a
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27 exit 1;
9fee6d81910d planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/iscc-sum commit 6db86b8b65a0e05b7f3541d505fbe900633fc72a
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28 fi &&
9fee6d81910d planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/iscc-sum commit 6db86b8b65a0e05b7f3541d505fbe900633fc72a
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29
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30 ## Output verification report
9fee6d81910d planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/iscc-sum commit 6db86b8b65a0e05b7f3541d505fbe900633fc72a
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31 if [ "\$GENERATED" = "\$EXPECTED" ]; then
9fee6d81910d planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/iscc-sum commit 6db86b8b65a0e05b7f3541d505fbe900633fc72a
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32 echo "OK - ISCC-CODEs match" > '${output_file}';
9fee6d81910d planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/iscc-sum commit 6db86b8b65a0e05b7f3541d505fbe900633fc72a
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33 else
9fee6d81910d planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/iscc-sum commit 6db86b8b65a0e05b7f3541d505fbe900633fc72a
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34 echo "FAILED - ISCC-CODEs do not match" > '${output_file}';
9fee6d81910d planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/iscc-sum commit 6db86b8b65a0e05b7f3541d505fbe900633fc72a
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35 fi &&
9fee6d81910d planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/iscc-sum commit 6db86b8b65a0e05b7f3541d505fbe900633fc72a
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36 echo "Expected: \$EXPECTED" >> '${output_file}' &&
9fee6d81910d planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/iscc-sum commit 6db86b8b65a0e05b7f3541d505fbe900633fc72a
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37 echo "Generated: \$GENERATED" >> '${output_file}' &&
9fee6d81910d planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/iscc-sum commit 6db86b8b65a0e05b7f3541d505fbe900633fc72a
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38 echo "" >> '${output_file}'
9fee6d81910d planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/iscc-sum commit 6db86b8b65a0e05b7f3541d505fbe900633fc72a
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39
9fee6d81910d planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/iscc-sum commit 6db86b8b65a0e05b7f3541d505fbe900633fc72a
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40 ]]></command>
9fee6d81910d planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/iscc-sum commit 6db86b8b65a0e05b7f3541d505fbe900633fc72a
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41
9fee6d81910d planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/iscc-sum commit 6db86b8b65a0e05b7f3541d505fbe900633fc72a
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42 <inputs>
9fee6d81910d planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/iscc-sum commit 6db86b8b65a0e05b7f3541d505fbe900633fc72a
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43 <param name="input_file" type="data" format="data" label="Dataset to verify"
9fee6d81910d planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/iscc-sum commit 6db86b8b65a0e05b7f3541d505fbe900633fc72a
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44 help="Verify this dataset's ISCC-CODE. When a collection is provided, each dataset is verified separately against the same expected ISCC-CODE."/>
9fee6d81910d planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/iscc-sum commit 6db86b8b65a0e05b7f3541d505fbe900633fc72a
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45 <param name="expected_code" type="text" label="Expected ISCC-CODE"
9fee6d81910d planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/iscc-sum commit 6db86b8b65a0e05b7f3541d505fbe900633fc72a
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46 help="The 55-character ISCC-CODE to verify against">
9fee6d81910d planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/iscc-sum commit 6db86b8b65a0e05b7f3541d505fbe900633fc72a
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47 <validator type="length" min="55" max="55" message="ISCC-CODE must be exactly 55 characters"/>
9fee6d81910d planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/iscc-sum commit 6db86b8b65a0e05b7f3541d505fbe900633fc72a
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48 </param>
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49 </inputs>
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50
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51 <outputs>
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52 <data name="output_file" format="txt" label="${tool.name} on ${on_string}"/>
9fee6d81910d planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/iscc-sum commit 6db86b8b65a0e05b7f3541d505fbe900633fc72a
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53 </outputs>
9fee6d81910d planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/iscc-sum commit 6db86b8b65a0e05b7f3541d505fbe900633fc72a
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54
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55 <tests>
9fee6d81910d planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/iscc-sum commit 6db86b8b65a0e05b7f3541d505fbe900633fc72a
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56 <!-- Test 1: Successful verification -->
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57 <test expect_num_outputs="1">
9fee6d81910d planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/iscc-sum commit 6db86b8b65a0e05b7f3541d505fbe900633fc72a
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58 <param name="input_file" value="test1.png"/>
9fee6d81910d planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/iscc-sum commit 6db86b8b65a0e05b7f3541d505fbe900633fc72a
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59 <param name="expected_code" value="K4AOMGOGQJA4Y46PAC4YPPA63GKD5RVFPR7FU3I4OOEW44TYXNYOTMY"/>
9fee6d81910d planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/iscc-sum commit 6db86b8b65a0e05b7f3541d505fbe900633fc72a
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60 <output name="output_file">
9fee6d81910d planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/iscc-sum commit 6db86b8b65a0e05b7f3541d505fbe900633fc72a
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61 <assert_contents>
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62 <has_text text="OK - ISCC-CODEs match"/>
9fee6d81910d planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/iscc-sum commit 6db86b8b65a0e05b7f3541d505fbe900633fc72a
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63 <has_text text="Expected: K4AOMGOGQJA4Y46PAC4YPPA63GKD5RVFPR7FU3I4OOEW44TYXNYOTMY"/>
9fee6d81910d planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/iscc-sum commit 6db86b8b65a0e05b7f3541d505fbe900633fc72a
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64 <has_text text="Generated: K4AOMGOGQJA4Y46PAC4YPPA63GKD5RVFPR7FU3I4OOEW44TYXNYOTMY"/>
9fee6d81910d planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/iscc-sum commit 6db86b8b65a0e05b7f3541d505fbe900633fc72a
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65 <has_n_lines n="4"/>
9fee6d81910d planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/iscc-sum commit 6db86b8b65a0e05b7f3541d505fbe900633fc72a
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66 </assert_contents>
9fee6d81910d planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/iscc-sum commit 6db86b8b65a0e05b7f3541d505fbe900633fc72a
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67 </output>
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68 </test>
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69
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70 <!-- Test 2: Failed verification -->
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71 <test expect_num_outputs="1">
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72 <param name="input_file" value="test1.png"/>
9fee6d81910d planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/iscc-sum commit 6db86b8b65a0e05b7f3541d505fbe900633fc72a
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73 <param name="expected_code" value="K4AGSPOSB5SS2X427WZ27QASTSBVTS55DXLMFDF7WOJKEOSTDEI3OXQ"/>
9fee6d81910d planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/iscc-sum commit 6db86b8b65a0e05b7f3541d505fbe900633fc72a
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74 <output name="output_file">
9fee6d81910d planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/iscc-sum commit 6db86b8b65a0e05b7f3541d505fbe900633fc72a
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75 <assert_contents>
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76 <has_text text="FAILED - ISCC-CODEs do not match"/>
9fee6d81910d planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/iscc-sum commit 6db86b8b65a0e05b7f3541d505fbe900633fc72a
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77 <has_text text="Expected: K4AGSPOSB5SS2X427WZ27QASTSBVTS55DXLMFDF7WOJKEOSTDEI3OXQ"/>
9fee6d81910d planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/iscc-sum commit 6db86b8b65a0e05b7f3541d505fbe900633fc72a
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78 <has_text text="Generated: K4AOMGOGQJA4Y46PAC4YPPA63GKD5RVFPR7FU3I4OOEW44TYXNYOTMY"/>
9fee6d81910d planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/iscc-sum commit 6db86b8b65a0e05b7f3541d505fbe900633fc72a
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79 <has_n_lines n="4"/>
9fee6d81910d planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/iscc-sum commit 6db86b8b65a0e05b7f3541d505fbe900633fc72a
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80 </assert_contents>
9fee6d81910d planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/iscc-sum commit 6db86b8b65a0e05b7f3541d505fbe900633fc72a
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81 </output>
9fee6d81910d planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/iscc-sum commit 6db86b8b65a0e05b7f3541d505fbe900633fc72a
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82 </test>
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83
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84 <!-- Test 3: FASTA file verification -->
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85 <test expect_num_outputs="1">
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86 <param name="input_file" value="test3.fasta"/>
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87 <param name="expected_code" value="K4AKF7PTZ7JTAAYZ7YZHZPR5RETKYXXE7RTBTJA4JX5GQQMSLZRC6QQ"/>
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88 <output name="output_file">
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89 <assert_contents>
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90 <has_text text="OK - ISCC-CODEs match"/>
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91 <has_text text="Expected: K4AKF7PTZ7JTAAYZ7YZHZPR5RETKYXXE7RTBTJA4JX5GQQMSLZRC6QQ"/>
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92 <has_text text="Generated: K4AKF7PTZ7JTAAYZ7YZHZPR5RETKYXXE7RTBTJA4JX5GQQMSLZRC6QQ"/>
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93 <has_n_lines n="4"/>
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94 </assert_contents>
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95 </output>
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96 </test>
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97 </tests>
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98
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99 <help><![CDATA[
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100 What it does
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101 ============
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102
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103 Verifies that a file (dataset) matches an expected ISCC-CODE (International Standard Content Code) for exact content verification. This tool uses ISCC-SUM, which generates an ISCC-CODE containing Data-Code and Instance-Code units for bit-level file comparison.
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104
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105 Exit Codes
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106 ==========
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107
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108 The tool uses exit codes for workflow logic:
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109
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110 - **0**: Verification successful (OK - ISCC-CODEs match)
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111 - **1**: Verification failed (FAILED - ISCC-CODEs do not match)
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112
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113 Dataset Mapping
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114 ===============
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115
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116 When you provide a collection, Galaxy automatically runs verification once per dataset. All datasets are verified against the same expected ISCC-CODE.
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117
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118 Output
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119 ======
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120
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121 A verification report containing:
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122
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123 - Filename (or element identifier)
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124 - Expected ISCC-CODE
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125 - Generated ISCC-CODE
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126 - Status: OK or FAILED
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127
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128 Example output::
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129 Status: OK - ISCC-CODEs match
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130
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131 Expected: K4AOMGOGQJA4Y46PAC4YPPA63GKD5RVFPR7FU3I4OOEW44TYXNYOTMY
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132 Generated: K4AOMGOGQJA4Y46PAC4YPPA63GKD5RVFPR7FU3I4OOEW44TYXNYOTMY
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133
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134 Use Cases
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135 =========
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136
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137 - Verify file integrity after transfer or storage
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138 - Confirm downloaded datasets match reference ISCC-CODEs
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139 - Validate that backups are identical to originals
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140 - Quality control for data archiving
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141
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142 Workflow Examples
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143 =================
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144
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145 Verify a single dataset
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146 -----------------------
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147
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148 ::
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149
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150 Input: document.pdf
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151 Expected ISCC-CODE: K4AOMG...
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152 ↓
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153 [Verify ISCC-CODE]
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154 ↓
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155 Output: "OK" or "FAILED"
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156
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157 Verify against reference table
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158 -------------------------------
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159
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160 Generate reference ISCC-CODEs first::
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161
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162 Original files → [Generate ISCC-CODE] → Reference ISCC-CODEs
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163
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164 Later verify::
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165
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166 New datasets → [Generate ISCC-CODE] → New ISCC-CODEs
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167 ↓
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168 [Join two Datasets] on filename
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169 ↓
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170 Compare ISCC-CODE columns
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171 ↓
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172 Result: Which files match/differ
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173
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174 Working with ISCC-CODE Files in Workflows
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175 ==========================================
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176
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177 If you have the expected ISCC-CODE in a dataset (e.g., from Generate ISCC tool):
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178
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179 1. In the workflow editor, connect the ISCC-CODE file to this tool
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180 2. The ISCC-CODE file content will be used automatically
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181 3. Or manually copy the ISCC-CODE from the file into the text field
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182
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183 Important Notes
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184 ===============
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185
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186 - **Exact match only**: Any change to the file will cause verification to fail
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187 - **Bit-level comparison**: Even metadata changes are detected
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188 - **For similarity detection**: Use "Find similar ISCC-CODEs" tool instead
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189
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190 More Information
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191 ================
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192
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193 For details about ISCC: https://sum.iscc.codes/ and https://iscc.codes/
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194 For ISCC structure and subtypes: https://ieps.iscc.codes/iep-0001/
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195 ]]></help>
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196 <expand macro="citations" />
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197 </tool>