Mercurial > repos > agpetit > calculate_diameter

annotate calculate_diameter.xml @ 13:f5064c93f7ab draft default tip

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"planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 83670d9ceed855c9f58e0fa63a682edcaace5354-dirty"
author agpetit
date Mon, 11 Jul 2022 13:17:18 +0000
parents 066606280457
children
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1 <tool id="calculate_diameter" name="calculate pore diameter of AQP" version="1.0.0" python_template_version="3.5" profile="@GALAXY_VERSION@" >
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2 <macros>
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3 <token name="@GALAXY_VERSION@">21.05</token>
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4 </macros>
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5 <requirements>
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6 <requirement type="package" version="2.1.0">mdanalysis</requirement>
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7 </requirements>
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8 <command detect_errors="exit_code"><![CDATA[
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9 ln -s '$gro_file' '$gro_file.element_identifier' &&
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10 ln -s '$xtc_file' '$xtc_file.element_identifier' &&
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11 python '$__tool_directory__/calculate_pore_diameter_aqp.py'
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12 --arr_one '$arr1'
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13 --arr_second '$arr2'
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14 --gro_file '$gro_file.element_identifier'
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15 --xtc_file '$xtc_file.element_identifier'
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16 --gro_file_ext '$gro_file.ext'
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17 --xtc_file_ext '$xtc_file.ext'
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18 --output '$table'
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19 --verbose
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20 --log_output '$tool_log'
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21 --output_directory 'out'
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22 2>&1
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23 ]]></command>
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24 <inputs>
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25 <param name="gro_file" type="data" format="gro" optional="False" help="Put your .gro file"/>
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26 <param name="xtc_file" type="data" format="xtc" optional="False" help="Put your .xtc file"/>
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27 <param name="arr1" type="text" optional="False" label="pattern1" help="Pattern1 is a sequence of four amino acids. The first amino acid of this sequence will be the one used for the pore diameter of measurement. Example : HSD LEU ALA THR">
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28 <validator type="regex" message="Syntax error. 4 amino acids requested separated by a space.">^(ALA|CYS|ASP|GLU|PHE|GLY|HIS|ILE|LYS|LEU|MET|ASN|PRO|GLN|ARG|SER|THR|VAL|TRP|TYR|HSD|HSP)( (ALA|CYS|ASP|GLU|PHE|GLY|HIS|ILE|LYS|LEU|MET|ASN|PRO|GLN|ARG|SER|THR|VAL|TRP|TYR|HSD|HSP))( (ALA|CYS|ASP|GLU|PHE|GLY|HIS|ILE|LYS|LEU|MET|ASN|PRO|GLN|ARG|SER|THR|VAL|TRP|TYR|HSD|HSP))( (ALA|CYS|ASP|GLU|PHE|GLY|HIS|ILE|LYS|LEU|MET|ASN|PRO|GLN|ARG|SER|THR|VAL|TRP|TYR|HSD|HSP))*$</validator>
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29 </param>
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30 <param name="arr2" type="text" optional="False" label="pattern2" help="Pattern2 is a sequence of four amino acids. The first amino acid of this sequence will be the one used for the pore diameter of measurement. Example : ARG SER PHE GLY">
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31 <validator type="regex" message="Syntax error. 4 amino acids requested separated by a space.">^(ALA|CYS|ASP|GLU|PHE|GLY|HIS|ILE|LYS|LEU|MET|ASN|PRO|GLN|ARG|SER|THR|VAL|TRP|TYR|HSD|HSP)( (ALA|CYS|ASP|GLU|PHE|GLY|HIS|ILE|LYS|LEU|MET|ASN|PRO|GLN|ARG|SER|THR|VAL|TRP|TYR|HSD|HSP))( (ALA|CYS|ASP|GLU|PHE|GLY|HIS|ILE|LYS|LEU|MET|ASN|PRO|GLN|ARG|SER|THR|VAL|TRP|TYR|HSD|HSP))( (ALA|CYS|ASP|GLU|PHE|GLY|HIS|ILE|LYS|LEU|MET|ASN|PRO|GLN|ARG|SER|THR|VAL|TRP|TYR|HSD|HSP))*$</validator>
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32 </param>
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33 </inputs>
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34 <outputs>
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35 <data name="table" format="tabular" from_work_dir="out/" label="${tool.name} (Tabular)"/>
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36 <data name="tool_log" format="txt" from_work_dir="out/*.log" label="${tool.name} (LOG)"/>
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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="gro_file" value="PIP2.1_test.gro" ftype="gro" />
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41 <param name="xtc_file" value="PIP2.1_test.xtc" ftype="xtc" />
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42 <param name="arr1" value="HSD LEU ALA THR"/>
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43 <param name="arr2" value="ARG SER PHE GLY"/>
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44 <output name="table" file="pair_dist_arr.tabular" />
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45 <output name="tool_log" file="calculate_pore_diameter_aqp.log" />
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46 </test>
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47 </tests>
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48 <help><![CDATA[
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49
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50 .. class:: infomark
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51
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52 **What it does**
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53
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54 This tool allows to launch a calculation of the pore diameter of an aquaporin as a function of time from a .gro file and an .xtc file. The calculation is made between the alpha carbons of two amino acids.
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55
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56 _____
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57
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58 .. class:: infomark
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59
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60 **Inputs**
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61
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62 - gro_file : .gro file created with GROMACS containing the system coordinates.
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63 - xtc_file : .xtc file created during a GROMACS simulation containing the trajectory for a given time of the system.
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64 - pattern1 : a sequence of 4 amino acids. Each amino acid is named according to its 3-letter code.
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65 - pattern2 : a sequence of 4 amino acids. Each amino acid is named according to its 3-letter code.
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66
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67 _____
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68
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69 .. class:: infomark
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70
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71 **Outputs**
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72
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
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73 - TSV file : contains all the distance measurements on a part of the trajectory and the average of these distances.
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
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74 - LOG file of the tool execution
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
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75
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
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76 ]]></help>
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
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77 <citations>
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
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78 <citation type="doi">10.1093/bioinformatics/btz107</citation>
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
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79 </citations>
e227d80e53be "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
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80 </tool>