Mercurial > repos > iuc > constava
annotate constava.xml @ 0:2ed0df0360e5 draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/constava commit 77814d75404602f3fb6b791dd79a17653de22d45
| author | iuc |
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| date | Wed, 08 Oct 2025 20:13:34 +0000 |
| parents | |
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| rev | line source |
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2ed0df0360e5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/constava commit 77814d75404602f3fb6b791dd79a17653de22d45
iuc
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1 <tool id="constava" name="Constava" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@" license="GPL-3.0-only"> |
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2ed0df0360e5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/constava commit 77814d75404602f3fb6b791dd79a17653de22d45
iuc
parents:
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2 <description> |
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2ed0df0360e5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/constava commit 77814d75404602f3fb6b791dd79a17653de22d45
iuc
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3 calculates conformational-state probabilities and variability in structural ensembles |
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2ed0df0360e5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/constava commit 77814d75404602f3fb6b791dd79a17653de22d45
iuc
parents:
diff
changeset
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4 </description> |
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2ed0df0360e5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/constava commit 77814d75404602f3fb6b791dd79a17653de22d45
iuc
parents:
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changeset
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5 <macros> |
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2ed0df0360e5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/constava commit 77814d75404602f3fb6b791dd79a17653de22d45
iuc
parents:
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6 <import>macros.xml</import> |
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2ed0df0360e5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/constava commit 77814d75404602f3fb6b791dd79a17653de22d45
iuc
parents:
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changeset
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7 </macros> |
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2ed0df0360e5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/constava commit 77814d75404602f3fb6b791dd79a17653de22d45
iuc
parents:
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8 <edam_topics> |
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2ed0df0360e5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/constava commit 77814d75404602f3fb6b791dd79a17653de22d45
iuc
parents:
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9 <edam_topic>topic_0130</edam_topic> |
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2ed0df0360e5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/constava commit 77814d75404602f3fb6b791dd79a17653de22d45
iuc
parents:
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changeset
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10 </edam_topics> |
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2ed0df0360e5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/constava commit 77814d75404602f3fb6b791dd79a17653de22d45
iuc
parents:
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11 <edam_operations> |
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2ed0df0360e5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/constava commit 77814d75404602f3fb6b791dd79a17653de22d45
iuc
parents:
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12 <edam_operation>operation_0249</edam_operation> |
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2ed0df0360e5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/constava commit 77814d75404602f3fb6b791dd79a17653de22d45
iuc
parents:
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changeset
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13 </edam_operations> |
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2ed0df0360e5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/constava commit 77814d75404602f3fb6b791dd79a17653de22d45
iuc
parents:
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14 <xrefs> |
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2ed0df0360e5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/constava commit 77814d75404602f3fb6b791dd79a17653de22d45
iuc
parents:
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15 <xref type="bio.tools">constava</xref> |
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2ed0df0360e5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/constava commit 77814d75404602f3fb6b791dd79a17653de22d45
iuc
parents:
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16 <!-- https://bio.tools/constava --> |
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2ed0df0360e5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/constava commit 77814d75404602f3fb6b791dd79a17653de22d45
iuc
parents:
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17 </xrefs> |
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2ed0df0360e5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/constava commit 77814d75404602f3fb6b791dd79a17653de22d45
iuc
parents:
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18 <expand macro="requirements"/> |
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2ed0df0360e5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/constava commit 77814d75404602f3fb6b791dd79a17653de22d45
iuc
parents:
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19 <version_command>constava --version</version_command> |
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2ed0df0360e5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/constava commit 77814d75404602f3fb6b791dd79a17653de22d45
iuc
parents:
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changeset
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20 <command detect_errors="aggressive" strict="true"> |
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2ed0df0360e5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/constava commit 77814d75404602f3fb6b791dd79a17653de22d45
iuc
parents:
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21 <![CDATA[ |
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2ed0df0360e5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/constava commit 77814d75404602f3fb6b791dd79a17653de22d45
iuc
parents:
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22 echo "[Galaxy command block at \$(date +'%Y-%m-%dT%H:%M:%S%z')] Starting Constava Tool execution from Galaxy Platform" && |
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2ed0df0360e5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/constava commit 77814d75404602f3fb6b791dd79a17653de22d45
iuc
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23 #for $input_file_id, $input_file in enumerate( $input_options.input_files ): |
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2ed0df0360e5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/constava commit 77814d75404602f3fb6b791dd79a17653de22d45
iuc
parents:
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24 #if $input_file |
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2ed0df0360e5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/constava commit 77814d75404602f3fb6b791dd79a17653de22d45
iuc
parents:
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25 #set ref_name = str($input_file.element_identifier) |
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2ed0df0360e5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/constava commit 77814d75404602f3fb6b791dd79a17653de22d45
iuc
parents:
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26 ln -sv '${input_file}' '$ref_name' && |
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2ed0df0360e5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/constava commit 77814d75404602f3fb6b791dd79a17653de22d45
iuc
parents:
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27 #end if |
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2ed0df0360e5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/constava commit 77814d75404602f3fb6b791dd79a17653de22d45
iuc
parents:
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28 #end for |
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2ed0df0360e5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/constava commit 77814d75404602f3fb6b791dd79a17653de22d45
iuc
parents:
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29 |
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2ed0df0360e5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/constava commit 77814d75404602f3fb6b791dd79a17653de22d45
iuc
parents:
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30 #set angle_units = $input_options.input_degrees |
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2ed0df0360e5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/constava commit 77814d75404602f3fb6b791dd79a17653de22d45
iuc
parents:
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31 echo "[Galaxy command block at \$(date +'%Y-%m-%dT%H:%M:%S%z')] Constava will use '$angle_units' as angle units (empty means Radians)" && |
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2ed0df0360e5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/constava commit 77814d75404602f3fb6b791dd79a17653de22d45
iuc
parents:
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32 |
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2ed0df0360e5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/constava commit 77814d75404602f3fb6b791dd79a17653de22d45
iuc
parents:
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33 #if str( $conformational_state_model_options.use_custom_model ) == "true": |
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2ed0df0360e5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/constava commit 77814d75404602f3fb6b791dd79a17653de22d45
iuc
parents:
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34 echo "[Galaxy command block \$(date +"%Y-%m-%dT%H:%M:%S%z")] Using custom model" && |
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2ed0df0360e5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/constava commit 77814d75404602f3fb6b791dd79a17653de22d45
iuc
parents:
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35 |
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2ed0df0360e5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/constava commit 77814d75404602f3fb6b791dd79a17653de22d45
iuc
parents:
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36 #if str( $conformational_state_model_options.use_custom_input_file ) == "true": |
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2ed0df0360e5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/constava commit 77814d75404602f3fb6b791dd79a17653de22d45
iuc
parents:
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37 echo "[Galaxy command block \$(date +"%Y-%m-%dT%H:%M:%S%z")] Using custom input file for data training: $conformational_state_model_options.custom_input_file.element_identifier" && |
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2ed0df0360e5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/constava commit 77814d75404602f3fb6b791dd79a17653de22d45
iuc
parents:
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38 |
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2ed0df0360e5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/constava commit 77814d75404602f3fb6b791dd79a17653de22d45
iuc
parents:
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39 #set custom_input_file_angle_units = $conformational_state_model_options.custom_input_file_degrees |
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2ed0df0360e5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/constava commit 77814d75404602f3fb6b791dd79a17653de22d45
iuc
parents:
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40 #set ref_name_train_data = str($conformational_state_model_options.custom_input_file.element_identifier) |
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2ed0df0360e5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/constava commit 77814d75404602f3fb6b791dd79a17653de22d45
iuc
parents:
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41 #if str( custom_input_file_angle_units ) != "": |
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2ed0df0360e5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/constava commit 77814d75404602f3fb6b791dd79a17653de22d45
iuc
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42 #set custom_input_parameter="--input " + str( $conformational_state_model_options.custom_input_file.element_identifier ) + " " + $custom_input_file_angle_units |
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2ed0df0360e5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/constava commit 77814d75404602f3fb6b791dd79a17653de22d45
iuc
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43 #else: |
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2ed0df0360e5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/constava commit 77814d75404602f3fb6b791dd79a17653de22d45
iuc
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44 #set custom_input_parameter="--input " + str( $conformational_state_model_options.custom_input_file.element_identifier ) |
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2ed0df0360e5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/constava commit 77814d75404602f3fb6b791dd79a17653de22d45
iuc
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45 #end if |
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2ed0df0360e5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/constava commit 77814d75404602f3fb6b791dd79a17653de22d45
iuc
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46 |
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2ed0df0360e5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/constava commit 77814d75404602f3fb6b791dd79a17653de22d45
iuc
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47 ln -sv '${conformational_state_model_options.custom_input_file}' '$ref_name_train_data' && |
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2ed0df0360e5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/constava commit 77814d75404602f3fb6b791dd79a17653de22d45
iuc
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48 #else: |
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2ed0df0360e5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/constava commit 77814d75404602f3fb6b791dd79a17653de22d45
iuc
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49 echo "[Galaxy command block \$(date +"%Y-%m-%dT%H:%M:%S%z")] Not using custom input file for data training" && |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/constava commit 77814d75404602f3fb6b791dd79a17653de22d45
iuc
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50 #set custom_input_parameter="" |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/constava commit 77814d75404602f3fb6b791dd79a17653de22d45
iuc
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51 #end if |
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2ed0df0360e5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/constava commit 77814d75404602f3fb6b791dd79a17653de22d45
iuc
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52 |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/constava commit 77814d75404602f3fb6b791dd79a17653de22d45
iuc
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53 #if str( $conformational_state_model_options.model_type ) == "kde": |
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2ed0df0360e5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/constava commit 77814d75404602f3fb6b791dd79a17653de22d45
iuc
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54 #set model_file = "custom_model.kde.pkl" |
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2ed0df0360e5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/constava commit 77814d75404602f3fb6b791dd79a17653de22d45
iuc
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55 #set load_model_param="--load-model custom_model.kde.pkl" |
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2ed0df0360e5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/constava commit 77814d75404602f3fb6b791dd79a17653de22d45
iuc
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56 echo "[Galaxy command block \$(date +"%Y-%m-%dT%H:%M:%S%z")] Invoking the 'constava fit-model' module command for KDE" && |
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2ed0df0360e5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/constava commit 77814d75404602f3fb6b791dd79a17653de22d45
iuc
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57 |
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2ed0df0360e5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/constava commit 77814d75404602f3fb6b791dd79a17653de22d45
iuc
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58 constava fit-model -vv |
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2ed0df0360e5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/constava commit 77814d75404602f3fb6b791dd79a17653de22d45
iuc
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59 --model-type kde |
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2ed0df0360e5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/constava commit 77814d75404602f3fb6b791dd79a17653de22d45
iuc
parents:
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60 --kde-bandwidth $conformational_state_model_options.bandwidth |
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2ed0df0360e5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/constava commit 77814d75404602f3fb6b791dd79a17653de22d45
iuc
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61 --output $model_file |
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2ed0df0360e5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/constava commit 77814d75404602f3fb6b791dd79a17653de22d45
iuc
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62 #if str( $custom_input_parameter ) != "": |
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2ed0df0360e5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/constava commit 77814d75404602f3fb6b791dd79a17653de22d45
iuc
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63 $custom_input_parameter |
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2ed0df0360e5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/constava commit 77814d75404602f3fb6b791dd79a17653de22d45
iuc
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64 #end if |
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2ed0df0360e5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/constava commit 77814d75404602f3fb6b791dd79a17653de22d45
iuc
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65 && |
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2ed0df0360e5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/constava commit 77814d75404602f3fb6b791dd79a17653de22d45
iuc
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66 echo "[Galaxy command block \$(date +"%Y-%m-%dT%H:%M:%S%z")] The 'constava fit-model' module command for KDE has finished" && |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/constava commit 77814d75404602f3fb6b791dd79a17653de22d45
iuc
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67 #else if str( $conformational_state_model_options.model_type ) == "grid": |
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2ed0df0360e5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/constava commit 77814d75404602f3fb6b791dd79a17653de22d45
iuc
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68 #set model_file = "custom_model.grid.pkl" |
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2ed0df0360e5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/constava commit 77814d75404602f3fb6b791dd79a17653de22d45
iuc
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69 #set load_model_param="--load-model custom_model.grid.pkl" |
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2ed0df0360e5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/constava commit 77814d75404602f3fb6b791dd79a17653de22d45
iuc
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70 echo "[Galaxy command block \$(date +"%Y-%m-%dT%H:%M:%S%z")] Preparing the 'constava fit-model' module command for GRID" && |
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2ed0df0360e5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/constava commit 77814d75404602f3fb6b791dd79a17653de22d45
iuc
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71 |
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2ed0df0360e5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/constava commit 77814d75404602f3fb6b791dd79a17653de22d45
iuc
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72 constava fit-model -vv |
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2ed0df0360e5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/constava commit 77814d75404602f3fb6b791dd79a17653de22d45
iuc
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73 --model-type grid |
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2ed0df0360e5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/constava commit 77814d75404602f3fb6b791dd79a17653de22d45
iuc
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74 --grid-points $custom_model_grid_points |
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2ed0df0360e5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/constava commit 77814d75404602f3fb6b791dd79a17653de22d45
iuc
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75 --kde-bandwidth $conformational_state_model_options.bandwidth |
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2ed0df0360e5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/constava commit 77814d75404602f3fb6b791dd79a17653de22d45
iuc
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76 --output $model_file |
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2ed0df0360e5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/constava commit 77814d75404602f3fb6b791dd79a17653de22d45
iuc
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77 #if str( $custom_input_parameter ) != "": |
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2ed0df0360e5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/constava commit 77814d75404602f3fb6b791dd79a17653de22d45
iuc
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78 $custom_input_parameter |
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79 #end if |
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80 && |
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81 echo "[Galaxy command block \$(date +"%Y-%m-%dT%H:%M:%S%z")] The 'constava fit-model' module command for GRID has finished" && |
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82 #else: |
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83 #set load_model_param="" |
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84 #end if |
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85 |
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86 #else: |
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87 echo "[Galaxy command block \$(date +"%Y-%m-%dT%H:%M:%S%z")] Not using custom model" && |
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88 #set load_model_param="" |
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89 #end if |
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90 |
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91 echo "[Galaxy command block \$(date +"%Y-%m-%dT%H:%M:%S%z")] Invoking the 'constava analyze' module command" && |
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92 |
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93 constava analyze -vv --precision $input_precision --input |
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94 #for $input_file_id, $input_file in enumerate( $input_files ): |
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95 #if $input_file: |
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96 #set ref_name = str($input_file.element_identifier) |
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97 #set input_format = str($input_file.ext) |
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98 $ref_name |
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99 #end if |
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100 #end for |
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101 --input-format $input_format |
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102 --output output_constava.csv |
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103 #if str( $subsampling_type ) == "window": |
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104 #if str( $return_window_series ) == "true": |
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105 --window-series $subsampling_options.window_size |
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106 #else: |
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107 --window $subsampling_options.window_size |
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108 #end if |
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109 #else if str( $subsampling_type ) == "bootstrap": |
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110 #if str( $return_bootstrap_series ) == "true": |
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111 --bootstrap-series $bootstrap_size |
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112 #else: |
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113 --bootstrap $bootstrap_size |
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114 #end if |
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115 --bootstrap-samples $bootstrap_samples --seed $bootstrap_seed |
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116 #end if |
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117 #if str ($load_model_param ) != "": |
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118 $load_model_param |
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119 #end if |
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120 #if str( $angle_units ) != "": |
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121 $angle_units |
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122 #end if |
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123 && |
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124 echo "[Galaxy command block at \$(date +'%Y-%m-%dT%H:%M:%S%z')] Constava execution from Galaxy has finished" |
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125 ]]></command> |
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126 <environment_variables> |
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127 <environment_variable name="MPLBACKEND">Agg</environment_variable> |
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128 <environment_variable name="TQDM_DISABLE">1</environment_variable> |
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129 <environment_variable name="PYTHON_TQDM_DISABLE">1</environment_variable> |
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130 </environment_variables> |
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131 <inputs> |
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132 <section name="input_options" title="Input Options" expanded="true" help="As input data the backbone dihedral angles extracted from the conformational ensemble need to be provided."> |
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133 <param name="input_files" type="data" format="csv,xvg" label="Dihedral angles file" help="Upload the input file(s) that contain the dihedral angles in CSV or XVG format (GROMACS' `gmx chi` module). Important: Given Constava extracts RESNAME and RESINDEX from filenames when using XVG format, your files must follow this regex 'ramaPhiPsi([A-Z][A-Z0-9][A-Z0-9])([0-9]+).xvg'" multiple="true" argument="input"/> |
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134 <param name="input_degrees" type="select" label="Are the dihedral angles in that file in radians or degrees?" help="Indicate if the dihedral angles are in radians or degrees." argument="degrees"> |
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135 <option value="--degrees">Degrees</option> |
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136 <option value="" selected="true">Radians</option> |
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137 </param> |
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138 <param name="input_precision" type="integer" label="Decimal precision" help="Sets the number of decimals in the output files." value="3" default_value="3" min="1" max="16" argument="precision"></param> |
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139 </section> |
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140 <section name="conformational_state_model_options" title="Kernel Options" help="By default, the conformational state models are generated on-the-fly when running Constava. In selected cases generating a model beforehand and loading it can be useful, though."> |
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141 <conditional name="custom_model"> |
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142 <param name="use_custom_model" type="select" label="Do you want to train a custom probabilistic model of conformational states?"> |
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143 <option value="false" selected="true">No</option> |
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144 <option value="true">Yes</option> |
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145 </param> |
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146 <when value="true"> <!-- Yes, train a custom probabilistic model of conformational states--> |
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147 <conditional name="model_type_options"> |
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148 <param name="model_type" type="select" label="Select a model type" help="We provide two model types. KDE models are the default. They are fast to fit but may be slow in the inference in large conformational ensembles (e.g. long-timescale MD simulations). The idea of Grid models is, to replace the continuous probability density function of the kde-Model by a fixed set of grid-points. The PDF for any sample is then estimated by linear interpolation between the nearest grid points. This is slightly less accurate than the kde-Model but speeds up inference significantly."> |
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149 <option value="kde">KDE model</option> |
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150 <option value="grid">Grid model</option> |
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151 </param> |
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152 <when value="kde"> |
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153 <param name="bandwidth" type="float" label="Which bandwidth do you want to use?" value="0.13" help="This flag controls the bandwidth of the Gaussian kernel density estimator. (default: 0.13)" argument="kde-bandwidth"/> |
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154 </when> |
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155 <when value="grid"> |
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156 <param name="bandwidth" type="float" label="Which bandwidth do you want to use?" value="0.13" help="This flag controls the bandwidth of the Gaussian kernel density estimator. (default: 0.13)" argument="kde-bandwidth"/> |
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157 <param name="custom_model_grid_points" type="integer" label="Grid points" value="10000" help="This flag controls how many grid points are used to describe the probability density function. (default: 10000)" argument="grid-points"/> |
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158 </when> |
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159 </conditional> |
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160 <conditional name="custom_input_json"> |
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161 <param name="use_custom_input_file" type="select" label="Do you want to train probability density functions with custom data?" help="If not, the default data from the publication will be used."> |
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162 <option value="false" selected="true">No</option> |
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163 <option value="true">Yes</option> |
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164 </param> |
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165 <when value="true"> |
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166 <param name="custom_input_file" type="data" format="json" label="File for pdf fitting in JSON format" help="The data to which the new conformational state models will be fitted. It should be provided as a JSON file. The top-most key should indicate the names of the conformational states. On the level below, lists of phi-psi pairs for each stat should be provided." argument="input"/> |
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167 <param name="custom_input_file_degrees" type="select" label="Are the dihedral angles in that file in radians or degrees?" help="Indicate if the dihedral angles of the training data file are in radians or degrees." argument="degrees"> |
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168 <option value="--degrees">Degrees</option> |
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169 <option value="" selected="true">Radians</option> |
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170 </param> |
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171 </when> |
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172 <when value="false"/> |
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173 </conditional> |
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174 </when> |
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175 <when value="false"/> |
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176 </conditional> |
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177 </section> |
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178 <section name="subsampling_options" title="Subsampling Options" help="Do inference using either a moving reading-frame of consecutive samples (sliding window) or using a moving reading-frame of consecutive samples (bootstrap)."> |
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179 <conditional name="sampling_options"> |
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180 <param name="subsampling_type" type="select" label="Select a subsampling method to configure" help="You must select and configure at least one subsampling option."> |
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181 <option value="window" selected="true">Sliding window</option> |
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182 <option value="bootstrap">Bootstrap sampling</option> |
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183 </param> |
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184 <when value="window"> |
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185 <param name="window_size" type="text" label="Window size (space-separated integers)" value="3" help="Specify window sizes for moving frame analysis, e.g., '3 5 7'. Each reading frame consists of consecutive samples. Multiple values can be provided." argument="window"> |
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186 <validator type="regex" message="Use one or more integers separated by single spaces.">^(\d+\s?)+$</validator> |
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187 </param> |
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188 <param name="return_window_series" type="boolean" label="Return the results for every window rather than the average." help="Return the results for every window rather than the average. This can result in very large output files." value="false" argument="window-series"/> |
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189 </when> |
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190 <when value="bootstrap"> |
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191 <param name="bootstrap_size" type="text" label="Bootstrap size (space-separated integers)" value="3" help="Do inference using N samples obtained through bootstrapping. Specify bootstrap sizes, e.g., '10 20 30'. Samples obtained through bootstrapping. Multiple values can be provided." argument="bootstrap"> |
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192 <validator type="regex" message="Use one or more integers separated by single spaces.">^(\d+\s?)+$</validator> |
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193 </param> |
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194 <param name="return_bootstrap_series" type="boolean" label="Return bootstrap series calculation" help="Return the results for every subsample rather than the average. This can result in very large output files." value="false" argument="bootstrap-series"/> |
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195 <param name="bootstrap_samples" type="integer" label="Bootstrap samples" value="10000" min="1" help="When bootstrapping, sample times from the input data."/> |
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196 <param name="bootstrap_seed" type="integer" label="Bootstrap seed" value="42" min="1" help="Set random seed for bootstrap sampling." argument="seed"/> |
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197 </when> |
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198 </conditional> |
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199 </section> |
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200 </inputs> |
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201 <outputs> |
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202 <data name="file_contents" format="csv" label="${tool.name} on ${on_string}: File Contents" from_work_dir="output_constava.csv"/> |
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203 </outputs> |
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204 <tests> |
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205 <!-- ======================================================================= --> |
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206 <!-- Test scenarios: Default PDF --> |
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207 <!-- ======================================================================= --> |
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208 |
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209 <!-- test_001: CSV Dihedrals in radians with window_size 3 using default PDF --> |
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210 <test expect_num_outputs="1"> |
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211 <section name="input_options"> |
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212 <param name="input_files" value="csv/dihedrals.mini.csv"/> |
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213 <param name="input_degrees" value=""/> |
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214 <param name="input_precision" value="10"/> |
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215 </section> |
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216 <assert_command> |
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217 <has_text text="constava analyze -vv --precision 10 --input dihedrals.mini.csv --input-format csv --output output_constava.csv --window 3"/> |
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218 <not_has_text text="constava fit-model"/> |
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219 </assert_command> |
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220 <output name="file_contents" file="expected/test_001.csv" ftype="csv"/> |
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221 </test> |
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222 |
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223 <!-- test_002: XVG Dihedrals in degrees with window_size 3 using default PDF --> |
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224 <test expect_num_outputs="1"> |
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225 <section name="input_options"> |
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226 <param name="input_files" value="xvg/ramaPhiPsiALA18.xvg,xvg/ramaPhiPsiGLY11.xvg,xvg/ramaPhiPsiLEU45.xvg,xvg/ramaPhiPsiTHR2.xvg,xvg/ramaPhiPsiALA19.xvg,xvg/ramaPhiPsiGLY22.xvg,xvg/ramaPhiPsiLYS16.xvg,xvg/ramaPhiPsiTHR4.xvg,xvg/ramaPhiPsiALA26.xvg,xvg/ramaPhiPsiGLY33.xvg,xvg/ramaPhiPsiLYS44.xvg,xvg/ramaPhiPsiTHR7.xvg,xvg/ramaPhiPsiARG29.xvg,xvg/ramaPhiPsiGLY36.xvg,xvg/ramaPhiPsiLYS48.xvg,xvg/ramaPhiPsiTRP31.xvg,xvg/ramaPhiPsiASN15.xvg,xvg/ramaPhiPsiGLY42.xvg,xvg/ramaPhiPsiLYS49.xvg,xvg/ramaPhiPsiTYR21.xvg,xvg/ramaPhiPsiASN27.xvg,xvg/ramaPhiPsiGLY50.xvg,xvg/ramaPhiPsiLYS9.xvg,xvg/ramaPhiPsiTYR5.xvg,xvg/ramaPhiPsiASN3.xvg,xvg/ramaPhiPsiILE17.xvg,xvg/ramaPhiPsiPHE40.xvg,xvg/ramaPhiPsiTYR6.xvg,xvg/ramaPhiPsiASN32.xvg,xvg/ramaPhiPsiILE34.xvg,xvg/ramaPhiPsiSER10.xvg,xvg/ramaPhiPsiVAL23.xvg,xvg/ramaPhiPsiASP12.xvg,xvg/ramaPhiPsiILE39.xvg,xvg/ramaPhiPsiSER24.xvg,xvg/ramaPhiPsiVAL25.xvg,xvg/ramaPhiPsiASP37.xvg,xvg/ramaPhiPsiILE46.xvg,xvg/ramaPhiPsiSER30.xvg,xvg/ramaPhiPsiVAL41.xvg,xvg/ramaPhiPsiGLN20.xvg,xvg/ramaPhiPsiLEU14.xvg,xvg/ramaPhiPsiSER35.xvg,xvg/ramaPhiPsiVAL47.xvg,xvg/ramaPhiPsiGLN43.xvg,xvg/ramaPhiPsiLEU28.xvg,xvg/ramaPhiPsiSER51.xvg,xvg/ramaPhiPsiVAL8.xvg,xvg/ramaPhiPsiGLY1.xvg,xvg/ramaPhiPsiLEU38.xvg,xvg/ramaPhiPsiTHR13.xvg" ftype="xvg"/> |
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227 <param name="input_degrees" value="--degrees"/> |
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228 <param name="input_precision" value="5"/> |
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229 </section> |
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230 <assert_command> |
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231 <has_text text="constava analyze -vv --precision 5 --input"/> |
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2ed0df0360e5
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232 <has_text text="ramaPhiPsiALA18.xvg"/> |
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2ed0df0360e5
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233 <has_text text="ramaPhiPsiGLY11.xvg"/> |
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2ed0df0360e5
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234 <has_text text="ramaPhiPsiLEU45.xvg"/> |
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2ed0df0360e5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/constava commit 77814d75404602f3fb6b791dd79a17653de22d45
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235 <has_text text="ramaPhiPsiTHR2.xvg"/> |
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2ed0df0360e5
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236 <has_text text="ramaPhiPsiALA19.xvg"/> |
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2ed0df0360e5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/constava commit 77814d75404602f3fb6b791dd79a17653de22d45
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237 <has_text text="ramaPhiPsiGLY22.xvg"/> |
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2ed0df0360e5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/constava commit 77814d75404602f3fb6b791dd79a17653de22d45
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238 <has_text text="ramaPhiPsiLYS16.xvg"/> |
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2ed0df0360e5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/constava commit 77814d75404602f3fb6b791dd79a17653de22d45
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239 <has_text text="ramaPhiPsiTHR4.xvg"/> |
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2ed0df0360e5
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240 <has_text text="ramaPhiPsiALA26.xvg"/> |
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2ed0df0360e5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/constava commit 77814d75404602f3fb6b791dd79a17653de22d45
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241 <has_text text="ramaPhiPsiGLY33.xvg"/> |
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2ed0df0360e5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/constava commit 77814d75404602f3fb6b791dd79a17653de22d45
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242 <has_text text="ramaPhiPsiLYS44.xvg"/> |
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2ed0df0360e5
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243 <has_text text="ramaPhiPsiTHR7.xvg"/> |
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2ed0df0360e5
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244 <has_text text="ramaPhiPsiARG29.xvg"/> |
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2ed0df0360e5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/constava commit 77814d75404602f3fb6b791dd79a17653de22d45
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245 <has_text text="ramaPhiPsiGLY36.xvg"/> |
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2ed0df0360e5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/constava commit 77814d75404602f3fb6b791dd79a17653de22d45
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246 <has_text text="ramaPhiPsiLYS48.xvg"/> |
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2ed0df0360e5
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247 <has_text text="ramaPhiPsiTRP31.xvg"/> |
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2ed0df0360e5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/constava commit 77814d75404602f3fb6b791dd79a17653de22d45
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248 <has_text text="ramaPhiPsiASN15.xvg"/> |
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2ed0df0360e5
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249 <has_text text="ramaPhiPsiGLY42.xvg"/> |
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2ed0df0360e5
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250 <has_text text="ramaPhiPsiLYS49.xvg"/> |
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2ed0df0360e5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/constava commit 77814d75404602f3fb6b791dd79a17653de22d45
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251 <has_text text="ramaPhiPsiTYR21.xvg"/> |
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2ed0df0360e5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/constava commit 77814d75404602f3fb6b791dd79a17653de22d45
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252 <has_text text="ramaPhiPsiASN27.xvg"/> |
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2ed0df0360e5
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253 <has_text text="ramaPhiPsiGLY50.xvg"/> |
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2ed0df0360e5
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254 <has_text text="ramaPhiPsiLYS9.xvg"/> |
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2ed0df0360e5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/constava commit 77814d75404602f3fb6b791dd79a17653de22d45
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255 <has_text text="ramaPhiPsiTYR5.xvg"/> |
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2ed0df0360e5
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256 <has_text text="ramaPhiPsiASN3.xvg"/> |
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2ed0df0360e5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/constava commit 77814d75404602f3fb6b791dd79a17653de22d45
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257 <has_text text="ramaPhiPsiILE17.xvg"/> |
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2ed0df0360e5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/constava commit 77814d75404602f3fb6b791dd79a17653de22d45
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258 <has_text text="ramaPhiPsiPHE40.xvg"/> |
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2ed0df0360e5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/constava commit 77814d75404602f3fb6b791dd79a17653de22d45
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259 <has_text text="ramaPhiPsiTYR6.xvg"/> |
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2ed0df0360e5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/constava commit 77814d75404602f3fb6b791dd79a17653de22d45
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260 <has_text text="ramaPhiPsiASN32.xvg"/> |
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2ed0df0360e5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/constava commit 77814d75404602f3fb6b791dd79a17653de22d45
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261 <has_text text="ramaPhiPsiILE34.xvg"/> |
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2ed0df0360e5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/constava commit 77814d75404602f3fb6b791dd79a17653de22d45
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262 <has_text text="ramaPhiPsiSER10.xvg"/> |
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2ed0df0360e5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/constava commit 77814d75404602f3fb6b791dd79a17653de22d45
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263 <has_text text="ramaPhiPsiVAL23.xvg"/> |
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2ed0df0360e5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/constava commit 77814d75404602f3fb6b791dd79a17653de22d45
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264 <has_text text="ramaPhiPsiASP12.xvg"/> |
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2ed0df0360e5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/constava commit 77814d75404602f3fb6b791dd79a17653de22d45
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265 <has_text text="ramaPhiPsiILE39.xvg"/> |
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2ed0df0360e5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/constava commit 77814d75404602f3fb6b791dd79a17653de22d45
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266 <has_text text="ramaPhiPsiSER24.xvg"/> |
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2ed0df0360e5
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267 <has_text text="ramaPhiPsiVAL25.xvg"/> |
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2ed0df0360e5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/constava commit 77814d75404602f3fb6b791dd79a17653de22d45
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268 <has_text text="ramaPhiPsiASP37.xvg"/> |
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2ed0df0360e5
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269 <has_text text="ramaPhiPsiILE46.xvg"/> |
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2ed0df0360e5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/constava commit 77814d75404602f3fb6b791dd79a17653de22d45
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270 <has_text text="ramaPhiPsiSER30.xvg"/> |
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271 <has_text text="ramaPhiPsiVAL41.xvg"/> |
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2ed0df0360e5
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272 <has_text text="ramaPhiPsiGLN20.xvg"/> |
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2ed0df0360e5
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273 <has_text text="ramaPhiPsiLEU14.xvg"/> |
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2ed0df0360e5
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274 <has_text text="ramaPhiPsiSER35.xvg"/> |
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2ed0df0360e5
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275 <has_text text="ramaPhiPsiVAL47.xvg"/> |
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2ed0df0360e5
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276 <has_text text="ramaPhiPsiGLN43.xvg"/> |
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2ed0df0360e5
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277 <has_text text="ramaPhiPsiLEU28.xvg"/> |
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2ed0df0360e5
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278 <has_text text="ramaPhiPsiSER51.xvg"/> |
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279 <has_text text="ramaPhiPsiVAL8.xvg"/> |
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2ed0df0360e5
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280 <has_text text="ramaPhiPsiGLY1.xvg"/> |
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2ed0df0360e5
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281 <has_text text="ramaPhiPsiLEU38.xvg"/> |
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2ed0df0360e5
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282 <has_text text="ramaPhiPsiTHR13.xvg"/> |
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2ed0df0360e5
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283 <has_text text="--input-format xvg --output output_constava.csv --window 3 --degrees"/> |
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284 <not_has_text text="constava fit-model"/> |
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2ed0df0360e5
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285 </assert_command> |
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286 <output name="file_contents" file="expected/test_002.csv" ftype="csv"/> |
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287 </test> |
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288 |
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289 <!-- ======================================================================= --> |
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290 <!-- Test scenarios: Custom PDF with default training data --> |
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291 <!-- ======================================================================= --> |
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292 |
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293 <!-- test_003: custom probability density functions: kde --> |
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294 <test expect_num_outputs="1"> |
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295 <section name="input_options"> |
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296 <param name="input_files" value="csv/dihedrals.mini.csv"/> |
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297 <param name="input_degrees" value=""/> |
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298 <param name="input_precision" value="5"/> |
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299 </section> |
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300 <section name="conformational_state_model_options"> |
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301 <conditional name="custom_model"> |
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302 <param name="use_custom_model" value="true"/> |
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303 <conditional name="model_type_options"> |
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304 <param name="model_type" value="kde"/> |
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305 <param name="bandwidth" value="0.15"/> |
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306 </conditional> |
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307 </conditional> |
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308 </section> |
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309 <assert_command> |
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310 <has_text text="constava fit-model -vv --model-type kde --kde-bandwidth 0.15 --output custom_model.kde.pkl"/> |
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2ed0df0360e5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/constava commit 77814d75404602f3fb6b791dd79a17653de22d45
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311 <has_text text="constava analyze -vv --precision 5 --input dihedrals.mini.csv --input-format csv --output output_constava.csv --window 3 --load-model custom_model.kde.pkl"/> |
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2ed0df0360e5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/constava commit 77814d75404602f3fb6b791dd79a17653de22d45
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312 </assert_command> |
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2ed0df0360e5
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313 <output name="file_contents" file="expected/test_003.csv" ftype="csv"/> |
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2ed0df0360e5
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314 </test> |
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315 |
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2ed0df0360e5
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316 <!-- test_004: custom probability density functions: grid --> |
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2ed0df0360e5
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317 <test expect_num_outputs="1"> |
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2ed0df0360e5
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318 <section name="input_options"> |
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2ed0df0360e5
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319 <param name="input_files" value="csv/dihedrals.mini.csv"/> |
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2ed0df0360e5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/constava commit 77814d75404602f3fb6b791dd79a17653de22d45
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320 <param name="input_degrees" value=""/> |
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2ed0df0360e5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/constava commit 77814d75404602f3fb6b791dd79a17653de22d45
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321 <param name="input_precision" value="5"/> |
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2ed0df0360e5
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322 </section> |
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323 <section name="conformational_state_model_options"> |
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2ed0df0360e5
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324 <conditional name="custom_model"> |
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2ed0df0360e5
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325 <param name="use_custom_model" value="true"/> |
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2ed0df0360e5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/constava commit 77814d75404602f3fb6b791dd79a17653de22d45
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326 <conditional name="model_type_options"> |
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2ed0df0360e5
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327 <param name="model_type" value="grid"/> |
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2ed0df0360e5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/constava commit 77814d75404602f3fb6b791dd79a17653de22d45
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328 <param name="bandwidth" value="0.15"/> |
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2ed0df0360e5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/constava commit 77814d75404602f3fb6b791dd79a17653de22d45
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329 <param name="custom_model_grid_points" value="1500"/> |
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2ed0df0360e5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/constava commit 77814d75404602f3fb6b791dd79a17653de22d45
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330 </conditional> |
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2ed0df0360e5
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331 </conditional> |
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2ed0df0360e5
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332 </section> |
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2ed0df0360e5
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333 <assert_command> |
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2ed0df0360e5
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334 <has_text text="constava fit-model -vv --model-type grid --grid-points 1500 --kde-bandwidth 0.15 --output custom_model.grid.pkl"/> |
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2ed0df0360e5
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335 <has_text text="constava analyze -vv --precision 5 --input dihedrals.mini.csv --input-format csv --output output_constava.csv --window 3 --load-model custom_model.grid.pkl"/> |
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2ed0df0360e5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/constava commit 77814d75404602f3fb6b791dd79a17653de22d45
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336 </assert_command> |
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337 <output name="file_contents" file="expected/test_004.csv" ftype="csv"/> |
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2ed0df0360e5
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338 </test> |
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339 |
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340 <!-- ======================================================================= --> |
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341 <!-- Test scenarios: Custom PDF with custom training data in JSON --> |
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342 <!-- ======================================================================= --> |
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343 |
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344 <!-- test_005: custom probability density functions with custom json: kde --> |
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345 <test expect_num_outputs="1"> |
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346 <section name="input_options"> |
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347 <param name="input_files" value="csv/dihedrals.mini.csv"/> |
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2ed0df0360e5
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348 <param name="input_degrees" value=""/> |
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2ed0df0360e5
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349 <param name="input_precision" value="5"/> |
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350 </section> |
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351 <section name="conformational_state_model_options"> |
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2ed0df0360e5
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352 <conditional name="custom_model"> |
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2ed0df0360e5
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353 <param name="use_custom_model" value="true"/> |
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2ed0df0360e5
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354 <conditional name="model_type_options"> |
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2ed0df0360e5
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355 <param name="model_type" value="kde"/> |
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2ed0df0360e5
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356 <param name="bandwidth" value="0.15"/> |
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2ed0df0360e5
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357 </conditional> |
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2ed0df0360e5
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358 <conditional name="custom_input_json"> |
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2ed0df0360e5
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359 <param name="use_custom_input_file" value="true"/> |
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2ed0df0360e5
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360 <param name="custom_input_file" value="custom-training-data/constava_csdata.mini.json"/> |
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2ed0df0360e5
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361 </conditional> |
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362 </conditional> |
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363 </section> |
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2ed0df0360e5
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364 <assert_command> |
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2ed0df0360e5
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365 <has_text text="constava fit-model -vv --model-type kde --kde-bandwidth 0.15 --output custom_model.kde.pkl --input constava_csdata.mini.json"/> |
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2ed0df0360e5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/constava commit 77814d75404602f3fb6b791dd79a17653de22d45
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366 <has_text text="constava analyze -vv --precision 5 --input dihedrals.mini.csv --input-format csv --output output_constava.csv --window 3 --load-model custom_model.kde.pkl"/> |
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2ed0df0360e5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/constava commit 77814d75404602f3fb6b791dd79a17653de22d45
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367 </assert_command> |
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368 <output name="file_contents" file="expected/test_005.csv" ftype="csv"/> |
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369 </test> |
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370 |
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371 <!-- test_006: custom probability density functions with custom json: grid --> |
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372 <test expect_num_outputs="1"> |
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373 <section name="input_options"> |
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374 <param name="input_files" value="csv/dihedrals.mini.csv"/> |
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2ed0df0360e5
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375 <param name="input_degrees" value=""/> |
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376 <param name="input_precision" value="5"/> |
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377 </section> |
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378 <section name="conformational_state_model_options"> |
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379 <conditional name="custom_model"> |
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380 <param name="use_custom_model" value="true"/> |
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2ed0df0360e5
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381 <conditional name="model_type_options"> |
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382 <param name="model_type" value="grid"/> |
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383 <param name="bandwidth" value="0.15"/> |
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384 <param name="custom_model_grid_points" value="1500"/> |
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2ed0df0360e5
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385 </conditional> |
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386 <conditional name="custom_input_json"> |
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387 <param name="use_custom_input_file" value="true"/> |
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2ed0df0360e5
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388 <param name="custom_input_file" value="custom-training-data/constava_csdata.mini.json"/> |
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2ed0df0360e5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/constava commit 77814d75404602f3fb6b791dd79a17653de22d45
iuc
parents:
diff
changeset
|
389 </conditional> |
|
2ed0df0360e5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/constava commit 77814d75404602f3fb6b791dd79a17653de22d45
iuc
parents:
diff
changeset
|
390 </conditional> |
|
2ed0df0360e5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/constava commit 77814d75404602f3fb6b791dd79a17653de22d45
iuc
parents:
diff
changeset
|
391 </section> |
|
2ed0df0360e5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/constava commit 77814d75404602f3fb6b791dd79a17653de22d45
iuc
parents:
diff
changeset
|
392 <assert_command> |
|
2ed0df0360e5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/constava commit 77814d75404602f3fb6b791dd79a17653de22d45
iuc
parents:
diff
changeset
|
393 <has_text text="constava fit-model -vv --model-type grid --grid-points 1500 --kde-bandwidth 0.15 --output custom_model.grid.pkl --input constava_csdata.mini.json"/> |
|
2ed0df0360e5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/constava commit 77814d75404602f3fb6b791dd79a17653de22d45
iuc
parents:
diff
changeset
|
394 <has_text text="constava analyze -vv --precision 5 --input dihedrals.mini.csv --input-format csv --output output_constava.csv --window 3 --load-model custom_model.grid.pkl"/> |
|
2ed0df0360e5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/constava commit 77814d75404602f3fb6b791dd79a17653de22d45
iuc
parents:
diff
changeset
|
395 </assert_command> |
|
2ed0df0360e5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/constava commit 77814d75404602f3fb6b791dd79a17653de22d45
iuc
parents:
diff
changeset
|
396 <output name="file_contents" file="expected/test_006.csv" ftype="csv"/> |
|
2ed0df0360e5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/constava commit 77814d75404602f3fb6b791dd79a17653de22d45
iuc
parents:
diff
changeset
|
397 </test> |
|
2ed0df0360e5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/constava commit 77814d75404602f3fb6b791dd79a17653de22d45
iuc
parents:
diff
changeset
|
398 <!-- ======================================================================= --> |
|
2ed0df0360e5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/constava commit 77814d75404602f3fb6b791dd79a17653de22d45
iuc
parents:
diff
changeset
|
399 <!-- Test scenarios: Default PDF with bootstrap --> |
|
2ed0df0360e5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/constava commit 77814d75404602f3fb6b791dd79a17653de22d45
iuc
parents:
diff
changeset
|
400 <!-- ======================================================================= --> |
|
2ed0df0360e5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/constava commit 77814d75404602f3fb6b791dd79a17653de22d45
iuc
parents:
diff
changeset
|
401 |
|
2ed0df0360e5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/constava commit 77814d75404602f3fb6b791dd79a17653de22d45
iuc
parents:
diff
changeset
|
402 <!-- test_007: CSV Dihedrals in radians with bootstrap with default train data --> |
|
2ed0df0360e5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/constava commit 77814d75404602f3fb6b791dd79a17653de22d45
iuc
parents:
diff
changeset
|
403 <test expect_num_outputs="1"> |
|
2ed0df0360e5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/constava commit 77814d75404602f3fb6b791dd79a17653de22d45
iuc
parents:
diff
changeset
|
404 <section name="input_options"> |
|
2ed0df0360e5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/constava commit 77814d75404602f3fb6b791dd79a17653de22d45
iuc
parents:
diff
changeset
|
405 <param name="input_files" value="csv/dihedrals.mini.csv"/> |
|
2ed0df0360e5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/constava commit 77814d75404602f3fb6b791dd79a17653de22d45
iuc
parents:
diff
changeset
|
406 <param name="input_degrees" value=""/> |
|
2ed0df0360e5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/constava commit 77814d75404602f3fb6b791dd79a17653de22d45
iuc
parents:
diff
changeset
|
407 <param name="input_precision" value="5"/> |
|
2ed0df0360e5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/constava commit 77814d75404602f3fb6b791dd79a17653de22d45
iuc
parents:
diff
changeset
|
408 </section> |
|
2ed0df0360e5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/constava commit 77814d75404602f3fb6b791dd79a17653de22d45
iuc
parents:
diff
changeset
|
409 <section name="conformational_state_model_options"> |
|
2ed0df0360e5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/constava commit 77814d75404602f3fb6b791dd79a17653de22d45
iuc
parents:
diff
changeset
|
410 <conditional name="custom_model"> |
|
2ed0df0360e5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/constava commit 77814d75404602f3fb6b791dd79a17653de22d45
iuc
parents:
diff
changeset
|
411 <param name="use_custom_model" value="false"/> |
|
2ed0df0360e5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/constava commit 77814d75404602f3fb6b791dd79a17653de22d45
iuc
parents:
diff
changeset
|
412 </conditional> |
|
2ed0df0360e5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/constava commit 77814d75404602f3fb6b791dd79a17653de22d45
iuc
parents:
diff
changeset
|
413 </section> |
|
2ed0df0360e5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/constava commit 77814d75404602f3fb6b791dd79a17653de22d45
iuc
parents:
diff
changeset
|
414 <section name="subsampling_options"> |
|
2ed0df0360e5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/constava commit 77814d75404602f3fb6b791dd79a17653de22d45
iuc
parents:
diff
changeset
|
415 <conditional name="sampling_options"> |
|
2ed0df0360e5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/constava commit 77814d75404602f3fb6b791dd79a17653de22d45
iuc
parents:
diff
changeset
|
416 <param name="subsampling_type" value="bootstrap"/> |
|
2ed0df0360e5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/constava commit 77814d75404602f3fb6b791dd79a17653de22d45
iuc
parents:
diff
changeset
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417 <param name="bootstrap_size" value="3"/> |
|
2ed0df0360e5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/constava commit 77814d75404602f3fb6b791dd79a17653de22d45
iuc
parents:
diff
changeset
|
418 <param name="return_bootstrap_series" value="false"/> |
|
2ed0df0360e5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/constava commit 77814d75404602f3fb6b791dd79a17653de22d45
iuc
parents:
diff
changeset
|
419 <param name="bootstrap_samples" value="10"/> |
|
2ed0df0360e5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/constava commit 77814d75404602f3fb6b791dd79a17653de22d45
iuc
parents:
diff
changeset
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420 <param name="bootstrap_seed" value="89"/> |
|
2ed0df0360e5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/constava commit 77814d75404602f3fb6b791dd79a17653de22d45
iuc
parents:
diff
changeset
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421 </conditional> |
|
2ed0df0360e5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/constava commit 77814d75404602f3fb6b791dd79a17653de22d45
iuc
parents:
diff
changeset
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422 </section> |
|
2ed0df0360e5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/constava commit 77814d75404602f3fb6b791dd79a17653de22d45
iuc
parents:
diff
changeset
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423 <assert_command> |
|
2ed0df0360e5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/constava commit 77814d75404602f3fb6b791dd79a17653de22d45
iuc
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changeset
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424 <has_text text="constava analyze -vv --precision 5 --input dihedrals.mini.csv --input-format csv --output output_constava.csv --bootstrap 3 --bootstrap-samples 10 --seed 89"/> |
|
2ed0df0360e5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/constava commit 77814d75404602f3fb6b791dd79a17653de22d45
iuc
parents:
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changeset
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425 <not_has_text text="constava fit-model"/> |
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2ed0df0360e5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/constava commit 77814d75404602f3fb6b791dd79a17653de22d45
iuc
parents:
diff
changeset
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426 </assert_command> |
|
2ed0df0360e5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/constava commit 77814d75404602f3fb6b791dd79a17653de22d45
iuc
parents:
diff
changeset
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427 <output name="file_contents" file="expected/test_007.csv" ftype="csv"/> |
|
2ed0df0360e5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/constava commit 77814d75404602f3fb6b791dd79a17653de22d45
iuc
parents:
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changeset
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428 </test> |
|
2ed0df0360e5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/constava commit 77814d75404602f3fb6b791dd79a17653de22d45
iuc
parents:
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changeset
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429 |
|
2ed0df0360e5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/constava commit 77814d75404602f3fb6b791dd79a17653de22d45
iuc
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changeset
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430 <!-- test_008: CSV Dihedrals in radians with bootstrap series with default train data --> |
|
2ed0df0360e5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/constava commit 77814d75404602f3fb6b791dd79a17653de22d45
iuc
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changeset
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431 <test expect_num_outputs="1"> |
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2ed0df0360e5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/constava commit 77814d75404602f3fb6b791dd79a17653de22d45
iuc
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changeset
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432 <section name="input_options"> |
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2ed0df0360e5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/constava commit 77814d75404602f3fb6b791dd79a17653de22d45
iuc
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changeset
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433 <param name="input_files" value="csv/dihedrals.mini.csv"/> |
|
2ed0df0360e5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/constava commit 77814d75404602f3fb6b791dd79a17653de22d45
iuc
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changeset
|
434 <param name="input_degrees" value=""/> |
|
2ed0df0360e5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/constava commit 77814d75404602f3fb6b791dd79a17653de22d45
iuc
parents:
diff
changeset
|
435 <param name="input_precision" value="5"/> |
|
2ed0df0360e5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/constava commit 77814d75404602f3fb6b791dd79a17653de22d45
iuc
parents:
diff
changeset
|
436 </section> |
|
2ed0df0360e5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/constava commit 77814d75404602f3fb6b791dd79a17653de22d45
iuc
parents:
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changeset
|
437 <section name="conformational_state_model_options"> |
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2ed0df0360e5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/constava commit 77814d75404602f3fb6b791dd79a17653de22d45
iuc
parents:
diff
changeset
|
438 <conditional name="custom_model"> |
|
2ed0df0360e5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/constava commit 77814d75404602f3fb6b791dd79a17653de22d45
iuc
parents:
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changeset
|
439 <param name="use_custom_model" value="false"/> |
|
2ed0df0360e5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/constava commit 77814d75404602f3fb6b791dd79a17653de22d45
iuc
parents:
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changeset
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440 </conditional> |
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2ed0df0360e5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/constava commit 77814d75404602f3fb6b791dd79a17653de22d45
iuc
parents:
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changeset
|
441 </section> |
|
2ed0df0360e5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/constava commit 77814d75404602f3fb6b791dd79a17653de22d45
iuc
parents:
diff
changeset
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442 <section name="subsampling_options"> |
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2ed0df0360e5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/constava commit 77814d75404602f3fb6b791dd79a17653de22d45
iuc
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diff
changeset
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443 <conditional name="sampling_options"> |
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2ed0df0360e5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/constava commit 77814d75404602f3fb6b791dd79a17653de22d45
iuc
parents:
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changeset
|
444 <param name="subsampling_type" value="bootstrap"/> |
|
2ed0df0360e5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/constava commit 77814d75404602f3fb6b791dd79a17653de22d45
iuc
parents:
diff
changeset
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445 <param name="bootstrap_size" value="3"/> |
|
2ed0df0360e5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/constava commit 77814d75404602f3fb6b791dd79a17653de22d45
iuc
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changeset
|
446 <param name="return_bootstrap_series" value="true"/> |
|
2ed0df0360e5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/constava commit 77814d75404602f3fb6b791dd79a17653de22d45
iuc
parents:
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changeset
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447 <param name="bootstrap_samples" value="10"/> |
|
2ed0df0360e5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/constava commit 77814d75404602f3fb6b791dd79a17653de22d45
iuc
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changeset
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448 <param name="bootstrap_seed" value="89"/> |
|
2ed0df0360e5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/constava commit 77814d75404602f3fb6b791dd79a17653de22d45
iuc
parents:
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changeset
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449 </conditional> |
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2ed0df0360e5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/constava commit 77814d75404602f3fb6b791dd79a17653de22d45
iuc
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changeset
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450 </section> |
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2ed0df0360e5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/constava commit 77814d75404602f3fb6b791dd79a17653de22d45
iuc
parents:
diff
changeset
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451 <assert_command> |
|
2ed0df0360e5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/constava commit 77814d75404602f3fb6b791dd79a17653de22d45
iuc
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changeset
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452 <has_text text="constava analyze -vv --precision 5 --input dihedrals.mini.csv --input-format csv --output output_constava.csv --bootstrap-series 3 --bootstrap-samples 10 --seed 89"/> |
|
2ed0df0360e5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/constava commit 77814d75404602f3fb6b791dd79a17653de22d45
iuc
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changeset
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453 <not_has_text text="constava fit-model"/> |
|
2ed0df0360e5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/constava commit 77814d75404602f3fb6b791dd79a17653de22d45
iuc
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changeset
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454 </assert_command> |
|
2ed0df0360e5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/constava commit 77814d75404602f3fb6b791dd79a17653de22d45
iuc
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changeset
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455 <output name="file_contents" file="expected/test_008.csv" ftype="csv"/> |
|
2ed0df0360e5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/constava commit 77814d75404602f3fb6b791dd79a17653de22d45
iuc
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changeset
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456 </test> |
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2ed0df0360e5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/constava commit 77814d75404602f3fb6b791dd79a17653de22d45
iuc
parents:
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changeset
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457 |
|
2ed0df0360e5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/constava commit 77814d75404602f3fb6b791dd79a17653de22d45
iuc
parents:
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changeset
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458 <!-- ======================================================================= --> |
|
2ed0df0360e5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/constava commit 77814d75404602f3fb6b791dd79a17653de22d45
iuc
parents:
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changeset
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459 <!-- Test scenarios: Custom PDF with bootstrap --> |
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2ed0df0360e5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/constava commit 77814d75404602f3fb6b791dd79a17653de22d45
iuc
parents:
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changeset
|
460 <!-- ======================================================================= --> |
|
2ed0df0360e5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/constava commit 77814d75404602f3fb6b791dd79a17653de22d45
iuc
parents:
diff
changeset
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461 |
|
2ed0df0360e5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/constava commit 77814d75404602f3fb6b791dd79a17653de22d45
iuc
parents:
diff
changeset
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462 <!-- test_009: CSV Dihedrals in radians with bootstrap using custom PDF (kde) using default data to train the PDF --> |
|
2ed0df0360e5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/constava commit 77814d75404602f3fb6b791dd79a17653de22d45
iuc
parents:
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changeset
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463 <test expect_num_outputs="1"> |
|
2ed0df0360e5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/constava commit 77814d75404602f3fb6b791dd79a17653de22d45
iuc
parents:
diff
changeset
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464 <section name="input_options"> |
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2ed0df0360e5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/constava commit 77814d75404602f3fb6b791dd79a17653de22d45
iuc
parents:
diff
changeset
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465 <param name="input_files" value="csv/dihedrals.mini.csv"/> |
|
2ed0df0360e5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/constava commit 77814d75404602f3fb6b791dd79a17653de22d45
iuc
parents:
diff
changeset
|
466 <param name="input_degrees" value=""/> |
|
2ed0df0360e5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/constava commit 77814d75404602f3fb6b791dd79a17653de22d45
iuc
parents:
diff
changeset
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467 <param name="input_precision" value="5"/> |
|
2ed0df0360e5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/constava commit 77814d75404602f3fb6b791dd79a17653de22d45
iuc
parents:
diff
changeset
|
468 </section> |
|
2ed0df0360e5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/constava commit 77814d75404602f3fb6b791dd79a17653de22d45
iuc
parents:
diff
changeset
|
469 <section name="conformational_state_model_options"> |
|
2ed0df0360e5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/constava commit 77814d75404602f3fb6b791dd79a17653de22d45
iuc
parents:
diff
changeset
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470 <conditional name="custom_model"> |
|
2ed0df0360e5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/constava commit 77814d75404602f3fb6b791dd79a17653de22d45
iuc
parents:
diff
changeset
|
471 <param name="use_custom_model" value="true"/> |
|
2ed0df0360e5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/constava commit 77814d75404602f3fb6b791dd79a17653de22d45
iuc
parents:
diff
changeset
|
472 <conditional name="model_type_options"> |
|
2ed0df0360e5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/constava commit 77814d75404602f3fb6b791dd79a17653de22d45
iuc
parents:
diff
changeset
|
473 <param name="model_type" value="kde"/> |
|
2ed0df0360e5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/constava commit 77814d75404602f3fb6b791dd79a17653de22d45
iuc
parents:
diff
changeset
|
474 <param name="bandwidth" value="0.15"/> |
|
2ed0df0360e5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/constava commit 77814d75404602f3fb6b791dd79a17653de22d45
iuc
parents:
diff
changeset
|
475 </conditional> |
|
2ed0df0360e5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/constava commit 77814d75404602f3fb6b791dd79a17653de22d45
iuc
parents:
diff
changeset
|
476 </conditional> |
|
2ed0df0360e5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/constava commit 77814d75404602f3fb6b791dd79a17653de22d45
iuc
parents:
diff
changeset
|
477 </section> |
|
2ed0df0360e5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/constava commit 77814d75404602f3fb6b791dd79a17653de22d45
iuc
parents:
diff
changeset
|
478 <section name="subsampling_options"> |
|
2ed0df0360e5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/constava commit 77814d75404602f3fb6b791dd79a17653de22d45
iuc
parents:
diff
changeset
|
479 <conditional name="sampling_options"> |
|
2ed0df0360e5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/constava commit 77814d75404602f3fb6b791dd79a17653de22d45
iuc
parents:
diff
changeset
|
480 <param name="subsampling_type" value="bootstrap"/> |
|
2ed0df0360e5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/constava commit 77814d75404602f3fb6b791dd79a17653de22d45
iuc
parents:
diff
changeset
|
481 <param name="bootstrap_size" value="3"/> |
|
2ed0df0360e5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/constava commit 77814d75404602f3fb6b791dd79a17653de22d45
iuc
parents:
diff
changeset
|
482 <param name="return_bootstrap_series" value="false"/> |
|
2ed0df0360e5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/constava commit 77814d75404602f3fb6b791dd79a17653de22d45
iuc
parents:
diff
changeset
|
483 <param name="bootstrap_samples" value="10"/> |
|
2ed0df0360e5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/constava commit 77814d75404602f3fb6b791dd79a17653de22d45
iuc
parents:
diff
changeset
|
484 <param name="bootstrap_seed" value="89"/> |
|
2ed0df0360e5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/constava commit 77814d75404602f3fb6b791dd79a17653de22d45
iuc
parents:
diff
changeset
|
485 </conditional> |
|
2ed0df0360e5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/constava commit 77814d75404602f3fb6b791dd79a17653de22d45
iuc
parents:
diff
changeset
|
486 </section> |
|
2ed0df0360e5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/constava commit 77814d75404602f3fb6b791dd79a17653de22d45
iuc
parents:
diff
changeset
|
487 <assert_command> |
|
2ed0df0360e5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/constava commit 77814d75404602f3fb6b791dd79a17653de22d45
iuc
parents:
diff
changeset
|
488 <has_text text="constava fit-model -vv --model-type kde --kde-bandwidth 0.15 --output custom_model.kde.pkl"/> |
|
2ed0df0360e5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/constava commit 77814d75404602f3fb6b791dd79a17653de22d45
iuc
parents:
diff
changeset
|
489 <has_text text="constava analyze -vv --precision 5 --input dihedrals.mini.csv --input-format csv --output output_constava.csv --bootstrap 3 --bootstrap-samples 10 --seed 89 --load-model custom_model.kde.pkl"/> |
|
2ed0df0360e5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/constava commit 77814d75404602f3fb6b791dd79a17653de22d45
iuc
parents:
diff
changeset
|
490 </assert_command> |
|
2ed0df0360e5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/constava commit 77814d75404602f3fb6b791dd79a17653de22d45
iuc
parents:
diff
changeset
|
491 <output name="file_contents" file="expected/test_009.csv" ftype="csv"/> |
|
2ed0df0360e5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/constava commit 77814d75404602f3fb6b791dd79a17653de22d45
iuc
parents:
diff
changeset
|
492 </test> |
|
2ed0df0360e5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/constava commit 77814d75404602f3fb6b791dd79a17653de22d45
iuc
parents:
diff
changeset
|
493 |
|
2ed0df0360e5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/constava commit 77814d75404602f3fb6b791dd79a17653de22d45
iuc
parents:
diff
changeset
|
494 <!-- test_010: CSV Dihedrals in radians with bootstrap using custom PDF (kde) using custom training data in json --> |
|
2ed0df0360e5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/constava commit 77814d75404602f3fb6b791dd79a17653de22d45
iuc
parents:
diff
changeset
|
495 <test expect_num_outputs="1"> |
|
2ed0df0360e5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/constava commit 77814d75404602f3fb6b791dd79a17653de22d45
iuc
parents:
diff
changeset
|
496 <section name="input_options"> |
|
2ed0df0360e5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/constava commit 77814d75404602f3fb6b791dd79a17653de22d45
iuc
parents:
diff
changeset
|
497 <param name="input_files" value="csv/dihedrals.mini.csv"/> |
|
2ed0df0360e5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/constava commit 77814d75404602f3fb6b791dd79a17653de22d45
iuc
parents:
diff
changeset
|
498 <param name="input_degrees" value=""/> |
|
2ed0df0360e5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/constava commit 77814d75404602f3fb6b791dd79a17653de22d45
iuc
parents:
diff
changeset
|
499 <param name="input_precision" value="5"/> |
|
2ed0df0360e5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/constava commit 77814d75404602f3fb6b791dd79a17653de22d45
iuc
parents:
diff
changeset
|
500 </section> |
|
2ed0df0360e5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/constava commit 77814d75404602f3fb6b791dd79a17653de22d45
iuc
parents:
diff
changeset
|
501 <section name="conformational_state_model_options"> |
|
2ed0df0360e5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/constava commit 77814d75404602f3fb6b791dd79a17653de22d45
iuc
parents:
diff
changeset
|
502 <conditional name="custom_model"> |
|
2ed0df0360e5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/constava commit 77814d75404602f3fb6b791dd79a17653de22d45
iuc
parents:
diff
changeset
|
503 <param name="use_custom_model" value="true"/> |
|
2ed0df0360e5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/constava commit 77814d75404602f3fb6b791dd79a17653de22d45
iuc
parents:
diff
changeset
|
504 <conditional name="model_type_options"> |
|
2ed0df0360e5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/constava commit 77814d75404602f3fb6b791dd79a17653de22d45
iuc
parents:
diff
changeset
|
505 <param name="model_type" value="kde"/> |
|
2ed0df0360e5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/constava commit 77814d75404602f3fb6b791dd79a17653de22d45
iuc
parents:
diff
changeset
|
506 <param name="bandwidth" value="0.15"/> |
|
2ed0df0360e5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/constava commit 77814d75404602f3fb6b791dd79a17653de22d45
iuc
parents:
diff
changeset
|
507 </conditional> |
|
2ed0df0360e5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/constava commit 77814d75404602f3fb6b791dd79a17653de22d45
iuc
parents:
diff
changeset
|
508 <conditional name="custom_input_json"> |
|
2ed0df0360e5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/constava commit 77814d75404602f3fb6b791dd79a17653de22d45
iuc
parents:
diff
changeset
|
509 <param name="use_custom_input_file" value="true"/> |
|
2ed0df0360e5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/constava commit 77814d75404602f3fb6b791dd79a17653de22d45
iuc
parents:
diff
changeset
|
510 <param name="custom_input_file" value="custom-training-data/constava_csdata.mini.json"/> |
|
2ed0df0360e5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/constava commit 77814d75404602f3fb6b791dd79a17653de22d45
iuc
parents:
diff
changeset
|
511 </conditional> |
|
2ed0df0360e5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/constava commit 77814d75404602f3fb6b791dd79a17653de22d45
iuc
parents:
diff
changeset
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512 </conditional> |
|
2ed0df0360e5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/constava commit 77814d75404602f3fb6b791dd79a17653de22d45
iuc
parents:
diff
changeset
|
513 </section> |
|
2ed0df0360e5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/constava commit 77814d75404602f3fb6b791dd79a17653de22d45
iuc
parents:
diff
changeset
|
514 <section name="subsampling_options"> |
|
2ed0df0360e5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/constava commit 77814d75404602f3fb6b791dd79a17653de22d45
iuc
parents:
diff
changeset
|
515 <conditional name="sampling_options"> |
|
2ed0df0360e5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/constava commit 77814d75404602f3fb6b791dd79a17653de22d45
iuc
parents:
diff
changeset
|
516 <param name="subsampling_type" value="bootstrap"/> |
|
2ed0df0360e5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/constava commit 77814d75404602f3fb6b791dd79a17653de22d45
iuc
parents:
diff
changeset
|
517 <param name="bootstrap_size" value="3"/> |
|
2ed0df0360e5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/constava commit 77814d75404602f3fb6b791dd79a17653de22d45
iuc
parents:
diff
changeset
|
518 <param name="return_bootstrap_series" value="false"/> |
|
2ed0df0360e5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/constava commit 77814d75404602f3fb6b791dd79a17653de22d45
iuc
parents:
diff
changeset
|
519 <param name="bootstrap_samples" value="10"/> |
|
2ed0df0360e5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/constava commit 77814d75404602f3fb6b791dd79a17653de22d45
iuc
parents:
diff
changeset
|
520 <param name="bootstrap_seed" value="89"/> |
|
2ed0df0360e5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/constava commit 77814d75404602f3fb6b791dd79a17653de22d45
iuc
parents:
diff
changeset
|
521 </conditional> |
|
2ed0df0360e5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/constava commit 77814d75404602f3fb6b791dd79a17653de22d45
iuc
parents:
diff
changeset
|
522 </section> |
|
2ed0df0360e5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/constava commit 77814d75404602f3fb6b791dd79a17653de22d45
iuc
parents:
diff
changeset
|
523 <assert_command> |
|
2ed0df0360e5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/constava commit 77814d75404602f3fb6b791dd79a17653de22d45
iuc
parents:
diff
changeset
|
524 <has_text text="constava fit-model -vv --model-type kde --kde-bandwidth 0.15 --output custom_model.kde.pkl --input constava_csdata.mini.json"/> |
|
2ed0df0360e5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/constava commit 77814d75404602f3fb6b791dd79a17653de22d45
iuc
parents:
diff
changeset
|
525 <has_text text="constava analyze -vv --precision 5 --input dihedrals.mini.csv --input-format csv --output output_constava.csv --bootstrap 3 --bootstrap-samples 10 --seed 89 --load-model custom_model.kde.pkl"/> |
|
2ed0df0360e5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/constava commit 77814d75404602f3fb6b791dd79a17653de22d45
iuc
parents:
diff
changeset
|
526 </assert_command> |
|
2ed0df0360e5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/constava commit 77814d75404602f3fb6b791dd79a17653de22d45
iuc
parents:
diff
changeset
|
527 <output name="file_contents" file="expected/test_010.csv" ftype="csv"/> |
|
2ed0df0360e5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/constava commit 77814d75404602f3fb6b791dd79a17653de22d45
iuc
parents:
diff
changeset
|
528 </test> |
|
2ed0df0360e5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/constava commit 77814d75404602f3fb6b791dd79a17653de22d45
iuc
parents:
diff
changeset
|
529 |
|
2ed0df0360e5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/constava commit 77814d75404602f3fb6b791dd79a17653de22d45
iuc
parents:
diff
changeset
|
530 <!-- test_011: CSV Dihedrals in radians with bootstrap series using custom PDF (kde) using default data to train the PDF --> |
|
2ed0df0360e5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/constava commit 77814d75404602f3fb6b791dd79a17653de22d45
iuc
parents:
diff
changeset
|
531 <test expect_num_outputs="1"> |
|
2ed0df0360e5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/constava commit 77814d75404602f3fb6b791dd79a17653de22d45
iuc
parents:
diff
changeset
|
532 <section name="input_options"> |
|
2ed0df0360e5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/constava commit 77814d75404602f3fb6b791dd79a17653de22d45
iuc
parents:
diff
changeset
|
533 <param name="input_files" value="csv/dihedrals.mini.csv"/> |
|
2ed0df0360e5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/constava commit 77814d75404602f3fb6b791dd79a17653de22d45
iuc
parents:
diff
changeset
|
534 <param name="input_degrees" value=""/> |
|
2ed0df0360e5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/constava commit 77814d75404602f3fb6b791dd79a17653de22d45
iuc
parents:
diff
changeset
|
535 <param name="input_precision" value="5"/> |
|
2ed0df0360e5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/constava commit 77814d75404602f3fb6b791dd79a17653de22d45
iuc
parents:
diff
changeset
|
536 </section> |
|
2ed0df0360e5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/constava commit 77814d75404602f3fb6b791dd79a17653de22d45
iuc
parents:
diff
changeset
|
537 <section name="conformational_state_model_options"> |
|
2ed0df0360e5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/constava commit 77814d75404602f3fb6b791dd79a17653de22d45
iuc
parents:
diff
changeset
|
538 <conditional name="custom_model"> |
|
2ed0df0360e5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/constava commit 77814d75404602f3fb6b791dd79a17653de22d45
iuc
parents:
diff
changeset
|
539 <param name="use_custom_model" value="true"/> |
|
2ed0df0360e5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/constava commit 77814d75404602f3fb6b791dd79a17653de22d45
iuc
parents:
diff
changeset
|
540 <conditional name="model_type_options"> |
|
2ed0df0360e5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/constava commit 77814d75404602f3fb6b791dd79a17653de22d45
iuc
parents:
diff
changeset
|
541 <param name="model_type" value="kde"/> |
|
2ed0df0360e5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/constava commit 77814d75404602f3fb6b791dd79a17653de22d45
iuc
parents:
diff
changeset
|
542 <param name="bandwidth" value="0.15"/> |
|
2ed0df0360e5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/constava commit 77814d75404602f3fb6b791dd79a17653de22d45
iuc
parents:
diff
changeset
|
543 </conditional> |
|
2ed0df0360e5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/constava commit 77814d75404602f3fb6b791dd79a17653de22d45
iuc
parents:
diff
changeset
|
544 </conditional> |
|
2ed0df0360e5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/constava commit 77814d75404602f3fb6b791dd79a17653de22d45
iuc
parents:
diff
changeset
|
545 </section> |
|
2ed0df0360e5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/constava commit 77814d75404602f3fb6b791dd79a17653de22d45
iuc
parents:
diff
changeset
|
546 <section name="subsampling_options"> |
|
2ed0df0360e5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/constava commit 77814d75404602f3fb6b791dd79a17653de22d45
iuc
parents:
diff
changeset
|
547 <conditional name="sampling_options"> |
|
2ed0df0360e5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/constava commit 77814d75404602f3fb6b791dd79a17653de22d45
iuc
parents:
diff
changeset
|
548 <param name="subsampling_type" value="bootstrap"/> |
|
2ed0df0360e5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/constava commit 77814d75404602f3fb6b791dd79a17653de22d45
iuc
parents:
diff
changeset
|
549 <param name="bootstrap_size" value="3"/> |
|
2ed0df0360e5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/constava commit 77814d75404602f3fb6b791dd79a17653de22d45
iuc
parents:
diff
changeset
|
550 <param name="return_bootstrap_series" value="true"/> |
|
2ed0df0360e5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/constava commit 77814d75404602f3fb6b791dd79a17653de22d45
iuc
parents:
diff
changeset
|
551 <param name="bootstrap_samples" value="10"/> |
|
2ed0df0360e5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/constava commit 77814d75404602f3fb6b791dd79a17653de22d45
iuc
parents:
diff
changeset
|
552 <param name="bootstrap_seed" value="89"/> |
|
2ed0df0360e5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/constava commit 77814d75404602f3fb6b791dd79a17653de22d45
iuc
parents:
diff
changeset
|
553 </conditional> |
|
2ed0df0360e5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/constava commit 77814d75404602f3fb6b791dd79a17653de22d45
iuc
parents:
diff
changeset
|
554 </section> |
|
2ed0df0360e5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/constava commit 77814d75404602f3fb6b791dd79a17653de22d45
iuc
parents:
diff
changeset
|
555 <assert_command> |
|
2ed0df0360e5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/constava commit 77814d75404602f3fb6b791dd79a17653de22d45
iuc
parents:
diff
changeset
|
556 <has_text text="constava fit-model -vv --model-type kde --kde-bandwidth 0.15 --output custom_model.kde.pkl"/> |
|
2ed0df0360e5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/constava commit 77814d75404602f3fb6b791dd79a17653de22d45
iuc
parents:
diff
changeset
|
557 <has_text text="constava analyze -vv --precision 5 --input dihedrals.mini.csv --input-format csv --output output_constava.csv --bootstrap-series 3 --bootstrap-samples 10 --seed 89 --load-model custom_model.kde.pkl"/> |
|
2ed0df0360e5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/constava commit 77814d75404602f3fb6b791dd79a17653de22d45
iuc
parents:
diff
changeset
|
558 </assert_command> |
|
2ed0df0360e5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/constava commit 77814d75404602f3fb6b791dd79a17653de22d45
iuc
parents:
diff
changeset
|
559 <output name="file_contents" file="expected/test_011.csv" ftype="csv"/> |
|
2ed0df0360e5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/constava commit 77814d75404602f3fb6b791dd79a17653de22d45
iuc
parents:
diff
changeset
|
560 </test> |
|
2ed0df0360e5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/constava commit 77814d75404602f3fb6b791dd79a17653de22d45
iuc
parents:
diff
changeset
|
561 |
|
2ed0df0360e5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/constava commit 77814d75404602f3fb6b791dd79a17653de22d45
iuc
parents:
diff
changeset
|
562 <!-- test_012: CSV Dihedrals in radians with bootstrap series using custom PDF (kde) using custom training data in json --> |
|
2ed0df0360e5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/constava commit 77814d75404602f3fb6b791dd79a17653de22d45
iuc
parents:
diff
changeset
|
563 <test expect_num_outputs="1"> |
|
2ed0df0360e5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/constava commit 77814d75404602f3fb6b791dd79a17653de22d45
iuc
parents:
diff
changeset
|
564 <section name="input_options"> |
|
2ed0df0360e5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/constava commit 77814d75404602f3fb6b791dd79a17653de22d45
iuc
parents:
diff
changeset
|
565 <param name="input_files" value="csv/dihedrals.mini.csv"/> |
|
2ed0df0360e5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/constava commit 77814d75404602f3fb6b791dd79a17653de22d45
iuc
parents:
diff
changeset
|
566 <param name="input_degrees" value=""/> |
|
2ed0df0360e5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/constava commit 77814d75404602f3fb6b791dd79a17653de22d45
iuc
parents:
diff
changeset
|
567 <param name="input_precision" value="5"/> |
|
2ed0df0360e5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/constava commit 77814d75404602f3fb6b791dd79a17653de22d45
iuc
parents:
diff
changeset
|
568 </section> |
|
2ed0df0360e5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/constava commit 77814d75404602f3fb6b791dd79a17653de22d45
iuc
parents:
diff
changeset
|
569 <section name="conformational_state_model_options"> |
|
2ed0df0360e5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/constava commit 77814d75404602f3fb6b791dd79a17653de22d45
iuc
parents:
diff
changeset
|
570 <conditional name="custom_model"> |
|
2ed0df0360e5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/constava commit 77814d75404602f3fb6b791dd79a17653de22d45
iuc
parents:
diff
changeset
|
571 <param name="use_custom_model" value="true"/> |
|
2ed0df0360e5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/constava commit 77814d75404602f3fb6b791dd79a17653de22d45
iuc
parents:
diff
changeset
|
572 <conditional name="model_type_options"> |
|
2ed0df0360e5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/constava commit 77814d75404602f3fb6b791dd79a17653de22d45
iuc
parents:
diff
changeset
|
573 <param name="model_type" value="kde"/> |
|
2ed0df0360e5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/constava commit 77814d75404602f3fb6b791dd79a17653de22d45
iuc
parents:
diff
changeset
|
574 <param name="bandwidth" value="0.15"/> |
|
2ed0df0360e5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/constava commit 77814d75404602f3fb6b791dd79a17653de22d45
iuc
parents:
diff
changeset
|
575 </conditional> |
|
2ed0df0360e5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/constava commit 77814d75404602f3fb6b791dd79a17653de22d45
iuc
parents:
diff
changeset
|
576 <conditional name="custom_input_json"> |
|
2ed0df0360e5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/constava commit 77814d75404602f3fb6b791dd79a17653de22d45
iuc
parents:
diff
changeset
|
577 <param name="use_custom_input_file" value="true"/> |
|
2ed0df0360e5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/constava commit 77814d75404602f3fb6b791dd79a17653de22d45
iuc
parents:
diff
changeset
|
578 <param name="custom_input_file" value="custom-training-data/constava_csdata.mini.json"/> |
|
2ed0df0360e5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/constava commit 77814d75404602f3fb6b791dd79a17653de22d45
iuc
parents:
diff
changeset
|
579 </conditional> |
|
2ed0df0360e5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/constava commit 77814d75404602f3fb6b791dd79a17653de22d45
iuc
parents:
diff
changeset
|
580 </conditional> |
|
2ed0df0360e5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/constava commit 77814d75404602f3fb6b791dd79a17653de22d45
iuc
parents:
diff
changeset
|
581 </section> |
|
2ed0df0360e5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/constava commit 77814d75404602f3fb6b791dd79a17653de22d45
iuc
parents:
diff
changeset
|
582 <section name="subsampling_options"> |
|
2ed0df0360e5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/constava commit 77814d75404602f3fb6b791dd79a17653de22d45
iuc
parents:
diff
changeset
|
583 <conditional name="sampling_options"> |
|
2ed0df0360e5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/constava commit 77814d75404602f3fb6b791dd79a17653de22d45
iuc
parents:
diff
changeset
|
584 <param name="subsampling_type" value="bootstrap"/> |
|
2ed0df0360e5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/constava commit 77814d75404602f3fb6b791dd79a17653de22d45
iuc
parents:
diff
changeset
|
585 <param name="bootstrap_size" value="3"/> |
|
2ed0df0360e5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/constava commit 77814d75404602f3fb6b791dd79a17653de22d45
iuc
parents:
diff
changeset
|
586 <param name="return_bootstrap_series" value="true"/> |
|
2ed0df0360e5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/constava commit 77814d75404602f3fb6b791dd79a17653de22d45
iuc
parents:
diff
changeset
|
587 <param name="bootstrap_samples" value="10"/> |
|
2ed0df0360e5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/constava commit 77814d75404602f3fb6b791dd79a17653de22d45
iuc
parents:
diff
changeset
|
588 <param name="bootstrap_seed" value="89"/> |
|
2ed0df0360e5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/constava commit 77814d75404602f3fb6b791dd79a17653de22d45
iuc
parents:
diff
changeset
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589 </conditional> |
|
2ed0df0360e5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/constava commit 77814d75404602f3fb6b791dd79a17653de22d45
iuc
parents:
diff
changeset
|
590 </section> |
|
2ed0df0360e5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/constava commit 77814d75404602f3fb6b791dd79a17653de22d45
iuc
parents:
diff
changeset
|
591 <assert_command> |
|
2ed0df0360e5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/constava commit 77814d75404602f3fb6b791dd79a17653de22d45
iuc
parents:
diff
changeset
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592 <has_text text="constava fit-model -vv --model-type kde --kde-bandwidth 0.15 --output custom_model.kde.pkl --input constava_csdata.mini.json"/> |
|
2ed0df0360e5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/constava commit 77814d75404602f3fb6b791dd79a17653de22d45
iuc
parents:
diff
changeset
|
593 <has_text text="constava analyze -vv --precision 5 --input dihedrals.mini.csv --input-format csv --output output_constava.csv --bootstrap-series 3 --bootstrap-samples 10 --seed 89 --load-model custom_model.kde.pkl"/> |
|
2ed0df0360e5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/constava commit 77814d75404602f3fb6b791dd79a17653de22d45
iuc
parents:
diff
changeset
|
594 </assert_command> |
|
2ed0df0360e5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/constava commit 77814d75404602f3fb6b791dd79a17653de22d45
iuc
parents:
diff
changeset
|
595 <output name="file_contents" file="expected/test_012.csv" ftype="csv"/> |
|
2ed0df0360e5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/constava commit 77814d75404602f3fb6b791dd79a17653de22d45
iuc
parents:
diff
changeset
|
596 </test> |
|
2ed0df0360e5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/constava commit 77814d75404602f3fb6b791dd79a17653de22d45
iuc
parents:
diff
changeset
|
597 |
|
2ed0df0360e5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/constava commit 77814d75404602f3fb6b791dd79a17653de22d45
iuc
parents:
diff
changeset
|
598 <!-- test_013: Testing the bootstrap validators --> |
|
2ed0df0360e5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/constava commit 77814d75404602f3fb6b791dd79a17653de22d45
iuc
parents:
diff
changeset
|
599 <test expect_num_outputs="1"> |
|
2ed0df0360e5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/constava commit 77814d75404602f3fb6b791dd79a17653de22d45
iuc
parents:
diff
changeset
|
600 <section name="input_options"> |
|
2ed0df0360e5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/constava commit 77814d75404602f3fb6b791dd79a17653de22d45
iuc
parents:
diff
changeset
|
601 <param name="input_files" value="csv/dihedrals.mini.csv"/> |
|
2ed0df0360e5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/constava commit 77814d75404602f3fb6b791dd79a17653de22d45
iuc
parents:
diff
changeset
|
602 <param name="input_degrees" value=""/> |
|
2ed0df0360e5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/constava commit 77814d75404602f3fb6b791dd79a17653de22d45
iuc
parents:
diff
changeset
|
603 <param name="input_precision" value="5"/> |
|
2ed0df0360e5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/constava commit 77814d75404602f3fb6b791dd79a17653de22d45
iuc
parents:
diff
changeset
|
604 </section> |
|
2ed0df0360e5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/constava commit 77814d75404602f3fb6b791dd79a17653de22d45
iuc
parents:
diff
changeset
|
605 <section name="conformational_state_model_options"> |
|
2ed0df0360e5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/constava commit 77814d75404602f3fb6b791dd79a17653de22d45
iuc
parents:
diff
changeset
|
606 <conditional name="custom_model"> |
|
2ed0df0360e5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/constava commit 77814d75404602f3fb6b791dd79a17653de22d45
iuc
parents:
diff
changeset
|
607 <param name="use_custom_model" value="true"/> |
|
2ed0df0360e5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/constava commit 77814d75404602f3fb6b791dd79a17653de22d45
iuc
parents:
diff
changeset
|
608 <conditional name="model_type_options"> |
|
2ed0df0360e5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/constava commit 77814d75404602f3fb6b791dd79a17653de22d45
iuc
parents:
diff
changeset
|
609 <param name="model_type" value="kde"/> |
|
2ed0df0360e5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/constava commit 77814d75404602f3fb6b791dd79a17653de22d45
iuc
parents:
diff
changeset
|
610 <param name="bandwidth" value="0.15"/> |
|
2ed0df0360e5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/constava commit 77814d75404602f3fb6b791dd79a17653de22d45
iuc
parents:
diff
changeset
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611 </conditional> |
|
2ed0df0360e5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/constava commit 77814d75404602f3fb6b791dd79a17653de22d45
iuc
parents:
diff
changeset
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612 </conditional> |
|
2ed0df0360e5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/constava commit 77814d75404602f3fb6b791dd79a17653de22d45
iuc
parents:
diff
changeset
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613 </section> |
|
2ed0df0360e5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/constava commit 77814d75404602f3fb6b791dd79a17653de22d45
iuc
parents:
diff
changeset
|
614 <section name="subsampling_options"> |
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2ed0df0360e5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/constava commit 77814d75404602f3fb6b791dd79a17653de22d45
iuc
parents:
diff
changeset
|
615 <conditional name="sampling_options"> |
|
2ed0df0360e5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/constava commit 77814d75404602f3fb6b791dd79a17653de22d45
iuc
parents:
diff
changeset
|
616 <param name="subsampling_type" value="bootstrap"/> |
|
2ed0df0360e5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/constava commit 77814d75404602f3fb6b791dd79a17653de22d45
iuc
parents:
diff
changeset
|
617 <param name="bootstrap_size" value="10 20"/> |
|
2ed0df0360e5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/constava commit 77814d75404602f3fb6b791dd79a17653de22d45
iuc
parents:
diff
changeset
|
618 <param name="return_bootstrap_series" value="false"/> |
|
2ed0df0360e5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/constava commit 77814d75404602f3fb6b791dd79a17653de22d45
iuc
parents:
diff
changeset
|
619 <param name="bootstrap_samples" value="10"/> |
|
2ed0df0360e5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/constava commit 77814d75404602f3fb6b791dd79a17653de22d45
iuc
parents:
diff
changeset
|
620 <param name="bootstrap_seed" value="18"/> |
|
2ed0df0360e5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/constava commit 77814d75404602f3fb6b791dd79a17653de22d45
iuc
parents:
diff
changeset
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621 </conditional> |
|
2ed0df0360e5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/constava commit 77814d75404602f3fb6b791dd79a17653de22d45
iuc
parents:
diff
changeset
|
622 </section> |
|
2ed0df0360e5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/constava commit 77814d75404602f3fb6b791dd79a17653de22d45
iuc
parents:
diff
changeset
|
623 <assert_command> |
|
2ed0df0360e5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/constava commit 77814d75404602f3fb6b791dd79a17653de22d45
iuc
parents:
diff
changeset
|
624 <has_text text="constava fit-model -vv --model-type kde --kde-bandwidth 0.15 --output custom_model.kde.pkl"/> |
|
2ed0df0360e5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/constava commit 77814d75404602f3fb6b791dd79a17653de22d45
iuc
parents:
diff
changeset
|
625 <has_text text="constava analyze -vv --precision 5 --input dihedrals.mini.csv --input-format csv --output output_constava.csv --bootstrap 10 20 --bootstrap-samples 10 --seed 18 --load-model custom_model.kde.pkl"/> |
|
2ed0df0360e5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/constava commit 77814d75404602f3fb6b791dd79a17653de22d45
iuc
parents:
diff
changeset
|
626 </assert_command> |
|
2ed0df0360e5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/constava commit 77814d75404602f3fb6b791dd79a17653de22d45
iuc
parents:
diff
changeset
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627 <output name="file_contents" file="expected/test_013.csv" ftype="csv"/> |
|
2ed0df0360e5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/constava commit 77814d75404602f3fb6b791dd79a17653de22d45
iuc
parents:
diff
changeset
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628 </test> |
|
2ed0df0360e5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/constava commit 77814d75404602f3fb6b791dd79a17653de22d45
iuc
parents:
diff
changeset
|
629 <!-- test_014: Testing the window validators --> |
|
2ed0df0360e5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/constava commit 77814d75404602f3fb6b791dd79a17653de22d45
iuc
parents:
diff
changeset
|
630 <test expect_num_outputs="1"> |
|
2ed0df0360e5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/constava commit 77814d75404602f3fb6b791dd79a17653de22d45
iuc
parents:
diff
changeset
|
631 <section name="input_options"> |
|
2ed0df0360e5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/constava commit 77814d75404602f3fb6b791dd79a17653de22d45
iuc
parents:
diff
changeset
|
632 <param name="input_files" value="csv/dihedrals.mini.csv"/> |
|
2ed0df0360e5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/constava commit 77814d75404602f3fb6b791dd79a17653de22d45
iuc
parents:
diff
changeset
|
633 <param name="input_degrees" value=""/> |
|
2ed0df0360e5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/constava commit 77814d75404602f3fb6b791dd79a17653de22d45
iuc
parents:
diff
changeset
|
634 <param name="input_precision" value="5"/> |
|
2ed0df0360e5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/constava commit 77814d75404602f3fb6b791dd79a17653de22d45
iuc
parents:
diff
changeset
|
635 </section> |
|
2ed0df0360e5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/constava commit 77814d75404602f3fb6b791dd79a17653de22d45
iuc
parents:
diff
changeset
|
636 <section name="conformational_state_model_options"> |
|
2ed0df0360e5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/constava commit 77814d75404602f3fb6b791dd79a17653de22d45
iuc
parents:
diff
changeset
|
637 <conditional name="custom_model"> |
|
2ed0df0360e5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/constava commit 77814d75404602f3fb6b791dd79a17653de22d45
iuc
parents:
diff
changeset
|
638 <param name="use_custom_model" value="true"/> |
|
2ed0df0360e5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/constava commit 77814d75404602f3fb6b791dd79a17653de22d45
iuc
parents:
diff
changeset
|
639 <conditional name="model_type_options"> |
|
2ed0df0360e5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/constava commit 77814d75404602f3fb6b791dd79a17653de22d45
iuc
parents:
diff
changeset
|
640 <param name="model_type" value="kde"/> |
|
2ed0df0360e5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/constava commit 77814d75404602f3fb6b791dd79a17653de22d45
iuc
parents:
diff
changeset
|
641 <param name="bandwidth" value="0.15"/> |
|
2ed0df0360e5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/constava commit 77814d75404602f3fb6b791dd79a17653de22d45
iuc
parents:
diff
changeset
|
642 </conditional> |
|
2ed0df0360e5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/constava commit 77814d75404602f3fb6b791dd79a17653de22d45
iuc
parents:
diff
changeset
|
643 </conditional> |
|
2ed0df0360e5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/constava commit 77814d75404602f3fb6b791dd79a17653de22d45
iuc
parents:
diff
changeset
|
644 </section> |
|
2ed0df0360e5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/constava commit 77814d75404602f3fb6b791dd79a17653de22d45
iuc
parents:
diff
changeset
|
645 <section name="subsampling_options"> |
|
2ed0df0360e5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/constava commit 77814d75404602f3fb6b791dd79a17653de22d45
iuc
parents:
diff
changeset
|
646 <conditional name="sampling_options"> |
|
2ed0df0360e5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/constava commit 77814d75404602f3fb6b791dd79a17653de22d45
iuc
parents:
diff
changeset
|
647 <param name="subsampling_type" value="window"/> |
|
2ed0df0360e5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/constava commit 77814d75404602f3fb6b791dd79a17653de22d45
iuc
parents:
diff
changeset
|
648 <param name="window_size" value="3 5 7"/> |
|
2ed0df0360e5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/constava commit 77814d75404602f3fb6b791dd79a17653de22d45
iuc
parents:
diff
changeset
|
649 </conditional> |
|
2ed0df0360e5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/constava commit 77814d75404602f3fb6b791dd79a17653de22d45
iuc
parents:
diff
changeset
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650 </section> |
|
2ed0df0360e5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/constava commit 77814d75404602f3fb6b791dd79a17653de22d45
iuc
parents:
diff
changeset
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651 <assert_command> |
|
2ed0df0360e5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/constava commit 77814d75404602f3fb6b791dd79a17653de22d45
iuc
parents:
diff
changeset
|
652 <has_text text="constava fit-model -vv --model-type kde --kde-bandwidth 0.15 --output custom_model.kde.pkl"/> |
|
2ed0df0360e5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/constava commit 77814d75404602f3fb6b791dd79a17653de22d45
iuc
parents:
diff
changeset
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653 <has_text text="constava analyze -vv --precision 5 --input dihedrals.mini.csv --input-format csv --output output_constava.csv --window 3 5 7 --load-model custom_model.kde.pkl"/> |
|
2ed0df0360e5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/constava commit 77814d75404602f3fb6b791dd79a17653de22d45
iuc
parents:
diff
changeset
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654 </assert_command> |
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2ed0df0360e5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/constava commit 77814d75404602f3fb6b791dd79a17653de22d45
iuc
parents:
diff
changeset
|
655 <output name="file_contents" file="expected/test_014.csv" ftype="csv"/> |
|
2ed0df0360e5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/constava commit 77814d75404602f3fb6b791dd79a17653de22d45
iuc
parents:
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changeset
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656 </test> |
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2ed0df0360e5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/constava commit 77814d75404602f3fb6b791dd79a17653de22d45
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diff
changeset
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657 <!-- test_015: Testing the window series validators --> |
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2ed0df0360e5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/constava commit 77814d75404602f3fb6b791dd79a17653de22d45
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changeset
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658 <test expect_num_outputs="1"> |
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2ed0df0360e5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/constava commit 77814d75404602f3fb6b791dd79a17653de22d45
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parents:
diff
changeset
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659 <section name="input_options"> |
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2ed0df0360e5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/constava commit 77814d75404602f3fb6b791dd79a17653de22d45
iuc
parents:
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changeset
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660 <param name="input_files" value="csv/dihedrals.mini.csv"/> |
|
2ed0df0360e5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/constava commit 77814d75404602f3fb6b791dd79a17653de22d45
iuc
parents:
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changeset
|
661 <param name="input_degrees" value=""/> |
|
2ed0df0360e5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/constava commit 77814d75404602f3fb6b791dd79a17653de22d45
iuc
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changeset
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662 <param name="input_precision" value="3"/> |
|
2ed0df0360e5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/constava commit 77814d75404602f3fb6b791dd79a17653de22d45
iuc
parents:
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changeset
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663 </section> |
|
2ed0df0360e5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/constava commit 77814d75404602f3fb6b791dd79a17653de22d45
iuc
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changeset
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664 <section name="conformational_state_model_options"> |
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2ed0df0360e5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/constava commit 77814d75404602f3fb6b791dd79a17653de22d45
iuc
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changeset
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665 <conditional name="custom_model"> |
|
2ed0df0360e5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/constava commit 77814d75404602f3fb6b791dd79a17653de22d45
iuc
parents:
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changeset
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666 <param name="use_custom_model" value="true"/> |
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2ed0df0360e5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/constava commit 77814d75404602f3fb6b791dd79a17653de22d45
iuc
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changeset
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667 <conditional name="model_type_options"> |
|
2ed0df0360e5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/constava commit 77814d75404602f3fb6b791dd79a17653de22d45
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parents:
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changeset
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668 <param name="model_type" value="kde"/> |
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2ed0df0360e5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/constava commit 77814d75404602f3fb6b791dd79a17653de22d45
iuc
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changeset
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669 <param name="bandwidth" value="0.15"/> |
|
2ed0df0360e5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/constava commit 77814d75404602f3fb6b791dd79a17653de22d45
iuc
parents:
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670 </conditional> |
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2ed0df0360e5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/constava commit 77814d75404602f3fb6b791dd79a17653de22d45
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671 </conditional> |
|
2ed0df0360e5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/constava commit 77814d75404602f3fb6b791dd79a17653de22d45
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672 </section> |
|
2ed0df0360e5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/constava commit 77814d75404602f3fb6b791dd79a17653de22d45
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changeset
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673 <section name="subsampling_options"> |
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2ed0df0360e5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/constava commit 77814d75404602f3fb6b791dd79a17653de22d45
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674 <conditional name="sampling_options"> |
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2ed0df0360e5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/constava commit 77814d75404602f3fb6b791dd79a17653de22d45
iuc
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675 <param name="subsampling_type" value="window"/> |
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2ed0df0360e5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/constava commit 77814d75404602f3fb6b791dd79a17653de22d45
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676 <param name="window_size" value="5 7 9 11"/> |
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2ed0df0360e5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/constava commit 77814d75404602f3fb6b791dd79a17653de22d45
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677 <param name="return_window_series" value="true"/> |
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2ed0df0360e5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/constava commit 77814d75404602f3fb6b791dd79a17653de22d45
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678 </conditional> |
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2ed0df0360e5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/constava commit 77814d75404602f3fb6b791dd79a17653de22d45
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679 </section> |
|
2ed0df0360e5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/constava commit 77814d75404602f3fb6b791dd79a17653de22d45
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680 <assert_command> |
|
2ed0df0360e5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/constava commit 77814d75404602f3fb6b791dd79a17653de22d45
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changeset
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681 <has_text text="constava fit-model -vv --model-type kde --kde-bandwidth 0.15 --output custom_model.kde.pkl"/> |
|
2ed0df0360e5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/constava commit 77814d75404602f3fb6b791dd79a17653de22d45
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changeset
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682 <has_text text="constava analyze -vv --precision 3 --input dihedrals.mini.csv --input-format csv --output output_constava.csv --window-series 5 7 9 11 --load-model custom_model.kde.pkl"/> |
|
2ed0df0360e5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/constava commit 77814d75404602f3fb6b791dd79a17653de22d45
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683 </assert_command> |
|
2ed0df0360e5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/constava commit 77814d75404602f3fb6b791dd79a17653de22d45
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684 <output name="file_contents" file="expected/test_015.csv" ftype="csv"/> |
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2ed0df0360e5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/constava commit 77814d75404602f3fb6b791dd79a17653de22d45
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685 </test> |
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2ed0df0360e5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/constava commit 77814d75404602f3fb6b791dd79a17653de22d45
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686 </tests> |
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2ed0df0360e5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/constava commit 77814d75404602f3fb6b791dd79a17653de22d45
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changeset
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687 <creator> |
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2ed0df0360e5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/constava commit 77814d75404602f3fb6b791dd79a17653de22d45
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688 <person name="José Gavalda-Garcia" honorificPrefix="Dr" identifier="0000-0001-6431-3442" url="https://orcid.org/0000-0001-6431-3442"/> |
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2ed0df0360e5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/constava commit 77814d75404602f3fb6b791dd79a17653de22d45
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689 <person name="David Bickel" honorificPrefix="Dr" identifier="0000-0003-0332-8338" url="https://orcid.org/0000-0003-0332-8338"/> |
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2ed0df0360e5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/constava commit 77814d75404602f3fb6b791dd79a17653de22d45
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690 <person name="Joel Roca-Martinez" honorificPrefix="Dr" identifier="0000-0002-4313-3845" url="https://orcid.org/0000-0002-4313-3845"/> |
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2ed0df0360e5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/constava commit 77814d75404602f3fb6b791dd79a17653de22d45
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691 <person name="Daniele Raimondi" honorificPrefix="Dr" identifier="0000-0003-1157-1899" url="https://orcid.org/0000-0003-1157-1899"/> |
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2ed0df0360e5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/constava commit 77814d75404602f3fb6b791dd79a17653de22d45
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692 <person name="Gabriele Orlando" honorificPrefix="Dr" identifier="0000-0002-5935-5258" url="https://orcid.org/0000-0002-5935-5258"/> |
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2ed0df0360e5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/constava commit 77814d75404602f3fb6b791dd79a17653de22d45
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693 <person name="Wim F. Vranken" honorificPrefix="Dr" email="wim.vranken@vub.be" identifier="0000-0001-7470-4324" url="https://orcid.org/0000-0001-7470-4324"/> |
|
2ed0df0360e5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/constava commit 77814d75404602f3fb6b791dd79a17653de22d45
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694 <person name="Iman Jouiad" /> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/constava commit 77814d75404602f3fb6b791dd79a17653de22d45
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695 <person name="Boris Depoortere" email="boris.depoortere@vib.be" identifier="0009-0002-2539-116X" url="https://orcid.org/0009-0002-2539-116X"/> |
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2ed0df0360e5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/constava commit 77814d75404602f3fb6b791dd79a17653de22d45
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696 <person name="Adrián Díaz" email="adrian.diaz@vub.be" identifier="0000-0003-0165-1318" url="https://orcid.org/0000-0003-0165-1318"/> |
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2ed0df0360e5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/constava commit 77814d75404602f3fb6b791dd79a17653de22d45
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697 <organization name="Bio2Byte, Vrije Universiteit Brussel (VUB)" address="Interuniversity Institute Bioinformatics Brussels, Université Libre de Bruxelles, 1050 Ixelles, Brussels, Belgium" url="https://bio2byte.be/rrmscorer" email="bio2byte@vub.be" image="https://0.gravatar.com/avatar/2b51fb7600d876086669bcc85a941b763a81d1c2bb3c667b8c83a1aa892cf740"/> |
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2ed0df0360e5
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698 </creator> |
|
2ed0df0360e5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/constava commit 77814d75404602f3fb6b791dd79a17653de22d45
iuc
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changeset
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699 <help><![CDATA[ |
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2ed0df0360e5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/constava commit 77814d75404602f3fb6b791dd79a17653de22d45
iuc
parents:
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changeset
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700 `Constava <https://pypi.org/project/constava/>`_ analyzes conformational ensembles to calculate **conformational state propensities** |
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2ed0df0360e5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/constava commit 77814d75404602f3fb6b791dd79a17653de22d45
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changeset
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701 and **conformational state variability**. |
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2ed0df0360e5
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changeset
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702 |
|
2ed0df0360e5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/constava commit 77814d75404602f3fb6b791dd79a17653de22d45
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changeset
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703 **Conformational state propensities** describe how likely each residue is to occupy a given conformational state, |
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2ed0df0360e5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/constava commit 77814d75404602f3fb6b791dd79a17653de22d45
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704 whereas **conformational state variability** measures the residue's ability to transition between conformational states. |
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changeset
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705 |
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2ed0df0360e5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/constava commit 77814d75404602f3fb6b791dd79a17653de22d45
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706 Each conformational state is represented by a statistical model derived from the backbone dihedral angles (φ, ψ). |
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2ed0df0360e5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/constava commit 77814d75404602f3fb6b791dd79a17653de22d45
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707 The default models were obtained from an analysis of NMR ensembles and chemical shifts. |
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2ed0df0360e5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/constava commit 77814d75404602f3fb6b791dd79a17653de22d45
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708 To perform an analysis, you must provide φ- and ψ-angles for each conformational state in the ensemble. |
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2ed0df0360e5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/constava commit 77814d75404602f3fb6b791dd79a17653de22d45
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changeset
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709 |
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710 The conformational states were defined according to residue behavior across NMR ensembles: |
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711 |
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712 - **Core helix** (column ``coreHelix``): Residues that exclusively adopt a helical conformation in all models of their associated ensemble, with shiftCrypt values ≤ 0.2 (N = 93,957 residues). |
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713 - **Surrounding helix** (column ``surrHelix``): Residues that adopt a helical conformation in the majority of models, with shiftCrypt values in the range (0.2, 0.4] (N = 8,180 residues). |
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714 - **Core sheet** (column ``coreSheet``): Residues that exclusively adopt an extended conformation in all models, with shiftCrypt values ≥ 0.8 (N = 47,280 residues). |
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715 - **Surrounding sheet** (column ``surrSheet``): Residues that adopt an extended conformation in most models, with shiftCrypt values in the range [0.6, 0.8) (N = 11,280 residues). |
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716 - **Turn** (column ``Turn``): Residues that adopt a turn conformation in most models, with shiftCrypt values in the range (0.4, 0.6) (N = 75,377 residues). |
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717 - **Other** (column ``Other``): Residues that adopt a coil conformation in most models, also with shiftCrypt values in the range (0.4, 0.6) (N = 74,542 residues). |
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718 |
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719 **Input Data and Parameters** |
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720 |
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721 *Constava* requires backbone dihedral angles extracted from the conformational ensemble as input data. |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/constava commit 77814d75404602f3fb6b791dd79a17653de22d45
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722 These angles can be generated with *GROMACS* using the ``gmx chi`` module (set the input format to `'xvg'`), |
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723 or they can be obtained using the Python submodule ``constava dihedrals``, which supports a wide range of molecular dynamics and structure formats. |
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724 |
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725 - **Input files:** Provide files containing the dihedral angles. Supported formats include CSV and XVG. |
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726 - **Angle units:** Specify whether the dihedral angles in your files are expressed in radians or degrees. |
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727 |
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728 .. class:: infomark |
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729 |
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730 **Example files:** Example datasets in both formats are available in the |
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731 `data directory on GitHub <https://github.com/Bio2Byte/constava/tree/main/constava/data>`_. |
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732 |
|
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733 The ``constava dihedrals`` submodule extracts backbone dihedral angles from conformational ensembles. |
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734 By default, it outputs the results in radians, which is the preferred format for ``constava analyze``. |
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|
735 |
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736 **Kernel Options** |
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|
737 |
|
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/constava commit 77814d75404602f3fb6b791dd79a17653de22d45
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738 Configure the probability density functions (PDFs) used in the analysis. You can choose predefined PDFs |
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739 or fit custom ones from your own data. |
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740 |
|
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741 **Subsampling Options** |
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742 |
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743 You can apply different subsampling strategies, such as window-based analysis or bootstrap sampling, |
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744 to assess data variability and statistical robustness. |
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745 |
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746 - **Window size:** Define the frame size for moving-window analyses (multiple consecutive samples). |
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747 - **Bootstrap size:** Specify the number of bootstrap samples to improve statistical confidence. |
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748 |
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749 **Results and Output Files** |
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750 |
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751 *Constava* produces an output file containing the calculated variability and propensity measures. |
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752 The file format and level of detail depend on your configuration and the selected subsampling options. |
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753 |
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754 - **Output precision:** Set the decimal places to include in the output file. |
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755 |
|
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756 .. class:: warningmark |
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757 |
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758 **Note:** Accurate results require careful parameter selection. Default settings are provided for convenience, |
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759 but they may need adjustment depending on your dataset and analysis goals. |
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760 |
|
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761 **Project Links** |
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762 |
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763 This tool uses the Python package `constava` available via PyPI and BioConda. |
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764 |
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765 - Source code repository on `GitHub <https://github.com/Bio2Byte/constava>`_ |
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766 - Python package on `PyPI <https://pypi.org/project/constava/>`_ |
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767 - Conda recipe on `BioConda <https://bioconda.github.io/recipes/constava/README.html>`_ |
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768 - Conda package on `Anaconda (BioConda channel) <https://anaconda.org/bioconda/constava>`_ |
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769 - Tool profile on `Bio.Tools <https://bio.tools/constava>`_ |
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770 ]]></help> |
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771 <citations> |
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772 <citation type="doi">10.1093/nargab/lqae082</citation> |
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773 <citation type="doi">10.1016/j.jmb.2024.168900</citation> |
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774 </citations> |
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775 </tool> |