| Previous changeset 4:5579659312e6 (2020-04-15) Next changeset 6:c8d2c0162b6e (2020-05-20) |
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Commit message:
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 3846f6c5a15ba0586afbd5c901229e237a4e4f17" |
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modified:
energy.xml macros.xml |
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added:
test-data/md_0_1.tabular |
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| diff -r 5579659312e6 -r 345c2a16b95f energy.xml --- a/energy.xml Wed Apr 15 14:25:30 2020 -0400 +++ b/energy.xml Fri May 08 07:45:15 2020 -0400 |
| [ |
| @@ -11,6 +11,11 @@ ln -s '$edr_input' ./edr_input.edr && echo #echo str($terms).replace(',', ' ')# | gmx energy -f ./edr_input.edr -o ./energy.xvg ## echo #echo ' '.join(str($terms).split(','))# | gmx energy -f ./edr_input.edr -o ./energy.xvg + #if $fmt == 'tabular': + && + grep '@\|#' energy.xvg && + grep -v '@\|#' energy.xvg | sed 's/[[:space:]]*//' | sed 's/ /\t/g' > energy.tabular + #end if ]]></command> @@ -67,21 +72,36 @@ <option value="48">Protein lambda values</option> <option value="49">Non-protein lambda values</option> </param> - + <param argument="fmt" type='select' label="Output format" help="Format for output; either standard GROMACS XVG, or Galaxy tabular file."> + <option value="xvg">GROMACS XVG format</option> + <option value="tabular" selected="true">Galaxy tabular</option> + </param> <expand macro="log" /> </inputs> <outputs> - <data name="output1" format="xvg" from_work_dir="energy.xvg"/> + <data name="output1" format="xvg" from_work_dir="energy.xvg"> + <filter>fmt == 'xvg'</filter> + </data> + <data name="output2" format="tabular" from_work_dir="energy.tabular"> + <filter>fmt == 'tabular'</filter> + </data> <expand macro="log_outputs" /> </outputs> <tests> <test> <param name="edr_input" value="md_0_1.edr" /> <param name="terms" value="10,12,13" /> + <param name="fmt" value="xvg" /> <output name="output1" file="md_0_1.xvg" ftype="xvg" lines_diff="12"/> </test> + <test> + <param name="edr_input" value="md_0_1.edr" /> + <param name="terms" value="10,12,13" /> + <param name="fmt" value="tabular" /> + <output name="output1" file="md_0_1.tabular" ftype="tabular"/> + </test> </tests> <help><![CDATA[ @@ -107,7 +127,7 @@ **Output** - - Tabular file containing selected terms and some header lines + - Tabular or XVG file containing selected terms and some header lines ]]></help> |
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| diff -r 5579659312e6 -r 345c2a16b95f macros.xml --- a/macros.xml Wed Apr 15 14:25:30 2020 -0400 +++ b/macros.xml Fri May 08 07:45:15 2020 -0400 |
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| @@ -1,5 +1,5 @@ <macros> - <token name="@VERSION@">2019.1.4</token> + <token name="@VERSION@">2019.1.5</token> <xml name="requirements"> <requirements> <requirement type="package" version="2019.1">gromacs</requirement> |
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| diff -r 5579659312e6 -r 345c2a16b95f test-data/md_0_1.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/md_0_1.tabular Fri May 08 07:45:15 2020 -0400 |
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| @@ -0,0 +1,11 @@ +0.000000 -593300.312500 -497358.281250 300.761719 +0.100000 -592522.125000 -497450.843750 298.032074 +0.200000 -593496.500000 -497942.718750 299.544647 +0.300000 -593921.062500 -497878.187500 301.077850 +0.400000 -593262.062500 -497926.406250 298.860870 +0.500000 -593674.437500 -498809.312500 297.385773 +0.600000 -594222.062500 -498825.562500 299.051605 +0.700000 -593496.625000 -498020.125000 299.302399 +0.800000 -593813.875000 -498131.031250 299.949219 +0.900000 -594351.437500 -498515.812500 300.428131 +1.000000 -595232.000000 -499672.000000 299.564087 |