# HG changeset patch # User galaxyp # Date 1500073337 14400 # Node ID 87077edf72c3d6b480c4399e940925e3ab487881 # Parent 38aae09ec59f3630462107cfdb7bde99cb945d2e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit daf6dfc513ede9b890125d9fff2c2657d834eea9 diff -r 38aae09ec59f -r 87077edf72c3 MetaboliteSpectralMatcher.xml --- a/MetaboliteSpectralMatcher.xml Thu Apr 27 13:00:19 2017 -0400 +++ b/MetaboliteSpectralMatcher.xml Fri Jul 14 19:02:17 2017 -0400 @@ -1,8 +1,8 @@ - - Find potential HMDB ids within the given mass error window. + + Perform a spectral library search. MetaboliteSpectralMatcher macros.xml @@ -15,6 +15,9 @@ #if $param_in: -in $param_in #end if +#if $param_database: + -database $param_database +#end if #if $param_out: -out $param_out #end if @@ -55,7 +58,8 @@ #end if - + + @@ -77,7 +81,7 @@ - Find potential HMDB ids within the given mass error window. + Perform a spectral library search. For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/UTILS_MetaboliteSpectralMatcher.html diff -r 38aae09ec59f -r 87077edf72c3 macros.xml --- a/macros.xml Thu Apr 27 13:00:19 2017 -0400 +++ b/macros.xml Fri Jul 14 19:02:17 2017 -0400 @@ -2,7 +2,7 @@ - openms + openms xtandem fido msgf_plus diff -r 38aae09ec59f -r 87077edf72c3 readme.md --- a/readme.md Thu Apr 27 13:00:19 2017 -0400 +++ b/readme.md Fri Jul 14 19:02:17 2017 -0400 @@ -14,15 +14,29 @@ Generating OpenMS wrappers ========================== - * install OpenMS (you can do this automatically through the Tool Shed) + * install OpenMS (you can do this automatically through Conda) * create a folder called CTD - * inside of your new installed openms/bin folder, execute the following command: + * if you installed openms as a binary in a specific directory, execute the following command in the `openms/bin` directory: ```bash for binary in `ls`; do ./$binary -write_ctd /PATH/TO/YOUR/CTD; done; ``` - * `MetaProSIP.ctd` includes a not supported character: To use it, search for `²` and replace it (e.g. with `^2`). + * if there is no binary release (e.g. as with version 2.2), download and unpack the Conda package, find the `bin` folder and create a list of the tools as follow: + + ```bash + ls >> tools.txt + ``` + + * search for the `bin` folder of your conda environment containing OpenMS and do: + + ```bash + while read p; do + ./PATH/TO/BIN/$p -write_ctd /PATH/TO/YOUR/CTD; + done -
- - -
- - @@ -22,13 +16,17 @@ + + +
+ @@ -44,7 +42,6 @@ - @@ -62,12 +59,14 @@ + + @@ -78,6 +77,7 @@ +
@@ -154,9 +154,7 @@ - -