Mercurial > repos > agpetit > cut_trajectory

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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 13:15:12 +0000
parents 763261d4720d
children
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9
adb40c1365a5 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 83670d9ceed855c9f58e0fa63a682edcaace5354-dirty"
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1 <tool id="cut_trajectory" name="cut trajectory" version="1.0.0" python_template_version="3.5" profile="@GALAXY_VERSION@">
0
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2 <macros>
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3 <token name="@TOOL_VERSION@">2022</token>
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4 <token name="@GALAXY_VERSION@">21.05</token>
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5 </macros>
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6 <requirements>
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7 <requirement type="package" version="1.1.0">joblib</requirement>
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8 <requirement type="package" version="@TOOL_VERSION@">gromacs</requirement>
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9 </requirements>
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10 <command detect_errors="exit_code"><![CDATA[
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11 ln -s '$gro_file' '$gro_file.element_identifier' &&
78f612cdb8e8 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
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12 ln -s '$xtc_file' '$xtc_file.element_identifier' &&
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13 #if $sub_traj.number_sub_traj == "file":
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14 ln -s '$sub_traj.nb_sub_traj_file' '$sub_traj.nb_sub_traj_file.element_identifier' &&
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15 #else:
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16 ln -s '$sub_traj.check_file_sub_traj' '$sub_traj.check_file_sub_traj.element_identifier' &&
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17 #end if
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18 python '$__tool_directory__/cut_trajectory.py'
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19 --verbose
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20 --gro_file '$gro_file.element_identifier'
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21 --xtc_file '$xtc_file.element_identifier'
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22 --log_output 'out_log/cut_trajectories.log'
78f612cdb8e8 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
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23 --output_directory 'out/'
78f612cdb8e8 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
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24 #if $sub_traj.number_sub_traj == "file":
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25 --nbr_sub_traj '$sub_traj.nb_sub_traj_file.element_identifier'
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26 #else:
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27 --nbr_sub_traj '$sub_traj.nb_sub_traj'
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28 --input_check '$sub_traj.check_file_sub_traj.element_identifier'
78f612cdb8e8 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
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29 --start_traj '$sub_traj.start_trajectory'
78f612cdb8e8 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
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30 --end_traj '$sub_traj.end_trajectory'
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31 #end if
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32 --group_output $group.select_group
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33 --number_cpus "\${GALAXY_SLOTS:-1}"
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34 ]]></command>
78f612cdb8e8 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
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35 <inputs>
9
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36 <param name="gro_file" type="data" format="gro" help="Put your .gro file"/>
0
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37 <param name="xtc_file" type="data" format="xtc" help="Put your .xtc file"/>
78f612cdb8e8 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
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38 <conditional name="sub_traj">
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39 <param name="number_sub_traj" type="select" label="Number of sub-trajectories">
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40 <option value="file">with estimation file</option>
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41 <option value="no_file">without estimation file</option>
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42 </param>
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43 <when value="file">
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44 <param name="nb_sub_traj_file" type="data" format="tabular" label="Number of sub-trajectories file"/>
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45 </when>
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46 <when value="no_file">
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47 <param name="check_file_sub_traj" type="data" format="txt" label="Check file" help="Enter the txt file produced with gmx check.">
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48 <validator type="expression" message="Wrong file type">value.extension == "txt"</validator>
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49 </param>
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50 <param name="nb_sub_traj" type="integer" value="2" label="Number of sub-trajectories"/>
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51 <param name="start_trajectory" type="integer" min="0" optional="true" label="Start trajectory" help="Choose the first frame of the trajectory (optional)"/>
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52 <param name="end_trajectory" type="integer" min="1" optional="true" label="End trajectory" help="Choose the last frame of the trajectory (optional)"/>
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53 </when>
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54 </conditional>
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55 <section name="group" title="Select a group for output">
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56 <param name="select_group" type="select" display="radio" label="Select a group:">
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57 <option value="0" selected="true">System</option>
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58 <option value="1">Protein</option>
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59 <option value="2">Protein-H</option>
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60 <option value="3">C-alpha</option>
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61 <option value="4">Backbone</option>
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62 <option value="5">MainChain</option>
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63 <option value="6">MainChain+Cb</option>
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64 <option value="7">MainChain+H</option>
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65 <option value="8">SideChain</option>
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66 <option value="9">SideChain-H</option>
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67 <option value="10">Prot-Masses</option>
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68 <option value="11">non-Protein</option>
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69 <option value="12">Other</option>
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70 <option value="13">POPC</option>
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71 <option value="14">POT</option>
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72 <option value="15">CLA</option>
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73 <option value="16">TIP3</option>
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74 </param>
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75 </section>
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76 </inputs>
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77 <outputs>
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78 <data name="cut_log" format="txt" from_work_dir="out_log/*.log" label="cut_trajectories.log"/>
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79 <collection name="output_traj" type="list" label="${tool.name} : output trajectories">
78f612cdb8e8 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
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80 <discover_datasets pattern="(?P&lt;name&gt;.+)\.xtc" directory="out/" ext="xtc"/>
78f612cdb8e8 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
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81 </collection>
78f612cdb8e8 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
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82 </outputs>
78f612cdb8e8 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
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83 <tests>
78f612cdb8e8 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
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84
78f612cdb8e8 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
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85 <test>
78f612cdb8e8 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
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86 <param name="select_mode" value="cut"/>
78f612cdb8e8 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
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87 <param name="gro_file" value="PIP2.1_test.gro"/>
78f612cdb8e8 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
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88 <param name="xtc_file" value="PIP2.1_test.xtc"/>
78f612cdb8e8 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
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89 <conditional name="sub_traj">
78f612cdb8e8 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
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90 <param name="number_sub_traj" value="file"/>
78f612cdb8e8 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
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91 <param name="nb_sub_traj_file" value="estimated_number_of_sub_trajectories.tsv"/>
78f612cdb8e8 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
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92 </conditional>
78f612cdb8e8 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
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93 <section name="group">
78f612cdb8e8 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
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94 <param name="select_group" value="0"/>
78f612cdb8e8 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
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95 </section>
78f612cdb8e8 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
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96 <output name="cut_log" file="cut_trajectories_file.log" ftype="txt" lines_diff="12">
78f612cdb8e8 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
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97 <assert_contents>
78f612cdb8e8 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
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98 <has_n_lines n="163"/>
78f612cdb8e8 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
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99 <has_text text="Start cut trajectory"/>
78f612cdb8e8 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
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100 <has_text text="Function search_nbr_sub_traj"/>
78f612cdb8e8 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
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101 <has_text text="End search_nbr_sub_traj function"/>
78f612cdb8e8 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
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102 <has_text text="Function cut_traj"/>
78f612cdb8e8 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
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103 <has_text text="End cut_traj function"/>
78f612cdb8e8 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
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104 <has_text text="gmx trjconv -f PIP2.1_test.xtc -s PIP2.1_test.gro -b 60 -e 80 -o out/PIP2.1_test_traj_3.xtc"/>
78f612cdb8e8 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
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105 <has_text text="Will write xtc: Compressed trajectory (portable xdr format): xtc"/>
78f612cdb8e8 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
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106 </assert_contents>
78f612cdb8e8 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
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107 </output>
78f612cdb8e8 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
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108 <output_collection name="output_traj" type="list">
78f612cdb8e8 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
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109 <element name="PIP2.1_test_traj_1" file="PIP2.1_test_traj_1.xtc"/>
78f612cdb8e8 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
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110 <element name="PIP2.1_test_traj_2" file="PIP2.1_test_traj_2.xtc"/>
78f612cdb8e8 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
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111 <element name="PIP2.1_test_traj_3" file="PIP2.1_test_traj_3.xtc"/>
78f612cdb8e8 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
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112 </output_collection>
78f612cdb8e8 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
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113 </test>
78f612cdb8e8 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
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114 <test>
78f612cdb8e8 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
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115 <param name="select_mode" value="cut"/>
78f612cdb8e8 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
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116 <param name="gro_file" value="PIP2.1_test.gro"/>
78f612cdb8e8 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
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117 <param name="xtc_file" value="PIP2.1_test.xtc"/>
78f612cdb8e8 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
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118 <conditional name="sub_traj">
78f612cdb8e8 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
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119 <param name="number_sub_traj" value="no_file"/>
78f612cdb8e8 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
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120 <param name="nb_sub_traj" value="3"/>
78f612cdb8e8 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
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121 <param name="check_file_sub_traj" value="PIP2.1_test_check.txt"/>
78f612cdb8e8 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
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122 <param name="start_trajectory" value="0"/>
78f612cdb8e8 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
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123 <param name="end_trajectory" value="10"/>
78f612cdb8e8 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
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124 </conditional>
78f612cdb8e8 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
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125 <section name="group">
78f612cdb8e8 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
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126 <param name="select_group" value="0"/>
78f612cdb8e8 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
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127 </section>
78f612cdb8e8 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
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128 <output name="cut_log" file="cut_trajectories_no_file.log" ftype="txt" lines_diff="12">
78f612cdb8e8 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
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129 <assert_contents>
78f612cdb8e8 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
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130 <has_n_lines n="161"/>
78f612cdb8e8 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
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131 <has_text text="Start cut trajectory"/>
78f612cdb8e8 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
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132 <has_text text="Function search_nbr_steps_time_step"/>
78f612cdb8e8 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
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133 <has_text text="End search_nbr_steps_time_step functions"/>
78f612cdb8e8 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
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134 <has_text text="Function cut_traj"/>
78f612cdb8e8 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
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135 <has_text text="End cut_traj function"/>
78f612cdb8e8 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
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136 <has_text text="gmx trjconv -f PIP2.1_test.xtc -s PIP2.1_test.gro -b 60 -e 80 -o out/PIP2.1_test_traj_3.xtc"/>
78f612cdb8e8 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
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137 <has_text text="Will write xtc: Compressed trajectory (portable xdr format): xtc"/>
78f612cdb8e8 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
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138 </assert_contents>
78f612cdb8e8 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
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139 </output>
78f612cdb8e8 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
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140 <output_collection name="output_traj" type="list">
78f612cdb8e8 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
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141 <element name="PIP2.1_test_traj_1" file="PIP2.1_test_traj_1.xtc"/>
78f612cdb8e8 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
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142 <element name="PIP2.1_test_traj_2" file="PIP2.1_test_traj_2.xtc"/>
78f612cdb8e8 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
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143 <element name="PIP2.1_test_traj_3" file="PIP2.1_test_traj_3.xtc"/>
78f612cdb8e8 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
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144 </output_collection>
78f612cdb8e8 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
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145 </test>
78f612cdb8e8 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
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146 </tests>
78f612cdb8e8 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
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147 <help><![CDATA[
78f612cdb8e8 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
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148
78f612cdb8e8 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
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149 .. class:: infomark
78f612cdb8e8 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
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150
78f612cdb8e8 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
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151 **What it does**
78f612cdb8e8 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
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152
78f612cdb8e8 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
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153 This tool allows allows to cut a path according to a desired number of sub-trajectories.
78f612cdb8e8 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
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154
78f612cdb8e8 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
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155 _____
78f612cdb8e8 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
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156
78f612cdb8e8 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
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157 .. class:: infomark
78f612cdb8e8 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
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158
78f612cdb8e8 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
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159 **Inputs**
78f612cdb8e8 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
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160
78f612cdb8e8 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
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161 - gro_file: -gro option. .gro file obtained with GROMACS.
78f612cdb8e8 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
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162 - xtc_file: -xtc option. .xtc file obtained with GROMACS.
78f612cdb8e8 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
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163 - with estimation file :
78f612cdb8e8 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
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164 - Number of sub-trajectories file: -s option. TSV file containing the number of sub-trajectories obtained with the 'Estimate number of sub-trajectories' mode of this tool.
78f612cdb8e8 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
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165 - without estimation file :
78f612cdb8e8 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
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166 - Number of sub-trajectories. Choose the number of sub-trajectories.
78f612cdb8e8 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
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167 - Start trajectory : -start. Choose the first frame of the trajectory (optional).
78f612cdb8e8 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
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168 - End trajectory : -end. Choose the last frame of the trajectory (optional).
78f612cdb8e8 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
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169 - Select a group for output. Select the group of atoms in which to cut the trajectory.
78f612cdb8e8 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
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170
78f612cdb8e8 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
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171 _____
78f612cdb8e8 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
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172
78f612cdb8e8 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
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173 .. class:: infomark
78f612cdb8e8 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
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174
78f612cdb8e8 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
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175 **Outputs**
78f612cdb8e8 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
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176
78f612cdb8e8 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
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177 - 'estimate sub-trajectories or cut trajectory : output trajectories' : collection that contains all the sub-trajectories.
78f612cdb8e8 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
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178 - 'cut_trajectories.log' : LOG file of the tool execution.
78f612cdb8e8 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
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179
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180 ]]></help>
78f612cdb8e8 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
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181 <citations>
78f612cdb8e8 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
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182 <citation type="doi">10.1093/bioinformatics/btz107</citation>
78f612cdb8e8 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
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183 </citations>
78f612cdb8e8 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
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184 </tool>