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"planemo upload commit fe7295ad48151648562b06d5b075a68d77747326"
author guerler
date Thu, 08 Apr 2021 18:22:14 +0000
parents e56e0f4c84fb
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1 <tool id="spring_model_all" name="SPRING Model-All" license="MIT" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.01">
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2 <description>complex structures</description>
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
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6 <expand macro="requirements" />
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7 <command detect_errors="exit_code"><![CDATA[
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8 spring_model_all.py
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9 -p '$pairs'
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10 @hhr_source@
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11 @pdb_source@
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12 -c '$crossreference'
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13 -o 'models'
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14 -g '$log'
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15 ]]> </command>
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16 <inputs>
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17 <param name="pairs" type="data" format="tabular" label="Interacting Pairs" help="Tabular 2-column file containing putative protein interaction pairs." />
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18 <param name="crossreference" type="data" format="tabular" label="Cross Reference" help="SPRING PDB Cross Reference as produced by SPRING Cross tool." />
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19 <expand macro="hhr_source" />
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20 <expand macro="pdb_source" />
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21 <expand macro="logfile" />
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22 </inputs>
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23 <outputs>
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24 <collection name="models" type="list" label="SPRING Model Structures">
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25 <discover_datasets pattern="__name_and_ext__" directory="models" />
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26 </collection>
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27 <data format="tabular" name="log" label="SPRING Model Log">
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28 <filter>logfile</filter>
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29 </data>
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30 </outputs>
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31 <tests>
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32 <test>
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33 <param name="pairs" value="model/pairs.txt" ftype="tabular" />
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34 <conditional name="hhr_source">
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35 <param name="hhr_source_selector" value="history" />
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36 <param name="ffindex" value="model/hhr.ffindex" />
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37 <param name="ffdata" value="model/hhr.ffdata" />
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38 </conditional>
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39 <conditional name="pdb_source">
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40 <param name="pdb_source_selector" value="history" />
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41 <param name="ffindex" value="model/pdb.ffindex" />
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42 <param name="ffdata" value="model/pdb.ffdata" />
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43 </conditional>
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44 <param name="crossreference" value="model/crossreference.txt" />
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45 <param name="logfile" value="true" />
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46 <output name="log" file="model/log.txt" />
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47 <output_collection name="models" type="list" count="1">
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48 <element name="sp|Q9BYF1|ACE2_HUMAN.sp|P0DTC2|SPIKE_SARS2" file="model/sp|Q9BYF1|ACE2_HUMAN.sp|P0DTC2|SPIKE_SARS2.pdb" />
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49 </output_collection>
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50 </test>
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51 <test>
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52 <param name="pairs" value="model/pairs.txt" ftype="tabular" />
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53 <conditional name="hhr_source">
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54 <param name="hhr_source_selector" value="indexed" />
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55 <param name="hhr" value="hhr_model" />
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56 </conditional>
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57 <conditional name="pdb_source">
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58 <param name="pdb_source_selector" value="indexed" />
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59 <param name="pdb" value="pdb01_model" />
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60 </conditional>
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61 <param name="crossreference" value="model/crossreference.txt" />
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62 <param name="logfile" value="true" />
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63 <output name="log" file="model/log.txt" />
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64 <output_collection name="models" type="list" count="1">
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65 <element name="sp|Q9BYF1|ACE2_HUMAN.sp|P0DTC2|SPIKE_SARS2" file="model/sp|Q9BYF1|ACE2_HUMAN.sp|P0DTC2|SPIKE_SARS2.pdb" />
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66 </output_collection>
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67 </test>
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68 </tests>
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69 <help><![CDATA[
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70
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71 **What it does**
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72
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73 Creates protein complex model from HHsearch threading results.
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74
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75 ]]> </help>
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76 <expand macro="citations" />
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77 </tool>