Mercurial > repos > chemteam > mdanalysis_distance

annotate distance.xml @ 0:c33b972fe040 draft

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planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit c32fe331f438df7760084b27bafad9f78f01edde
author chemteam
date Mon, 08 Oct 2018 13:16:12 -0400
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c33b972fe040 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit c32fe331f438df7760084b27bafad9f78f01edde
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1 <tool id="mdanalysis_distance" name="Distance Analysis" version="@VERSION@">
c33b972fe040 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit c32fe331f438df7760084b27bafad9f78f01edde
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2 <description>Time series using MDAnalysis</description>
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3 <macros>
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4 <import>macros.xml</import>
c33b972fe040 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit c32fe331f438df7760084b27bafad9f78f01edde
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5 </macros>
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6 <expand macro="requirements" />
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7 <command detect_errors="exit_code">
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8 <![CDATA[
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9 python '$__tool_directory__/distance.py'
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10 --idcd '$dcdin'
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11 --ipdb '$pdbin'
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12 --isegid1 '$segid1'
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13 --iresid1 '$resid1'
c33b972fe040 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit c32fe331f438df7760084b27bafad9f78f01edde
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14 --iname1 '$name1'
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15 --isegid2 '$segid2'
c33b972fe040 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit c32fe331f438df7760084b27bafad9f78f01edde
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16 --iresid2 '$resid2'
c33b972fe040 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit c32fe331f438df7760084b27bafad9f78f01edde
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17 --iname2 '$name2'
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18 --output '$output'
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19 --odistance_plot '$distance_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"/>
c33b972fe040 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit c32fe331f438df7760084b27bafad9f78f01edde
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24 <param name="segid1" type="text" value="PRO" label="Segid of atom 1"/>
c33b972fe040 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit c32fe331f438df7760084b27bafad9f78f01edde
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25 <param name="resid1" type="text" value="212" label="Resid of atom 1"/>
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26 <param name="name1" type="text" value="OE2" label="Atom name of atom 1"/>
c33b972fe040 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit c32fe331f438df7760084b27bafad9f78f01edde
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27 <param name="segid2" type="text" value="HET" label="Segid of atom 2"/>
c33b972fe040 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit c32fe331f438df7760084b27bafad9f78f01edde
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28 <param name="resid2" type="text" value="3" label="Resid of atom 2"/>
c33b972fe040 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit c32fe331f438df7760084b27bafad9f78f01edde
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29 <param name="name2" type="text" value="C1" label="Atom name of atom 2"/>
c33b972fe040 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit c32fe331f438df7760084b27bafad9f78f01edde
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30 </inputs>
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31 <outputs>
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32 <data format="tabular" name="output" label="Distance Analysis raw data"/>
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33 <data format="png" name="distance_plot" label="Distance Analysis Plot"/>
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34 </outputs>
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35 <tests>
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36 <test>
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37 <expand macro="tests_inputs"/>
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38 <param name="segid1" value="PRO"/>
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39 <param name="resid1" value="212"/>
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40 <param name="name1" value="OE2"/>
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41 <param name="segid2" value="HET"/>
c33b972fe040 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit c32fe331f438df7760084b27bafad9f78f01edde
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42 <param name="resid2" value="3"/>
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43 <param name="name2" value="C1"/>
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44 <output name="output">
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45 <assert_contents>
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46 <has_n_columns n="2" />
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47 </assert_contents>
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48 </output>
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49 </test>
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50 </tests>
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51 <help><![CDATA[
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52 .. class:: infomark
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53
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54 **What it does**
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55
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56 This tool calculates and plot distance between the two atoms.
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57
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58 _____
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59
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60
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61 .. class:: infomark
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62
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63 **Input**
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64
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65 - Trajectory file (DCD).
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66 - PDB file.
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67 - Segids, resids and names of two atoms to calculate distances.
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68
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69 _____
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70
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71
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72 .. class:: infomark
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73
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74 **Output**
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75
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76 - Tab-separated file of raw data of distance between two atoms calculated for each frame.
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77 - Image (as png) of the time series graph.
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78
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79
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80 ]]></help>
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81 <expand macro="citations" />
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82 </tool>