Mercurial > repos > agpetit > cut_trajectory
diff cut_trajectory.xml @ 0:78f612cdb8e8 draft
"planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
| author | agpetit |
|---|---|
| date | Mon, 30 May 2022 14:04:45 +0000 |
| parents | |
| children | b9fb306ccb2a |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/cut_trajectory.xml Mon May 30 14:04:45 2022 +0000 @@ -0,0 +1,184 @@ +<tool id="cut_trajectory" name="Cut trajectory" version="0.1.0" python_template_version="3.5" profile="@GALAXY_VERSION@"> + <macros> + <token name="@TOOL_VERSION@">2022</token> + <token name="@GALAXY_VERSION@">21.05</token> + </macros> + <requirements> + <requirement type="package" version="1.1.0">joblib</requirement> + <requirement type="package" version="@TOOL_VERSION@">gromacs</requirement> + </requirements> + <command detect_errors="exit_code"><![CDATA[ + ln -s '$gro_file' '$gro_file.element_identifier' && + ln -s '$xtc_file' '$xtc_file.element_identifier' && + #if $sub_traj.number_sub_traj == "file": + ln -s '$sub_traj.nb_sub_traj_file' '$sub_traj.nb_sub_traj_file.element_identifier' && + #else: + ln -s '$sub_traj.check_file_sub_traj' '$sub_traj.check_file_sub_traj.element_identifier' && + #end if + python '$__tool_directory__/cut_trajectory.py' + --verbose + --gro_file '$gro_file.element_identifier' + --xtc_file '$xtc_file.element_identifier' + --log_output 'out_log/cut_trajectories.log' + --output_directory 'out/' + #if $sub_traj.number_sub_traj == "file": + --nbr_sub_traj '$sub_traj.nb_sub_traj_file.element_identifier' + #else: + --nbr_sub_traj '$sub_traj.nb_sub_traj' + --input_check '$sub_traj.check_file_sub_traj.element_identifier' + --start_traj '$sub_traj.start_trajectory' + --end_traj '$sub_traj.end_trajectory' + #end if + --group_output $group.select_group + --number_cpus "\${GALAXY_SLOTS:-1}" + ]]></command> + <inputs> + <param name="gro_file" type="data" format="gro" help="Put your .gro file"/> + <param name="xtc_file" type="data" format="xtc" help="Put your .xtc file"/> + <conditional name="sub_traj"> + <param name="number_sub_traj" type="select" label="Number of sub-trajectories"> + <option value="file">with estimation file</option> + <option value="no_file">without estimation file</option> + </param> + <when value="file"> + <param name="nb_sub_traj_file" type="data" format="tabular" label="Number of sub-trajectories file"/> + </when> + <when value="no_file"> + <param name="check_file_sub_traj" type="data" format="txt" label="Check file" help="Enter the txt file produced with gmx check."> + <validator type="expression" message="Wrong file type">value.extension == "txt"</validator> + </param> + <param name="nb_sub_traj" type="integer" value="2" label="Number of sub-trajectories"/> + <param name="start_trajectory" type="integer" min="0" optional="true" label="Start trajectory" help="Choose the first frame of the trajectory (optional)"/> + <param name="end_trajectory" type="integer" min="1" optional="true" label="End trajectory" help="Choose the last frame of the trajectory (optional)"/> + </when> + </conditional> + <section name="group" title="Select a group for output"> + <param name="select_group" type="select" display="radio" label="Select a group:"> + <option value="0" selected="true">System</option> + <option value="1">Protein</option> + <option value="2">Protein-H</option> + <option value="3">C-alpha</option> + <option value="4">Backbone</option> + <option value="5">MainChain</option> + <option value="6">MainChain+Cb</option> + <option value="7">MainChain+H</option> + <option value="8">SideChain</option> + <option value="9">SideChain-H</option> + <option value="10">Prot-Masses</option> + <option value="11">non-Protein</option> + <option value="12">Other</option> + <option value="13">POPC</option> + <option value="14">POT</option> + <option value="15">CLA</option> + <option value="16">TIP3</option> + </param> + </section> + </inputs> + <outputs> + <data name="cut_log" format="txt" from_work_dir="out_log/*.log" label="cut_trajectories.log"/> + <collection name="output_traj" type="list" label="${tool.name} : output trajectories"> + <discover_datasets pattern="(?P<name>.+)\.xtc" directory="out/" ext="xtc"/> + </collection> + </outputs> + <tests> + + <test> + <param name="select_mode" value="cut"/> + <param name="gro_file" value="PIP2.1_test.gro"/> + <param name="xtc_file" value="PIP2.1_test.xtc"/> + <conditional name="sub_traj"> + <param name="number_sub_traj" value="file"/> + <param name="nb_sub_traj_file" value="estimated_number_of_sub_trajectories.tsv"/> + </conditional> + <section name="group"> + <param name="select_group" value="0"/> + </section> + <output name="cut_log" file="cut_trajectories_file.log" ftype="txt" lines_diff="12"> + <assert_contents> + <has_n_lines n="163"/> + <has_text text="Start cut trajectory"/> + <has_text text="Function search_nbr_sub_traj"/> + <has_text text="End search_nbr_sub_traj function"/> + <has_text text="Function cut_traj"/> + <has_text text="End cut_traj function"/> + <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"/> + <has_text text="Will write xtc: Compressed trajectory (portable xdr format): xtc"/> + </assert_contents> + </output> + <output_collection name="output_traj" type="list"> + <element name="PIP2.1_test_traj_1" file="PIP2.1_test_traj_1.xtc"/> + <element name="PIP2.1_test_traj_2" file="PIP2.1_test_traj_2.xtc"/> + <element name="PIP2.1_test_traj_3" file="PIP2.1_test_traj_3.xtc"/> + </output_collection> + </test> + <test> + <param name="select_mode" value="cut"/> + <param name="gro_file" value="PIP2.1_test.gro"/> + <param name="xtc_file" value="PIP2.1_test.xtc"/> + <conditional name="sub_traj"> + <param name="number_sub_traj" value="no_file"/> + <param name="nb_sub_traj" value="3"/> + <param name="check_file_sub_traj" value="PIP2.1_test_check.txt"/> + <param name="start_trajectory" value="0"/> + <param name="end_trajectory" value="10"/> + </conditional> + <section name="group"> + <param name="select_group" value="0"/> + </section> + <output name="cut_log" file="cut_trajectories_no_file.log" ftype="txt" lines_diff="12"> + <assert_contents> + <has_n_lines n="161"/> + <has_text text="Start cut trajectory"/> + <has_text text="Function search_nbr_steps_time_step"/> + <has_text text="End search_nbr_steps_time_step functions"/> + <has_text text="Function cut_traj"/> + <has_text text="End cut_traj function"/> + <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"/> + <has_text text="Will write xtc: Compressed trajectory (portable xdr format): xtc"/> + </assert_contents> + </output> + <output_collection name="output_traj" type="list"> + <element name="PIP2.1_test_traj_1" file="PIP2.1_test_traj_1.xtc"/> + <element name="PIP2.1_test_traj_2" file="PIP2.1_test_traj_2.xtc"/> + <element name="PIP2.1_test_traj_3" file="PIP2.1_test_traj_3.xtc"/> + </output_collection> + </test> + </tests> + <help><![CDATA[ + +.. class:: infomark + +**What it does** + +This tool allows allows to cut a path according to a desired number of sub-trajectories. + +_____ + +.. class:: infomark + +**Inputs** + + - gro_file: -gro option. .gro file obtained with GROMACS. + - xtc_file: -xtc option. .xtc file obtained with GROMACS. + - with estimation file : + - 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. + - without estimation file : + - Number of sub-trajectories. Choose the number of sub-trajectories. + - Start trajectory : -start. Choose the first frame of the trajectory (optional). + - End trajectory : -end. Choose the last frame of the trajectory (optional). + - Select a group for output. Select the group of atoms in which to cut the trajectory. + +_____ + +.. class:: infomark + +**Outputs** + + - 'estimate sub-trajectories or cut trajectory : output trajectories' : collection that contains all the sub-trajectories. + - 'cut_trajectories.log' : LOG file of the tool execution. + + ]]></help> + <citations> + <citation type="doi">10.1093/bioinformatics/btz107</citation> + </citations> +</tool>