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annotate spring_model.xml @ 2:3fd0f313665b draft default tip

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"planemo upload commit fe7295ad48151648562b06d5b075a68d77747326"
author guerler
date Thu, 08 Apr 2021 18:23:33 +0000
parents 719931bce361
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1 <tool id="spring_model" name="SPRING Model" 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.py
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9 -a '$first_target'
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10 -b '$second_target'
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11 @pdb_source@
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12 -c '$cross'
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13 -o '$output'
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14 ]]> </command>
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15 <inputs>
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16 <param name="first_target" format="hhr" type="data" label="First HHR target file" help="Threading result for target sequence using HHsearch." />
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17 <param name="second_target" format="hhr" type="data" label="Second HHR target file" help="Threading result for target sequence using HHsearch." />
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18 <param name="cross" format="tabular" type="data" label="Cross Reference" help="SPRING PDB Cross Reference as produced by SPRING Cross tool." />
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19 <expand macro="pdb_source" />
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20 </inputs>
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21 <outputs>
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22 <data format="pdb" name="output" label="SPRING Model Structure" />
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23 </outputs>
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24 <tests>
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25 <test>
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26 <param name="first_target" value="model/ACE2_HUMAN.hhr" ftype="hhr" />
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27 <param name="second_target" value="model/SPIKE_SARS2.hhr" ftype="hhr" />
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28 <conditional name="pdb_source">
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29 <param name="pdb_source_selector" value="history" />
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30 <param name="ffindex" value="model/pdb.ffindex" />
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31 <param name="ffdata" value="model/pdb.ffdata" />
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32 </conditional>
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33 <param name="cross" value="model/crossreference.txt" />
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34 <output name="output" file="model/sp|Q9BYF1|ACE2_HUMAN.sp|P0DTC2|SPIKE_SARS2.pdb" />
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35 </test>
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36 <test>
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37 <param name="first_target" value="model/ACE2_HUMAN.hhr" ftype="hhr" />
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38 <param name="second_target" value="model/SPIKE_SARS2.hhr" ftype="hhr" />
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39 <conditional name="pdb_source">
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40 <param name="pdb_source_selector" value="indexed" />
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41 <param name="pdb" value="pdb01_model" />
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42 </conditional>
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43 <param name="cross" value="model/crossreference.txt" />
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44 <output name="output" file="model/sp|Q9BYF1|ACE2_HUMAN.sp|P0DTC2|SPIKE_SARS2.pdb" />
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45 </test>
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46 <test>
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47 <param name="first_target" value="model/ACE2_HUMAN.hhr" ftype="hhr" />
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48 <param name="second_target" value="model/SPIKE_SARS2.hhr" ftype="hhr" />
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49 <conditional name="pdb_source">
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50 <param name="pdb_source_selector" value="indexed" />
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51 <param name="pdb" value="pdb02_model" />
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52 <param name="zipped" value="gz" />
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53 </conditional>
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54 <param name="cross" value="model/crossreference.txt" />
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55 <output name="output" file="model/sp|Q9BYF1|ACE2_HUMAN.sp|P0DTC2|SPIKE_SARS2_1.pdb" />
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56 </test>
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57 </tests>
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58 <help><![CDATA[
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59
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60 **What it does**
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61
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62 Creates protein complex model from HHsearch threading results.
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63
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64 ]]> </help>
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65 <expand macro="citations" />
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66 </tool>