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annotate rmsf.xml @ 0:f261fded9631 draft default tip

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planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 1310371ed706e7cf287c848363102f8a476647de
author chemteam
date Mon, 24 Oct 2022 22:35:01 +0000
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f261fded9631 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 1310371ed706e7cf287c848363102f8a476647de
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1 <tool id="gmx_rmsf" name="GROMACS RMSF calculation" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="21.09">
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2 <description>of molecular structures</description>
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3 <macros>
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4 <import>macros.xml</import>
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5 <token name="@GALAXY_VERSION@">0</token>
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6 </macros>
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7 <expand macro="requirements"/>
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8 <command detect_errors="exit_code"><![CDATA[
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9
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10 ln -s '$traj_input' ./traj_input.${traj_input.ext} &&
f261fded9631 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 1310371ed706e7cf287c848363102f8a476647de
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11 ln -s '$structure_input' ./structure_input.${structure_input.ext} &&
f261fded9631 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 1310371ed706e7cf287c848363102f8a476647de
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12 #if $ndx_input:
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13 ln -s '$ndx_input' ./ndx_input.${ndx_input.ext} &&
f261fded9631 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 1310371ed706e7cf287c848363102f8a476647de
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14 #end if
f261fded9631 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 1310371ed706e7cf287c848363102f8a476647de
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15 echo '$index' | gmx rmsf
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16
f261fded9631 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 1310371ed706e7cf287c848363102f8a476647de
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17 ##inputs
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18 -f ./traj_input.${traj_input.ext}
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19 -s ./structure_input.${structure_input.ext}
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20 #if $ndx_input:
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21 -n ./ndx_input.${ndx_input.ext}
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22 #end if
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23 -xvg '$outputformat'
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24
f261fded9631 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 1310371ed706e7cf287c848363102f8a476647de
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25 ## other options
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26 #if $resavg == 'true':
f261fded9631 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 1310371ed706e7cf287c848363102f8a476647de
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27 -res
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28 #end if
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29
f261fded9631 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 1310371ed706e7cf287c848363102f8a476647de
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30 >> verbose.txt 2>&1
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31
f261fded9631 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 1310371ed706e7cf287c848363102f8a476647de
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32 ]]></command>
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33 <inputs>
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34 <param name="traj_input" type="data" format="trr,xtc" label="Trajectory file" help="In XTC or TRR format"/>
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35 <param name="structure_input" type="data" format="tpr,pdb,gro" label="Structure file" help="In TPR, PDB, or GRO format. Use a tpr file if your system contains nonstandard atom types, as atomic masses may not be directly obtained from PDB or GRO files."/>
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36 <param name="ndx_input" type="data" format="ndx" optional="true" label="Index (NDX) file" help="Index file (optional) containing your system's different atomic and molecular groups. If not specified, GROMACS uses a default set of groups."/>
f261fded9631 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 1310371ed706e7cf287c848363102f8a476647de
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37 <param name="index" type="integer" value="0" min="0" label="Index of group" help="Index of group for calculating the Root Mean Square Fluctuation (RMSF) - i.e. the group's position in the ndx file (using zero-based numbering, so the first group has index 0)."/>
f261fded9631 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 1310371ed706e7cf287c848363102f8a476647de
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38 <param name="resavg" type="select" label="Calculate average RMSF for entire residues?" help="This option works best if the selected index group mainly includes whole residues.">
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39 <option value="false">No</option>
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40 <option value="true">Yes</option>
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41 </param>
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42 <param name="outputformat" type="select" label="Output format" help="The default XVG format is compatible with XMGRACE and includes all of the graph's parameters. The raw data just includes 2 columns, one for the frame index and second for the corresponding RMSF value.">
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43 <option value="xmgrace" selected="true">XVG</option>
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44 <option value="none">Raw Data</option>
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45 </param>
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46 <expand macro="log"/>
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47 </inputs>
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48 <outputs>
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49 <data name="rmsf_output" format="xvg" from_work_dir="rmsf.xvg" label="GROMACS calculation of RMSF on ${on_string}"/>
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50 <expand macro="log_outputs"/>
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51 </outputs>
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52 <tests>
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53 <test expect_num_outputs="1">
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54 <param name="traj_input" value="npt.xtc"/>
f261fded9631 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 1310371ed706e7cf287c848363102f8a476647de
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55 <param name="structure_input" value="npt.tpr" ftype="tpr"/>
f261fded9631 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 1310371ed706e7cf287c848363102f8a476647de
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56 <param name="ndx_input" value="index.ndx" ftype="ndx"/>
f261fded9631 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 1310371ed706e7cf287c848363102f8a476647de
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57 <param name="index" value="3"/>
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58 <param name="outputformat" value="xmgrace"/>
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59 <output name="rmsf_output" ftype="xvg">
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60 <assert_contents>
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61 <has_text text="5 0.0113"/>
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62 <has_text text="27 0.0136"/>
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63 <has_text text="43 0.0134"/>
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64 </assert_contents>
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65 </output>
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66 </test>
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67 <test expect_num_outputs="1">
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68 <param name="traj_input" value="npt.xtc"/>
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69 <param name="structure_input" value="npt.tpr" ftype="tpr"/>
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70 <param name="ndx_input" value="index.ndx" ftype="ndx"/>
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71 <param name="index" value="1"/>
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72 <param name="resavg" value="true"/>
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73 <param name="outputformat" value="none"/>
f261fded9631 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 1310371ed706e7cf287c848363102f8a476647de
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74 <output name="rmsf_output" ftype="xvg">
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75 <assert_contents>
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76 <has_text text="1 0.0263"/>
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77 <has_text text="2 0.0230"/>
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78 <has_text text="3 0.0201"/>
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79 </assert_contents>
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80 </output>
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81 </test>
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82 <!-- test without optional ndx -->
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83 <test expect_num_outputs="1">
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84 <param name="traj_input" value="npt.xtc"/>
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85 <param name="structure_input" value="npt.tpr" ftype="tpr"/>
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86 <param name="index" value="1"/>
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87 <param name="resavg" value="true"/>
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88 <param name="outputformat" value="none"/>
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89 <output name="rmsf_output" ftype="xvg">
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90 <assert_contents>
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91 <has_text text="1 0.0263"/>
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92 <has_text text="2 0.0230"/>
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93 <has_text text="3 0.0201"/>
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94 </assert_contents>
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95 </output>
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96 </test>
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97 </tests>
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98 <help><![CDATA[
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99
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100 .. class:: infomark
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101
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102 **What it does**
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103
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104 This tool calculates a structure's Root Mean Square Fluctuation (RMSF), using GROMACS.
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105
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106 _____
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107
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108 .. class:: infomark
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109
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110 **Input**
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111
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112 - GRO, PDB, or TPR structure file.
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113 - TRR or XTC trajectory file.
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114
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115
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116 _____
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117
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118
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119 .. class:: infomark
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120
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121 **Output**
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122
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123 - XVG file containing RMSF results.
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124
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125 ]]></help>
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126 <expand macro="citations"/>
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127 </tool>