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comparison makendx.xml @ 0:48dcca6f45ce draft

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"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
author chemteam
date Wed, 20 Nov 2019 11:11:48 -0500
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children d9eb276dfa32
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-1:000000000000 0:48dcca6f45ce
1 <tool id="gmx_makendx" name="Create GROMACS index files" version="@VERSION@">
2 <description>using make_ndx</description>
3 <macros>
4 <import>macros.xml</import>
5 </macros>
6
7 <expand macro="requirements" />
8
9 <command detect_errors="exit_code"><![CDATA[
10
11 ln -s '$input_file' ./input.$input_file.ext &&
12 (echo '$sel'; echo 'q') | gmx make_ndx -f ./input.$input_file.ext -o ./ndx.ndx &>> verbose.txt &&
13 cp ./ndx.ndx '$ndx'
14
15 ]]></command>
16
17 <inputs>
18 <param argument="input_file" type="data" format='gro,pdb' label="Input structure"/>
19 <param argument="sel" type="text" label="Selection command" help="Selection for the new index group, e.g. 'r34' to select residue 34. Use the operators '|' (or) and &amp; (and) to combine predefined groups.">
20 <sanitizer>
21 <valid>
22 <add value="|" />
23 <add value="&amp;" />
24 <add value="!" />
25 </valid>
26 </sanitizer>
27 </param>
28
29 <expand macro="log" />
30
31 </inputs>
32 <outputs>
33 <data name="ndx" format="ndx"/>
34 <expand macro="log_outputs" />
35 </outputs>
36 <tests>
37 <test>
38 <param name="input_file" value="md_0_1.gro" ftype="gro"/>
39 <param name="sel" value="! 1 &amp; 14" />
40 <output name="ndx" file="md_0_1.ndx">
41 <assert_contents>
42 <has_line line="[ !Protein_&amp;_non-Water ]"/>
43 <has_text text="38369 38370 38371 38372 38373 38374 38375 38376"/>
44 </assert_contents>
45 </output>
46 </test>
47 </tests>
48 <help><![CDATA[
49
50 .. class:: infomark
51
52 **What it does**
53
54 Generates GROMACS custom index files.
55
56 _____
57
58 .. class:: infomark
59
60 **Input**
61
62 - A PDB or GRO file.
63 - A selection command for the new index group to be included in the output file. Combine previously defined groups using identifying values with the operators '|' (or) and & (and). For example, '1 | 4' will create a new index group containing all atoms contained within the first and fourth index groups already specified (according to their position in the input file).
64
65 _____
66
67 .. class:: infomark
68
69 **Output**
70
71 - A GROMACS index (ndx) file, containing the 'default' index groups and the new group at the end of the file.
72
73 ]]></help>
74
75 <expand macro="citations" />
76 </tool>