Mercurial > repos > chemteam > gmx_trj
changeset 16:32052c6c3310 draft default tip
planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 4bffc6aa89cd0e6d6435a6e571b3836eaab076f1
| author | chemteam |
|---|---|
| date | Mon, 24 Oct 2022 22:36:40 +0000 |
| parents | 4a303225d447 |
| children | |
| files | test-data/trjconv_skip2.xtc trj.xml |
| diffstat | 2 files changed, 113 insertions(+), 56 deletions(-) [+] |
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line diff
--- a/trj.xml Tue Jul 12 12:45:39 2022 +0000 +++ b/trj.xml Mon Oct 24 22:36:40 2022 +0000 @@ -1,8 +1,8 @@ -<tool id="gmx_trj" name="Modify/convert GROMACS trajectories" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@"> +<tool id="gmx_trj" name="Modify/convert and concatate GROMACS trajectories" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="21.09"> <description>using trjconv and trjcat</description> <macros> <import>macros.xml</import> - <token name="@GALAXY_VERSION@">1</token> + <token name="@GALAXY_VERSION@">2</token> <xml name="fit_when" token_option="none"> <when value="@OPTION@"> <param name="index_fit" type="text" label="Index of group to use for fitting" help="Index of group to use for fitting - i.e. the group's position in the ndx file (using zero-based numbering, so the first group has index 0)."> @@ -11,18 +11,33 @@ </when> </xml> </macros> - - <expand macro="requirements" /> - + <expand macro="requirements"/> <command detect_errors="exit_code"><![CDATA[ #if $trj.trj_op == 'trjcat': mkdir trajs && - #for $value, $file in enumerate($trj_input): - ln -s '$file' trajs/traj_${str(value).rjust(10, '0')}.${file.ext} && + #set $file_count = 0 ## sets 1st input to 0 + #set $file_list = [] + #for $file_count, $file in enumerate($trj_input): ## enumerates each input file, starting from 0 + #set $filename = "trajs/traj_%i.%s" % ($file_count, $file.ext) + #silent $file_list.append($filename) + ln -s '$file' '$filename' && + #end for + + ## runs inputs from a repeat block. By choosing each input, this allows the user to select individual input files at a time, as well as ensure the proper order. + #for $traj_repeat in $trj.inputtrajs: + #for $file in $traj_repeat.trj_input: + #set $file_count = $file_count + 1 ## inputs from this repeat block will be numbered at + 1 ahead of inputs from first multiple select above + #set $filename = "trajs/traj_%i.%s" % ($file_count, $file.ext) + #silent $file_list.append($filename) + ln -s '$file' '$filename' && + #end for #end for gmx trjcat - -f trajs/traj* ## here we assume that they all have the same ext, probably reasonable + -f + #for $filename in $file_list: + '$filename' + #end for $trj.cat -e '$time.e' @@ -58,18 +73,20 @@ #if $time.e != -1: -e '$time.e' #end if + #if $trj.skip: + -skip $trj.skip + #end if #end if -b '$time.b' -dt '$time.dt' - -o ./output.${output_format} && - &>> verbose.txt + -o ./output.${output_format} + >> verbose.txt 2>&1 #if not $trj.sep: && mv ./output.${output_format} '$output' #end if ]]></command> - <inputs> <conditional name="trj"> <param name="trj_op" type="select" label="Modify a trajectory or concatenate multiple trajectories?"> @@ -77,9 +94,9 @@ <option value="trjcat">Concatenate (trjcat)</option> </param> <when value="trjconv"> - <param name="trj_input" type="data" format='xtc,trr,pdb,gro' label="Input trajectory" help="In XTC or TRR format; structure files with PDB or GRO format can also be used."/> - <param name="str_input" type="data" format='pdb,gro,tpr' label="Input structure" help="In PDB, GRO or TPR format."/> - <param name="ndx_input" type="data" format='ndx' label="Index (NDX) file" optional="true" help="In NDX format. Optional."/> + <param name="trj_input" type="data" format="xtc,trr,pdb,gro" label="Input trajectory" help="In XTC or TRR format; structure files with PDB or GRO format can also be used."/> + <param name="str_input" type="data" format="pdb,gro,tpr" label="Input structure" help="In PDB, GRO or TPR format."/> + <param name="ndx_input" type="data" format="ndx" label="Index (NDX) file" optional="true" help="In NDX format. Optional."/> <param name="index_output" value="0" type="text" label="Index of group to save in the output" help="Index of group to save in the output - i.e. the group's position in the ndx file (using zero-based numbering, so the first group has index 0)."> <validator type="regex" message="Only numeric values allowed">^[0-9]*$</validator> </param> @@ -91,7 +108,7 @@ <option value="sep">Yes, write each frame separately</option> </param> <conditional name="pbc"> - <param name="pbc" type="select" label="PBC treatment" > + <param name="pbc" type="select" label="PBC treatment"> <option value="none">none</option> <option value="mol">mol</option> <option value="res">res</option> @@ -105,25 +122,26 @@ <validator type="regex" message="Only numeric values allowed">^[0-9]*$</validator> </param> </when> - <when value="none" /> - <when value="mol" /> - <when value="res" /> - <when value="atom" /> - <when value="nojump" /> - <when value="whole" /> + <when value="none"/> + <when value="mol"/> + <when value="res"/> + <when value="atom"/> + <when value="nojump"/> + <when value="whole"/> </conditional> <param name="ur" type="select" label="Unit cell representation" help="Only has effect in combination with PBC treatment of mol, res or atom"> <option value="rect" selected="true">rect</option> <option value="tric">tric</option> <option value="compact">compact</option> </param> - <param name="boxcenter" type="select" label="Center for PBC and centering treatment" > + <param name="skip" type="integer" min="1" value="1" label="Number of frames to skip" help="This allows you to compress a trajectory file, by reducing the amount of frames written out into the new trajectory file."/> + <param name="boxcenter" type="select" label="Center for PBC and centering treatment"> <option value="rect">rect</option> <option value="tric" selected="true">tric</option> <option value="zero">zero</option> </param> <conditional name="fit"> - <param name="fit" type="select" label="Fit molecule to reference structure in the reference file?" > + <param name="fit" type="select" label="Fit molecule to reference structure in the reference file?"> <option value="none" selected="true">No fitting</option> <option value="rot+trans">rot+trans</option> <option value="rotxy+transxy">rotxy+transxy</option> @@ -140,23 +158,27 @@ </conditional> </when> <when value="trjcat"> - <param name="trj_input" type="data" format='xtc,trr' label="Input trajectories" help="In XTC or TRR format, but please do not mix the two. Please note that if you want to take order into account when concatenating, you must use a collection as input." multiple="true"/> + <param name="trj_input" type="data" format="xtc,trr" label="Input trajectories" help="In XTC or TRR format, but please do not mix the two. Please note that the order of concatenation is the same as the consecutive order of these selected inputs." multiple="true"/> + <repeat name="inputtrajs" title="Select input trajectories" min="0"> + <param name="trj_input" type="data" format="xtc,trr" label="Input trajectories" help="In XTC or TRR format, but please do not mix the two. Please note that the order of concatenation is the same as the consecutive order of these selected inputs." multiple="true"/> + </repeat> <param name="cat" type="boolean" label="Do not discard double time frames" truevalue="-cat" falsevalue="-nocat"/> - <param name="sep" type="hidden" value="" /> + <param name="sep" type="hidden" value=""/> </when> </conditional> - <param name="output_format" type="select" label="Output format" > + <param name="output_format" type="select" label="Output format"> <option value="xtc">XTC</option> <option value="trr">TRR</option> <option value="pdb">PDB</option> <option value="gro">GRO</option> </param> - <section title="Time" name='time' expanded="true"> + <section title="Time" name="time" expanded="true"> <param name="b" type="integer" label="Start time" help="Time (ps) of first frame to read from trajectory" value="0" min="0"/> - <param name="e" type="integer" label="End time" help="Time (ps) of last frame to read from trajectory" value="-1" min="-1"/> <!-- stupidly this has different default values for trjconv and trjcat --> - <param name="dt" type="integer" label="Write frames at this time interval (ps)" help="Only write frame when t is exactly divisible by this value. Leave as 0 to record all frames." value="0" min="0"/> + <param name="e" type="integer" label="End time" help="Time (ps) of last frame to read from trajectory" value="-1" min="-1"/> + <!-- stupidly this has different default values for trjconv and trjcat --> + <param name="dt" type="integer" label="Write frames at this time interval (ps)" help="Only write frame when t is exactly divisible by this value. Leave as 0 to record all frames." value="0" min="0"/> </section> - <expand macro="log" /> + <expand macro="log"/> </inputs> <outputs> <data name="output" format="xtc"> @@ -176,45 +198,80 @@ <filter>trj.get("sep") and output_format == 'pdb'</filter> <discover_datasets pattern="(?P<designation>^output[0-9]{9}\.pdb$)" ext="pdb"/> </collection> - <expand macro="log_outputs" /> + <expand macro="log_outputs"/> </outputs> <tests> <test> <!-- gmx trjcat -f npt.xtc nvt.xtc -cat -o test.xtc --> - <param name="trj_op" value="trjcat" /> - <param name="trj_input" value="npt.xtc,nvt.xtc" /> - <param name="b" value="0" /> - <param name="e" value="-1" /> - <param name="dt" value="0" /> - <param name="cat" value="true" /> + <param name="trj_op" value="trjcat"/> + <param name="trj_input" value="npt.xtc,nvt.xtc"/> + <param name="b" value="0"/> + <param name="e" value="-1"/> + <param name="dt" value="0"/> + <param name="cat" value="true"/> + <output name="output" file="trjcat.xtc" ftype="xtc"/> + </test> + <test> + <!-- gmx trjcat -f npt.xtc nvt.xtc -cat -o test.xtc --> + <conditional name="trj"> + <param name="trj_op" value="trjcat"/> + <param name="trj_input" value="npt.xtc"/> + <repeat name="inputtrajs"> + <param name="trj_input" value="nvt.xtc"/> + </repeat> + <param name="cat" value="true"/> + </conditional> + <param name="output_format" value="xtc"/> + <section name="time"> + <param name="b" value="0"/> + <param name="e" value="-1"/> + <param name="dt" value="0"/> + </section> <output name="output" file="trjcat.xtc" ftype="xtc"/> </test> <test> <!-- echo '1 1' | gmx trjconv -f npt.xtc -s npt.tpr -n -center -pbc mol -ur compact -o npt_c.xtc --> <!-- <param name="trj_op" value="trjconv" /> --> - <param name="trj_input" value="npt.xtc" /> + <param name="trj_input" value="npt.xtc"/> <param name="str_input" value="npt.tpr" ftype="tpr"/> - <param name="ndx_input" value="index.ndx" /> - <param name="b" value="0" /> - <param name="e" value="-1" /> - <param name="dt" value="0" /> - <param name="index_output" value="1" /> - <param name="index_center" value="1" /> - <param name="pbc" value="mol" /> - <param name="ur" value="tric" /> + <param name="ndx_input" value="index.ndx"/> + <param name="b" value="0"/> + <param name="e" value="-1"/> + <param name="dt" value="0"/> + <param name="index_output" value="1"/> + <param name="index_center" value="1"/> + <param name="pbc" value="mol"/> + <param name="ur" value="tric"/> <output name="output" file="trjconv.xtc" ftype="xtc"/> </test> <test> - <!-- test sep flag --> - <param name="trj_input" value="npt.xtc" /> + <!-- testing skip --> + <!-- echo '1 1' | gmx trjconv -f npt.xtc -s npt.tpr -n -center -pbc mol -ur compact -skip 2 -o npt_c.xtc --> + <!-- <param name="trj_op" value="trjconv" /> --> + <param name="trj_input" value="npt.xtc"/> <param name="str_input" value="npt.tpr" ftype="tpr"/> - <param name="ndx_input" value="index.ndx" /> - <param name="b" value="0" /> - <param name="e" value="-1" /> - <param name="dt" value="0" /> - <param name="index_output" value="0" /> - <param name="sep" value="sep" /> - <param name="output_format" value="pdb" /> + <param name="ndx_input" value="index.ndx"/> + <param name="b" value="0"/> + <param name="e" value="-1"/> + <param name="dt" value="0"/> + <param name="index_output" value="1"/> + <param name="index_center" value="1"/> + <param name="pbc" value="mol"/> + <param name="ur" value="compact"/> + <param name="skip" value="2"/> + <output name="output" file="trjconv_skip2.xtc" ftype="xtc"/> + </test> + <test> + <!-- test sep flag --> + <param name="trj_input" value="npt.xtc"/> + <param name="str_input" value="npt.tpr" ftype="tpr"/> + <param name="ndx_input" value="index.ndx"/> + <param name="b" value="0"/> + <param name="e" value="-1"/> + <param name="dt" value="0"/> + <param name="index_output" value="0"/> + <param name="sep" value="sep"/> + <param name="output_format" value="pdb"/> <output_collection name="pdb_frames" type="list"> <element name="output000000007.pdb" ftype="pdb" file="frame7.pdb"/> </output_collection> @@ -250,5 +307,5 @@ ]]></help> - <expand macro="citations" /> + <expand macro="citations"/> </tool>