Mercurial > repos > chemteam > gmx_restraints

comparison restraints.xml @ 6:ca6a4740114e draft

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"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 7a25958195ccc8f448dd64ddcc36e8f5e5979d8b"
author chemteam
date Wed, 20 May 2020 13:01:45 -0400
parents 72c2b7992c26
children
comparison
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5:a550cfa43262 6:ca6a4740114e
1 <tool id="gmx_restraints" name="Create GROMACS position restraints files" version="@VERSION@"> 1 <tool id="gmx_restraints" name="Create GROMACS position restraints files" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@">
2 <description>using genrestr</description> 2 <description>using genrestr</description>
3 <macros> 3 <macros>
4 <import>macros.xml</import> 4 <import>macros.xml</import>
5 <token name="@GALAXY_VERSION@">0</token>
5 </macros> 6 </macros>
6 7
7 <expand macro="requirements" /> 8 <expand macro="requirements" />
8 9
9 <command detect_errors="exit_code"><![CDATA[ 10 <command detect_errors="exit_code"><![CDATA[
10 11
11 ln -s '$gro_input' ./gro_input.gro && 12 ln -s '$gro_input' ./gro_input.gro &&
12 ln -s '$ndx_input' ./ndx_input.ndx && 13 ln -s '$ndx_input' ./ndx_input.ndx &&
13 echo '$index' | gmx genrestr -f ./gro_input.gro -n ./ndx_input.ndx -o posre.itp -fc $fc &>> verbose.txt 14 echo '$index' | gmx genrestr -f ./gro_input.gro -n ./ndx_input.ndx -o tmp.itp -fc $fc &>> verbose.txt &&
14 15 tail -n +2 tmp.itp > posre.itp
15 ]]></command> 16 ]]></command>
16 17
17 <inputs> 18 <inputs>
18 <param argument="gro_input" type="data" format='gro' label="GRO input file" help="Input structure"/> 19 <param argument="gro_input" type="data" format='gro' label="GRO input file" help="Input structure"/>
19 <param argument="ndx_input" type="data" format='ndx' label="Index (NDX) file" help="Index file containing the atoms which should be restrained"/> 20 <param argument="ndx_input" type="data" format='ndx' label="Index (NDX) file" help="Index file containing the atoms which should be restrained"/>
31 <data name="output1" format="itp" from_work_dir="posre.itp"/> 32 <data name="output1" format="itp" from_work_dir="posre.itp"/>
32 <expand macro="log_outputs" /> 33 <expand macro="log_outputs" />
33 </outputs> 34 </outputs>
34 <tests> 35 <tests>
35 <test> 36 <test>
36 <param name="gro_input" value="md_0_1.gro" /> 37 <param name="gro_input" value="str_ions.gro" />
37 <param name="ndx_input" value="md_0_1.ndx" /> 38 <param name="ndx_input" value="index.ndx" />
38 <param name="fc" value="500 600 700" /> 39 <param name="fc" value="500 600 700" />
39 <param name="index" value="16" /> 40 <param name="index" value="13" />
40 <output name="output1" file="posre_cl.itp" ftype="itp"/> 41 <!-- Galaxy seems to think this output is a binary (?) -->
42 <output name="output1" file="posre_cl.itp" lines_diff="2"/>
41 </test> 43 </test>
42 </tests> 44 </tests>
43 <help><![CDATA[ 45 <help><![CDATA[
44 46
45 .. class:: infomark 47 .. class:: infomark