annotate end-to-end.xml @ 1:ce9dc91ff87f draft

"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 45fe75a3a8ca80f799c85e194429c4c7f38bb5f6"
author chemteam
date Wed, 28 Oct 2020 21:37:06 +0000
parents 78aa3659fcd1
children
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1 <tool id="mdanalysis_endtoend" name="End-to-End Analysis" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@">
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2 <description>- End-to-End distance timeseries and histogram for the given selections</description>
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3 <macros>
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4 <import>macros.xml</import>
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5 <token name="@GALAXY_VERSION@">0</token>
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6 </macros>
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7 <expand macro="requirements"/>
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8 <command detect_errors="exit_code">
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9 <![CDATA[
78aa3659fcd1 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 1b23e024af45cc0999d9142d07de6897d4189ec2"
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10 python '$__tool_directory__/end-to-end.py'
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11 --itraj '$trajin'
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12 --istr '$strin'
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13 --itrajext '$trajin.ext'
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14 --istrext '$strin.ext'
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15 --isegid1 '$segid1'
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16 --ilabel '$label1'
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17 --ititle1 '$title1'
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18 --output1 '$output1'
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19 --o_plot '$o_plot'
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20 2>&1
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21 ]]></command>
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22 <inputs>
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23 <expand macro="analysis_inputs"/>
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24 <param name="segid1" type="text" value="PROA" label="Segment ID of the protein" help="A valid segment ID selection for the current molecular system">
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25 <validator type="regex" message="Maximum of 8 characters allowed.">^[a-zA-Z0-9]{1,8}$</validator>
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26 </param>
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27 <param name="label1" type="text" value="N-C" label="Data series label">
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28 <validator type="regex" message="Maximum of 8 characters allowed.">^[a-zA-Z0-9\- ]{1,8}$</validator>
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29 </param>
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30 <param name="title1" type="text" value="End-to-End timeseries and histogram" label="Plot title" help="Plot title, to be included in image output">
78aa3659fcd1 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 1b23e024af45cc0999d9142d07de6897d4189ec2"
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31 <validator type="regex" message="Maximum of 36 characters allowed.">^[a-zA-Z0-9\- ]{1,36}$</validator>
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32 </param>
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33 </inputs>
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34 <outputs>
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35 <data format="tabular" name="output1" label="timeseries raw data"/>
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36 <data format="png" name="o_plot" label="End-to-End Timeseries and Histogram Plot"/>
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37 </outputs>
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38 <tests>
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39 <test>
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40 <param name="trajin" value="test.dcd" ftype="dcd"/>
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41 <param name="strin" value="test.pdb" ftype="pdb"/>
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42 <param name="segid1" value="PRO"/>
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43 <output name="output1">
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44 <assert_contents>
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45 <has_text text="3.921"/>
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46 <has_text text="3.938"/>
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47 </assert_contents>
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48 </output>
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49 <output name="o_plot">
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50 <assert_contents>
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51 <has_size value="39991" delta="3000"/>
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52 </assert_contents>
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53 </output>
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54 </test>
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55 </tests>
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56 <help>
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57 <![CDATA[
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58 .. class:: infomark
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59
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60 **What it does**
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61
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62 End-to-End distance timeseries and histogram for proteins. The termini are chosen as ends with the N atom of the N-terminus and the C atom of the C-terminus chosen.
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63
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64 _____
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65
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66
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67 .. class:: infomark
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68
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69 **Input**
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70
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71 - Trajectory file (DCD).
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72 - PDB file.
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73 - Segment ID for the protein
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74 - Graph series label and title
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75
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76 Note that a MDAnalysis 'segment' is a larger organizational unit, for example one protein or all the solvent molecules or simply the whole system.
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77
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78 _____
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79
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80
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81 .. class:: infomark
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82
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83 **Output**
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84
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85 - Tab-separated file of timeseries raw data
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86 - Image (as png) of the end-to-end timeseries and histogram
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87
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88 ]]>
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89 </help>
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90 <expand macro="citations"/>
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91 </tool>