Mercurial > repos > agpetit > visualize_pore_diameter_aqp

annotate visualize_pore_diameter_aqp.xml @ 14:1f08a90393be 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 13:13:06 +0000
parents a03c7dd0650e
children
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14
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agpetit
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1 <tool id="visualize_pore_diameter_aqp" name="visualize pore diameter of AQP" 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="@GALAXY_VERSION@">21.05</token>
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4 </macros>
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5 <requirements>
1
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6 <requirement type="package" version="1.20.3">r-getopt</requirement>
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7 <requirement type="package" version="3.3.6">r-ggplot2</requirement>
c860709ebc6e "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
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8 <requirement type="package" version="1.3.1">r-tidyverse</requirement>
2
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9 <requirement type="package" version="0.4.0">r-ggpubr</requirement>
0
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10 </requirements>
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11 <command detect_errors="exit_code"><![CDATA[
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12 ln -s '$input_file' '$input_file.element_identifier' &&
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13 Rscript '$__tool_directory__/visualize_pore_diameter_aqp.R'
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14 -i '$input_file.element_identifier'
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15 #if 'aqp' in $select_graph:
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16 -a TRUE
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17 #else:
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18 -a FALSE
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19 #end if
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20 #if 'protomer' in $select_graph:
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21 -p TRUE
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22 #else:
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23 -p FALSE
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24 #end if
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25 #if 'all' in $select_graph :
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26 -d TRUE
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27 #else:
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28 -d FALSE
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29 #end if
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30 #if $pdf == 'yes' :
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31 -f TRUE
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32 #else:
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33 -f FALSE
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34 #end if
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35 ]]></command>
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36 <inputs>
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37 <param name="input_file" type="data" format="tabular" label="Aquaporin pore diameter table" help="Put your table containing the means and standard deviations of aquaporins pore diameter"/>
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38 <param name="select_graph" type="select" multiple="true" display="checkboxes" label="Choose which graphics you want to get">
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39 <option value="aqp" selected="true">Distance distribution by aquaporin</option>
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40 <option value="protomer" selected="true">Distance distribution by protomer</option>
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41 <option value="all" selected="true">Distance distribution by aquaporin and by protomer</option>
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42 </param>
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43 <param name="pdf" type="select" label="Do you want a pdf file that contains all the selected graphics?">
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44 <option value="yes" selected="true">Yes</option>
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45 <option value="no">No</option>
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46 </param>
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47 </inputs>
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48 <outputs>
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49 <data name="out_file" format="png" from_work_dir="./Distance_distribution_by_aquaporin.png" label="Distance_distribution_by_aquaporin.png">
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50 <filter>"aqp" in select_graph</filter>
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51 </data>
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52 <data name="out_file2" format="png" from_work_dir="./Distance_distribution_by_protomer.png" label="Distance_distribution_by_protomer.png">
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53 <filter>"protomer" in select_graph</filter>
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54 </data>
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55 <data name="out_file3" format="png" from_work_dir="./Distance_distribution_on_all_protomers.png" label="Distance_distribution_on_all_protomers.png">
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56 <filter>"all" in select_graph</filter>
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57 </data>
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58 <data name="out_file4" format="pdf" from_work_dir="./*.pdf" label="Distance distribution (PDF)">
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59 <filter>pdf == "yes"</filter>
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60 </data>
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61 </outputs>
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62 <tests>
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63 <test>
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64 <param name="input_file" value="table_sort_pore_diameter_aqp.tabular" ftype="tabular"/>
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65 <param name="select_graph" value="aqp,protomer,all"/>
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66 <param name="pdf" value="yes"/>
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67 <output name="out_file" file="Distance_distribution_by_aquaporin.png"/>
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68 <output name="out_file2" file="Distance_distribution_by_protomer.png"/>
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69 <output name="out_file3" file="Distance_distribution_on_all_protomers.png"/>
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70 <output name="out_file4" file="all_graphics_distribution.pdf"/>
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71 </test>
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72 </tests>
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73 <help><![CDATA[
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74
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75 .. class:: infomark
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76
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77 **What it does**
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78
113c9904d083 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
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79 This tool allows to visualize the pore diameter of an aquaporin over time.
113c9904d083 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
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80
113c9904d083 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
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81 _____
113c9904d083 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
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82
113c9904d083 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
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83 .. class:: infomark
113c9904d083 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
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84
113c9904d083 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
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85 **Inputs**
113c9904d083 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
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86
113c9904d083 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
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87 - Aquaporin pore diameter table : table containing the average distance and standard deviation of each subpath for a complete trajectory
113c9904d083 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
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88 - Choose which graphics you want to get :
113c9904d083 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
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89 - Distance distribution by aquaporin : for each aquaporin, a ribbon graph is created showing the distance distribution over time
113c9904d083 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
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90 - Distance distribution by protomer : for each protomer, a ribbon graph is created showing the distance distribution over time
113c9904d083 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
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91 - Distance distribution by aquaporin and by protomer : for each protomer of each aquaporin, a ribbon graph is created showing the distribution of the distance over time
113c9904d083 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
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92 - Do you want a pdf file that contains all the selected graphics? :
113c9904d083 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
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93 - Yes : a PDF file containing all the selected graphics will be created in addition to the PNG files of the graphics
113c9904d083 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
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94 - No : only PNG files of the graphics will be created
113c9904d083 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
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95
113c9904d083 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
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96 _____
113c9904d083 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
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97
113c9904d083 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
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98 .. class:: infomark
113c9904d083 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
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99
113c9904d083 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
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100 **Outputs**
113c9904d083 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
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101
113c9904d083 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
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102 - PNG file for each selected graphic type
113c9904d083 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
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103 - PDF file containing all selected graphics
113c9904d083 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
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104
113c9904d083 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
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105 ]]></help>
113c9904d083 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
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106 <citations>
113c9904d083 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
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107 <citation type="doi">10.1093/bioinformatics/btz107</citation>
113c9904d083 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
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108 </citations>
113c9904d083 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
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109 </tool>