Mercurial > repos > chemteam > gmx_energy

comparison energy.xml @ 5:345c2a16b95f draft

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"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 3846f6c5a15ba0586afbd5c901229e237a4e4f17"
author chemteam
date Fri, 08 May 2020 07:45:15 -0400
parents 5b0e6c2039a7
children c8d2c0162b6e
comparison
equal deleted inserted replaced
4:5579659312e6 5:345c2a16b95f
9 <command detect_errors="exit_code"><![CDATA[ 9 <command detect_errors="exit_code"><![CDATA[
10 10
11 ln -s '$edr_input' ./edr_input.edr && 11 ln -s '$edr_input' ./edr_input.edr &&
12 echo #echo str($terms).replace(',', ' ')# | gmx energy -f ./edr_input.edr -o ./energy.xvg 12 echo #echo str($terms).replace(',', ' ')# | gmx energy -f ./edr_input.edr -o ./energy.xvg
13 ## echo #echo ' '.join(str($terms).split(','))# | gmx energy -f ./edr_input.edr -o ./energy.xvg 13 ## echo #echo ' '.join(str($terms).split(','))# | gmx energy -f ./edr_input.edr -o ./energy.xvg
14 #if $fmt == 'tabular':
15 &&
16 grep '@\|#' energy.xvg &&
17 grep -v '@\|#' energy.xvg | sed 's/[[:space:]]*//' | sed 's/ /\t/g' > energy.tabular
18 #end if
14 19
15 ]]></command> 20 ]]></command>
16 21
17 <inputs> 22 <inputs>
18 <param argument="edr_input" type="data" format="edr" label="EDR file" help="GROMACS energy binary file"/> 23 <param argument="edr_input" type="data" format="edr" label="EDR file" help="GROMACS energy binary file"/>
65 <option value="46">Protein temperature</option> 70 <option value="46">Protein temperature</option>
66 <option value="47">Non-protein temperature</option> 71 <option value="47">Non-protein temperature</option>
67 <option value="48">Protein lambda values</option> 72 <option value="48">Protein lambda values</option>
68 <option value="49">Non-protein lambda values</option> 73 <option value="49">Non-protein lambda values</option>
69 </param> 74 </param>
70 75 <param argument="fmt" type='select' label="Output format" help="Format for output; either standard GROMACS XVG, or Galaxy tabular file.">
76 <option value="xvg">GROMACS XVG format</option>
77 <option value="tabular" selected="true">Galaxy tabular</option>
78 </param>
71 79
72 <expand macro="log" /> 80 <expand macro="log" />
73 81
74 </inputs> 82 </inputs>
75 <outputs> 83 <outputs>
76 <data name="output1" format="xvg" from_work_dir="energy.xvg"/> 84 <data name="output1" format="xvg" from_work_dir="energy.xvg">
85 <filter>fmt == 'xvg'</filter>
86 </data>
87 <data name="output2" format="tabular" from_work_dir="energy.tabular">
88 <filter>fmt == 'tabular'</filter>
89 </data>
77 <expand macro="log_outputs" /> 90 <expand macro="log_outputs" />
78 </outputs> 91 </outputs>
79 <tests> 92 <tests>
80 <test> 93 <test>
81 <param name="edr_input" value="md_0_1.edr" /> 94 <param name="edr_input" value="md_0_1.edr" />
82 <param name="terms" value="10,12,13" /> 95 <param name="terms" value="10,12,13" />
96 <param name="fmt" value="xvg" />
83 <output name="output1" file="md_0_1.xvg" ftype="xvg" lines_diff="12"/> 97 <output name="output1" file="md_0_1.xvg" ftype="xvg" lines_diff="12"/>
98 </test>
99 <test>
100 <param name="edr_input" value="md_0_1.edr" />
101 <param name="terms" value="10,12,13" />
102 <param name="fmt" value="tabular" />
103 <output name="output1" file="md_0_1.tabular" ftype="tabular"/>
84 </test> 104 </test>
85 </tests> 105 </tests>
86 <help><![CDATA[ 106 <help><![CDATA[
87 107
88 .. class:: infomark 108 .. class:: infomark
105 125
106 .. class:: infomark 126 .. class:: infomark
107 127
108 **Output** 128 **Output**
109 129
110 - Tabular file containing selected terms and some header lines 130 - Tabular or XVG file containing selected terms and some header lines
111 131
112 ]]></help> 132 ]]></help>
113 133
114 <expand macro="citations" /> 134 <expand macro="citations" />
115 </tool> 135 </tool>