Mercurial > repos > chemteam > bio3d_rmsf

annotate rmsf.xml @ 1:057daf00ca31 draft

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planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit 8e1fece3eaef36823e90f5d10f8bb8b809544c55
author chemteam
date Sun, 13 Jan 2019 03:21:33 -0500
parents e838317708a6
children 6bcb804a54c3
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e838317708a6 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit 580d80c3fd856bb3ae18ef7b5458eb3b5e2c7374
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1 <tool id="bio3d_rmsf" name="RMSF Analysis" version="@VERSION@">
e838317708a6 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit 580d80c3fd856bb3ae18ef7b5458eb3b5e2c7374
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2 <description>rmsf using Bio3D</description>
e838317708a6 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit 580d80c3fd856bb3ae18ef7b5458eb3b5e2c7374
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3 <macros>
e838317708a6 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit 580d80c3fd856bb3ae18ef7b5458eb3b5e2c7374
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4 <import>macros.xml</import>
e838317708a6 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit 580d80c3fd856bb3ae18ef7b5458eb3b5e2c7374
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5 </macros>
e838317708a6 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit 580d80c3fd856bb3ae18ef7b5458eb3b5e2c7374
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6 <expand macro="requirements" />
e838317708a6 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit 580d80c3fd856bb3ae18ef7b5458eb3b5e2c7374
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7 <command detect_errors="exit_code">
e838317708a6 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit 580d80c3fd856bb3ae18ef7b5458eb3b5e2c7374
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8 <![CDATA[
e838317708a6 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit 580d80c3fd856bb3ae18ef7b5458eb3b5e2c7374
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9 Rscript '$__tool_directory__/rmsf.R'
e838317708a6 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit 580d80c3fd856bb3ae18ef7b5458eb3b5e2c7374
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10 '$dcdin'
e838317708a6 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit 580d80c3fd856bb3ae18ef7b5458eb3b5e2c7374
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11 '$pdbin'
e838317708a6 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit 580d80c3fd856bb3ae18ef7b5458eb3b5e2c7374
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12 #if $rmsf.sele == 'calpha':
e838317708a6 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit 580d80c3fd856bb3ae18ef7b5458eb3b5e2c7374
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13 "string"
e838317708a6 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit 580d80c3fd856bb3ae18ef7b5458eb3b5e2c7374
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14 "calpha"
e838317708a6 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit 580d80c3fd856bb3ae18ef7b5458eb3b5e2c7374
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15 #end if
e838317708a6 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit 580d80c3fd856bb3ae18ef7b5458eb3b5e2c7374
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16 #if $rmsf.sele == 'cbeta':
e838317708a6 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit 580d80c3fd856bb3ae18ef7b5458eb3b5e2c7374
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17 "string"
e838317708a6 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit 580d80c3fd856bb3ae18ef7b5458eb3b5e2c7374
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18 '$rmsf.cbeta'
e838317708a6 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit 580d80c3fd856bb3ae18ef7b5458eb3b5e2c7374
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19 #end if
e838317708a6 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit 580d80c3fd856bb3ae18ef7b5458eb3b5e2c7374
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20 #if $rmsf.sele == 'backbone':
e838317708a6 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit 580d80c3fd856bb3ae18ef7b5458eb3b5e2c7374
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21 "string"
e838317708a6 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit 580d80c3fd856bb3ae18ef7b5458eb3b5e2c7374
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22 "backbone"
e838317708a6 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit 580d80c3fd856bb3ae18ef7b5458eb3b5e2c7374
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23 #end if
e838317708a6 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit 580d80c3fd856bb3ae18ef7b5458eb3b5e2c7374
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24 #if $rmsf.sele == 'sidechain':
e838317708a6 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit 580d80c3fd856bb3ae18ef7b5458eb3b5e2c7374
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25 "string"
e838317708a6 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit 580d80c3fd856bb3ae18ef7b5458eb3b5e2c7374
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26 '$rmsf.sidechain'
e838317708a6 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit 580d80c3fd856bb3ae18ef7b5458eb3b5e2c7374
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27 #end if
e838317708a6 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit 580d80c3fd856bb3ae18ef7b5458eb3b5e2c7374
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28 #if $rmsf.sele == 'protein':
e838317708a6 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit 580d80c3fd856bb3ae18ef7b5458eb3b5e2c7374
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29 "string"
e838317708a6 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit 580d80c3fd856bb3ae18ef7b5458eb3b5e2c7374
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30 "protein"
e838317708a6 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit 580d80c3fd856bb3ae18ef7b5458eb3b5e2c7374
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31 #end if
e838317708a6 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit 580d80c3fd856bb3ae18ef7b5458eb3b5e2c7374
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32 #if $rmsf.sele == 'ligand':
e838317708a6 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit 580d80c3fd856bb3ae18ef7b5458eb3b5e2c7374
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33 "string"
e838317708a6 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit 580d80c3fd856bb3ae18ef7b5458eb3b5e2c7374
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34 "ligand"
e838317708a6 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit 580d80c3fd856bb3ae18ef7b5458eb3b5e2c7374
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35 #end if
e838317708a6 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit 580d80c3fd856bb3ae18ef7b5458eb3b5e2c7374
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36 #if $rmsf.sele == 'nucleic':
e838317708a6 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit 580d80c3fd856bb3ae18ef7b5458eb3b5e2c7374
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37 "string"
e838317708a6 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit 580d80c3fd856bb3ae18ef7b5458eb3b5e2c7374
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38 "nucleic"
e838317708a6 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit 580d80c3fd856bb3ae18ef7b5458eb3b5e2c7374
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39 #end if
e838317708a6 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit 580d80c3fd856bb3ae18ef7b5458eb3b5e2c7374
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40 #if $rmsf.sele == 'water':
e838317708a6 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit 580d80c3fd856bb3ae18ef7b5458eb3b5e2c7374
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41 "string"
e838317708a6 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit 580d80c3fd856bb3ae18ef7b5458eb3b5e2c7374
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42 "water"
e838317708a6 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit 580d80c3fd856bb3ae18ef7b5458eb3b5e2c7374
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43 #end if
e838317708a6 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit 580d80c3fd856bb3ae18ef7b5458eb3b5e2c7374
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44 #if $rmsf.sele == 'hyd':
e838317708a6 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit 580d80c3fd856bb3ae18ef7b5458eb3b5e2c7374
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45 "string"
e838317708a6 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit 580d80c3fd856bb3ae18ef7b5458eb3b5e2c7374
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46 "hyd"
e838317708a6 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit 580d80c3fd856bb3ae18ef7b5458eb3b5e2c7374
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47 #end if
e838317708a6 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit 580d80c3fd856bb3ae18ef7b5458eb3b5e2c7374
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48 #if $rmsf.sele == 'noh':
e838317708a6 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit 580d80c3fd856bb3ae18ef7b5458eb3b5e2c7374
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49 "string"
e838317708a6 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit 580d80c3fd856bb3ae18ef7b5458eb3b5e2c7374
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50 "noh"
e838317708a6 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit 580d80c3fd856bb3ae18ef7b5458eb3b5e2c7374
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51 #end if
e838317708a6 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit 580d80c3fd856bb3ae18ef7b5458eb3b5e2c7374
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52 #if $rmsf.sele == 'loop':
e838317708a6 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit 580d80c3fd856bb3ae18ef7b5458eb3b5e2c7374
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53 "resno"
e838317708a6 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit 580d80c3fd856bb3ae18ef7b5458eb3b5e2c7374
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54 '$rmsf.res1'
e838317708a6 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit 580d80c3fd856bb3ae18ef7b5458eb3b5e2c7374
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55 '$rmsf.res2'
e838317708a6 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit 580d80c3fd856bb3ae18ef7b5458eb3b5e2c7374
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56 #end if
e838317708a6 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit 580d80c3fd856bb3ae18ef7b5458eb3b5e2c7374
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57 #if $rmsf.sele == "elety":
e838317708a6 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit 580d80c3fd856bb3ae18ef7b5458eb3b5e2c7374
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58 "elety"
e838317708a6 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit 580d80c3fd856bb3ae18ef7b5458eb3b5e2c7374
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59 '$rmsf.elety'
e838317708a6 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit 580d80c3fd856bb3ae18ef7b5458eb3b5e2c7374
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60 #end if
e838317708a6 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit 580d80c3fd856bb3ae18ef7b5458eb3b5e2c7374
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61 #if $rmsf.sele == "resid":
e838317708a6 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit 580d80c3fd856bb3ae18ef7b5458eb3b5e2c7374
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62 "resid"
e838317708a6 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit 580d80c3fd856bb3ae18ef7b5458eb3b5e2c7374
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63 '$rmsf.resid'
e838317708a6 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit 580d80c3fd856bb3ae18ef7b5458eb3b5e2c7374
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64 #end if
e838317708a6 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit 580d80c3fd856bb3ae18ef7b5458eb3b5e2c7374
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65 #if $rmsf.sele == "segid":
e838317708a6 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit 580d80c3fd856bb3ae18ef7b5458eb3b5e2c7374
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66 "segid"
e838317708a6 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit 580d80c3fd856bb3ae18ef7b5458eb3b5e2c7374
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67 '$rmsf.segid'
e838317708a6 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit 580d80c3fd856bb3ae18ef7b5458eb3b5e2c7374
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68 #end if
e838317708a6 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit 580d80c3fd856bb3ae18ef7b5458eb3b5e2c7374
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69 '$output'
e838317708a6 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit 580d80c3fd856bb3ae18ef7b5458eb3b5e2c7374
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70 '$rmsf_plot'
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71 2>&1
e838317708a6 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit 580d80c3fd856bb3ae18ef7b5458eb3b5e2c7374
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72 ]]></command>
e838317708a6 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit 580d80c3fd856bb3ae18ef7b5458eb3b5e2c7374
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73 <inputs>
e838317708a6 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit 580d80c3fd856bb3ae18ef7b5458eb3b5e2c7374
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74 <expand macro="analysis_inputs"/>
e838317708a6 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit 580d80c3fd856bb3ae18ef7b5458eb3b5e2c7374
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75 <conditional name="rmsf">
e838317708a6 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit 580d80c3fd856bb3ae18ef7b5458eb3b5e2c7374
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76 <param name="sele" type="select" label="Select domains">
e838317708a6 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit 580d80c3fd856bb3ae18ef7b5458eb3b5e2c7374
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77 <option value="calpha">Calpha</option>
e838317708a6 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit 580d80c3fd856bb3ae18ef7b5458eb3b5e2c7374
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78 <option value="cbeta">Cbeta</option>
e838317708a6 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit 580d80c3fd856bb3ae18ef7b5458eb3b5e2c7374
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79 <option value="backbone">Backbone</option>
e838317708a6 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit 580d80c3fd856bb3ae18ef7b5458eb3b5e2c7374
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80 <option value="sidechain">Sidechain</option>
e838317708a6 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit 580d80c3fd856bb3ae18ef7b5458eb3b5e2c7374
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81 <option value="protein">Protein</option>
e838317708a6 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit 580d80c3fd856bb3ae18ef7b5458eb3b5e2c7374
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82 <option value="ligand">Ligand</option>
e838317708a6 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit 580d80c3fd856bb3ae18ef7b5458eb3b5e2c7374
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83 <option value="nucleic">Nucleic Acids</option>
e838317708a6 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit 580d80c3fd856bb3ae18ef7b5458eb3b5e2c7374
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84 <option value="loop">Loop</option>
e838317708a6 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit 580d80c3fd856bb3ae18ef7b5458eb3b5e2c7374
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85 <option value="water">Water</option>
e838317708a6 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit 580d80c3fd856bb3ae18ef7b5458eb3b5e2c7374
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86 <option value="hyd">Hydrogens</option>
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87 <option value="noh">Non Hydrogens</option>
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88 <option value="elety">Atom Names</option>
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89 <option value="resid">Resid</option>
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90 <option value="segid">Segid</option>
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91 </param>
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92 <when value="calpha">
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93 </when>
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94 <when value="cbeta">
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95 </when>
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96 <when value="backbone">
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97 </when>
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98 <when value="sidechain">
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99 </when>
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100 <when value="protein">
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101 </when>
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102 <when value="ligand">
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103 </when>
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104 <when value="nucleic">
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105 </when>
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106 <when value="loop">
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107 <param name="res1" type="text" label="Resid of the loop starting residue"/>
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108 <param name="res2" type="text" label="Resid of the loop ending residue"/>
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109 </when>
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110 <when value="water">
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111 </when>
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112 <when value="hyd">
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113 </when>
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114 <when value="noh">
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115 </when>
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116 <when value="elety">
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117 <param name="elety" type="text" value="CA" label="Atom Name"/>
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118 </when>
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119 <when value="resid">
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120 <param name="resid" type="text" value="BGLC" label="Resid"/>
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121 </when>
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122 <when value="segid">
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123 <param name="segid" type="text" value="SUBS" label="Segid"/>
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124 </when>
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125 </conditional>
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126 </inputs>
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127 <outputs>
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128 <data format="tabular" name="output" label="rmsf raw data"/>
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129 <data format="png" name="rmsf_plot" label="rmsf plot"/>
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130 </outputs>
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131 <tests>
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132 <test>
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133 <expand macro="tests_inputs"/>
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134 <param name="sele" value="calpha"/>
1
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135 <output name="output" file="rmsf_raw_data.tabular" />
0
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136 </test>
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137 </tests>
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138 <help><![CDATA[
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139
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140 .. class:: infomark
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141
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142 **What it does**
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143
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144 The Root Mean Square Fluctuation (RMSF) conformational variance that analysis can analyze the
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145 portions of structure that are fluctuating from their mean structure the most (or least). This tool can calculate and plot the RMSF of the selected section.
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146
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147 _____
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148
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149 .. class:: infomark
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150
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151 **Input**
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152
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153 - Input file in PDB format
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154 - Input file in DCD format
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155
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156 _____
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157
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158 .. class:: infomark
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159
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160 **Output**
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161
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162 - Image (as PNG) of the rmsf plot
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163 - Tab-separated file of raw data
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164
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165
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166 ]]></help>
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167 <expand macro="citations" />
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168 </tool>