Mercurial > repos > imgteam > highdicom_dicom2text

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planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/highdicom/ commit 3a064f9bbb0eb56d752df40eb467b74da31711ce
author imgteam
date Thu, 01 Jan 2026 10:26:58 +0000
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199de6887566 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/highdicom/ commit 3a064f9bbb0eb56d752df40eb467b74da31711ce
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1 <tool id="highdicom_dicom2text" name="Export DICOM metadata" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="24.01">
199de6887566 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/highdicom/ commit 3a064f9bbb0eb56d752df40eb467b74da31711ce
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2 <expand macro="description"/>
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3 <macros>
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4 <import>macros.xml</import>
199de6887566 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/highdicom/ commit 3a064f9bbb0eb56d752df40eb467b74da31711ce
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5 <import>creators.xml</import>
199de6887566 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/highdicom/ commit 3a064f9bbb0eb56d752df40eb467b74da31711ce
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6 </macros>
199de6887566 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/highdicom/ commit 3a064f9bbb0eb56d752df40eb467b74da31711ce
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7 <creator>
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8 <expand macro="creators/bmcv"/>
199de6887566 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/highdicom/ commit 3a064f9bbb0eb56d752df40eb467b74da31711ce
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9 <expand macro="creators/kostrykin"/>
199de6887566 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/highdicom/ commit 3a064f9bbb0eb56d752df40eb467b74da31711ce
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10 </creator>
199de6887566 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/highdicom/ commit 3a064f9bbb0eb56d752df40eb467b74da31711ce
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11 <edam_operations>
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12 <edam_operation>operation_3443</edam_operation>
199de6887566 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/highdicom/ commit 3a064f9bbb0eb56d752df40eb467b74da31711ce
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13 </edam_operations>
199de6887566 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/highdicom/ commit 3a064f9bbb0eb56d752df40eb467b74da31711ce
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14 <expand macro="xrefs"/>
199de6887566 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/highdicom/ commit 3a064f9bbb0eb56d752df40eb467b74da31711ce
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15 <expand macro="requirements"/>
199de6887566 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/highdicom/ commit 3a064f9bbb0eb56d752df40eb467b74da31711ce
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16 <command><![CDATA[
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17
199de6887566 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/highdicom/ commit 3a064f9bbb0eb56d752df40eb467b74da31711ce
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18 python '$__tool_directory__/dicom2text.py'
199de6887566 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/highdicom/ commit 3a064f9bbb0eb56d752df40eb467b74da31711ce
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19 '$input'
199de6887566 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/highdicom/ commit 3a064f9bbb0eb56d752df40eb467b74da31711ce
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20
199de6887566 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/highdicom/ commit 3a064f9bbb0eb56d752df40eb467b74da31711ce
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21 #if $export_to == "json"
199de6887566 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/highdicom/ commit 3a064f9bbb0eb56d752df40eb467b74da31711ce
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22 ./output.json
199de6887566 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/highdicom/ commit 3a064f9bbb0eb56d752df40eb467b74da31711ce
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23 #elif $export_to == "yaml"
199de6887566 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/highdicom/ commit 3a064f9bbb0eb56d752df40eb467b74da31711ce
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24 ./output.yaml
199de6887566 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/highdicom/ commit 3a064f9bbb0eb56d752df40eb467b74da31711ce
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25 #end if
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26
199de6887566 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/highdicom/ commit 3a064f9bbb0eb56d752df40eb467b74da31711ce
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27 ]]>
199de6887566 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/highdicom/ commit 3a064f9bbb0eb56d752df40eb467b74da31711ce
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28 </command>
199de6887566 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/highdicom/ commit 3a064f9bbb0eb56d752df40eb467b74da31711ce
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29 <inputs>
199de6887566 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/highdicom/ commit 3a064f9bbb0eb56d752df40eb467b74da31711ce
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30 <param name="input" type="data" format="binary" label="DICOM dataset"/>
199de6887566 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/highdicom/ commit 3a064f9bbb0eb56d752df40eb467b74da31711ce
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31 <param name="export_to" type="select" label="Export to">
199de6887566 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/highdicom/ commit 3a064f9bbb0eb56d752df40eb467b74da31711ce
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32 <option value="json" selected="true">JSON</option>
199de6887566 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/highdicom/ commit 3a064f9bbb0eb56d752df40eb467b74da31711ce
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33 <option value="yaml">YAML</option>
199de6887566 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/highdicom/ commit 3a064f9bbb0eb56d752df40eb467b74da31711ce
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34 </param>
199de6887566 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/highdicom/ commit 3a064f9bbb0eb56d752df40eb467b74da31711ce
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35 </inputs>
199de6887566 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/highdicom/ commit 3a064f9bbb0eb56d752df40eb467b74da31711ce
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36 <outputs>
199de6887566 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/highdicom/ commit 3a064f9bbb0eb56d752df40eb467b74da31711ce
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37 <data format="json" name="output_json" from_work_dir="output.json" label="${tool.name} on ${on_string} (JSON)">
199de6887566 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/highdicom/ commit 3a064f9bbb0eb56d752df40eb467b74da31711ce
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38 <filter>export_to == 'json'</filter>
199de6887566 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/highdicom/ commit 3a064f9bbb0eb56d752df40eb467b74da31711ce
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39 </data>
199de6887566 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/highdicom/ commit 3a064f9bbb0eb56d752df40eb467b74da31711ce
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40 <data format="yaml" name="output_yaml" from_work_dir="output.yaml" label="${tool.name} on ${on_string} (YAML)">
199de6887566 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/highdicom/ commit 3a064f9bbb0eb56d752df40eb467b74da31711ce
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41 <filter>export_to == 'yaml'</filter>
199de6887566 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/highdicom/ commit 3a064f9bbb0eb56d752df40eb467b74da31711ce
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42 </data>
199de6887566 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/highdicom/ commit 3a064f9bbb0eb56d752df40eb467b74da31711ce
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43 </outputs>
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44 <tests>
199de6887566 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/highdicom/ commit 3a064f9bbb0eb56d752df40eb467b74da31711ce
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45 <test expect_num_outputs="1">
199de6887566 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/highdicom/ commit 3a064f9bbb0eb56d752df40eb467b74da31711ce
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46 <param name="input" value="highdicom/ct_image.dcm"/>
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47 <param name="export_to" value="json"/>
199de6887566 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/highdicom/ commit 3a064f9bbb0eb56d752df40eb467b74da31711ce
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48 <output name="output_json" ftype="json">
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49 <assert_contents>
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50 <has_json_property_with_value property="00080080" value='{"vr": "LO", "Value": ["JFK IMAGING CENTER"]}'/>
199de6887566 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/highdicom/ commit 3a064f9bbb0eb56d752df40eb467b74da31711ce
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51 </assert_contents>
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52 </output>
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53 </test>
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54 <test expect_num_outputs="1">
199de6887566 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/highdicom/ commit 3a064f9bbb0eb56d752df40eb467b74da31711ce
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55 <param name="input" value="highdicom/sm_image.dcm"/>
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56 <param name="export_to" value="yaml"/>
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57 <output name="output_yaml" ftype="yaml">
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58 <assert_contents>
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59 <has_text_matching expression="00080104:\n +Value:\n +- Brightfield illumination\n"/>
199de6887566 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/highdicom/ commit 3a064f9bbb0eb56d752df40eb467b74da31711ce
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60 </assert_contents>
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61 </output>
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62 </test>
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63 </tests>
199de6887566 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/highdicom/ commit 3a064f9bbb0eb56d752df40eb467b74da31711ce
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64 <help>
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65
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66 **Exports the metadata of a DICOM dataset as JSON or YAML.**
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67
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68 @DICOM_INTRO@
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69
199de6887566 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/highdicom/ commit 3a064f9bbb0eb56d752df40eb467b74da31711ce
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70 </help>
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71 <expand macro="citations"/>
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72 </tool>