| Previous changeset 15:4a303225d447 (2022-07-12) |
|
Commit message:
planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 4bffc6aa89cd0e6d6435a6e571b3836eaab076f1 |
|
modified:
trj.xml |
|
added:
test-data/trjconv_skip2.xtc |
| b |
| diff -r 4a303225d447 -r 32052c6c3310 test-data/trjconv_skip2.xtc |
| b |
| Binary file test-data/trjconv_skip2.xtc has changed |
| b |
| diff -r 4a303225d447 -r 32052c6c3310 trj.xml --- a/trj.xml Tue Jul 12 12:45:39 2022 +0000 +++ b/trj.xml Mon Oct 24 22:36:40 2022 +0000 |
| [ |
| b'@@ -1,8 +1,8 @@\n-<tool id="gmx_trj" name="Modify/convert GROMACS trajectories" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@">\n+<tool id="gmx_trj" name="Modify/convert and concatate GROMACS trajectories" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="21.09">\n <description>using trjconv and trjcat</description>\n <macros>\n <import>macros.xml</import>\n- <token name="@GALAXY_VERSION@">1</token>\n+ <token name="@GALAXY_VERSION@">2</token>\n <xml name="fit_when" token_option="none">\n <when value="@OPTION@">\n <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).">\n@@ -11,18 +11,33 @@\n </when>\n </xml>\n </macros>\n-\n- <expand macro="requirements" />\n-\n+ <expand macro="requirements"/>\n <command detect_errors="exit_code"><![CDATA[\n #if $trj.trj_op == \'trjcat\':\n mkdir trajs &&\n- #for $value, $file in enumerate($trj_input):\n- ln -s \'$file\' trajs/traj_${str(value).rjust(10, \'0\')}.${file.ext} &&\n+ #set $file_count = 0 ## sets 1st input to 0\n+ #set $file_list = []\n+ #for $file_count, $file in enumerate($trj_input): ## enumerates each input file, starting from 0\n+ #set $filename = "trajs/traj_%i.%s" % ($file_count, $file.ext)\n+ #silent $file_list.append($filename)\n+ ln -s \'$file\' \'$filename\' &&\n+ #end for\n+ \n+ ## 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.\n+ #for $traj_repeat in $trj.inputtrajs:\n+ #for $file in $traj_repeat.trj_input:\n+ #set $file_count = $file_count + 1 ## inputs from this repeat block will be numbered at + 1 ahead of inputs from first multiple select above\n+ #set $filename = "trajs/traj_%i.%s" % ($file_count, $file.ext)\n+ #silent $file_list.append($filename)\n+ ln -s \'$file\' \'$filename\' &&\n+ #end for\n #end for\n \n gmx trjcat\n- -f trajs/traj* ## here we assume that they all have the same ext, probably reasonable\n+ -f \n+ #for $filename in $file_list:\n+ \'$filename\'\n+ #end for\n $trj.cat\n -e \'$time.e\'\n \n@@ -58,18 +73,20 @@\n #if $time.e != -1:\n -e \'$time.e\'\n #end if\n+ #if $trj.skip:\n+ -skip $trj.skip\n+ #end if\n #end if\n \n -b \'$time.b\'\n -dt \'$time.dt\'\n- -o ./output.${output_format} &&\n- &>> verbose.txt\n+ -o ./output.${output_format} \n+ >> verbose.txt 2>&1\n #if not $trj.sep:\n &&\n mv ./output.${output_format} \'$output\'\n #end if\n ]]></command>\n-\n <inputs>\n <conditional name="trj">\n <param name="trj_op" type="select" label="Modify a trajectory or concatenate multiple trajectories?">\n@@ -77,9 +94,9 @@\n <option value="trjcat">Concatenate (trjcat)</option>\n </param>\n <when value="trjconv">\n- <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."/>\n- <param name="str_input" type="data" format=\'pdb,gro,tpr\' label="Input structure" help="In PDB, GRO or TPR format."/>\n- <param name="ndx_input" type="data" format=\'ndx\' label="Index (NDX) file" optional="true" help="In NDX format. Optional."/>\n+ <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."/>\n+ <param name="str_input" type="data" format="pdb,gr'..b' name="trj">\n+ <param name="trj_op" value="trjcat"/>\n+ <param name="trj_input" value="npt.xtc"/>\n+ <repeat name="inputtrajs">\n+ <param name="trj_input" value="nvt.xtc"/>\n+ </repeat>\n+ <param name="cat" value="true"/>\n+ </conditional>\n+ <param name="output_format" value="xtc"/>\n+ <section name="time">\n+ <param name="b" value="0"/>\n+ <param name="e" value="-1"/>\n+ <param name="dt" value="0"/>\n+ </section>\n <output name="output" file="trjcat.xtc" ftype="xtc"/>\n </test>\n <test>\n <!-- echo \'1 1\' | gmx trjconv -f npt.xtc -s npt.tpr -n -center -pbc mol -ur compact -o npt_c.xtc -->\n <!-- <param name="trj_op" value="trjconv" /> -->\n- <param name="trj_input" value="npt.xtc" />\n+ <param name="trj_input" value="npt.xtc"/>\n <param name="str_input" value="npt.tpr" ftype="tpr"/>\n- <param name="ndx_input" value="index.ndx" />\n- <param name="b" value="0" />\n- <param name="e" value="-1" />\n- <param name="dt" value="0" />\n- <param name="index_output" value="1" />\n- <param name="index_center" value="1" />\n- <param name="pbc" value="mol" />\n- <param name="ur" value="tric" />\n+ <param name="ndx_input" value="index.ndx"/>\n+ <param name="b" value="0"/>\n+ <param name="e" value="-1"/>\n+ <param name="dt" value="0"/>\n+ <param name="index_output" value="1"/>\n+ <param name="index_center" value="1"/>\n+ <param name="pbc" value="mol"/>\n+ <param name="ur" value="tric"/>\n <output name="output" file="trjconv.xtc" ftype="xtc"/>\n </test>\n <test>\n- <!-- test sep flag -->\n- <param name="trj_input" value="npt.xtc" />\n+ <!-- testing skip -->\n+ <!-- echo \'1 1\' | gmx trjconv -f npt.xtc -s npt.tpr -n -center -pbc mol -ur compact -skip 2 -o npt_c.xtc -->\n+ <!-- <param name="trj_op" value="trjconv" /> -->\n+ <param name="trj_input" value="npt.xtc"/>\n <param name="str_input" value="npt.tpr" ftype="tpr"/>\n- <param name="ndx_input" value="index.ndx" />\n- <param name="b" value="0" />\n- <param name="e" value="-1" />\n- <param name="dt" value="0" />\n- <param name="index_output" value="0" />\n- <param name="sep" value="sep" />\n- <param name="output_format" value="pdb" />\n+ <param name="ndx_input" value="index.ndx"/>\n+ <param name="b" value="0"/>\n+ <param name="e" value="-1"/>\n+ <param name="dt" value="0"/>\n+ <param name="index_output" value="1"/>\n+ <param name="index_center" value="1"/>\n+ <param name="pbc" value="mol"/>\n+ <param name="ur" value="compact"/>\n+ <param name="skip" value="2"/>\n+ <output name="output" file="trjconv_skip2.xtc" ftype="xtc"/>\n+ </test>\n+ <test>\n+ <!-- test sep flag -->\n+ <param name="trj_input" value="npt.xtc"/>\n+ <param name="str_input" value="npt.tpr" ftype="tpr"/>\n+ <param name="ndx_input" value="index.ndx"/>\n+ <param name="b" value="0"/>\n+ <param name="e" value="-1"/>\n+ <param name="dt" value="0"/>\n+ <param name="index_output" value="0"/>\n+ <param name="sep" value="sep"/>\n+ <param name="output_format" value="pdb"/>\n <output_collection name="pdb_frames" type="list">\n <element name="output000000007.pdb" ftype="pdb" file="frame7.pdb"/>\n </output_collection>\n@@ -250,5 +307,5 @@\n \n \n ]]></help>\n- <expand macro="citations" />\n+ <expand macro="citations"/>\n </tool>\n' |