| Previous changeset 1:cd0746ee4796 (2017-08-09) Next changeset 3:61bc5fb43781 (2017-10-28) |
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Commit message:
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 1e51bed3a1c10c67ef0404216608e9333db04c64 |
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modified:
XTandemAdapter.xml macros.xml readme.md |
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removed:
repository_dependencies.xml |
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| diff -r cd0746ee4796 -r 22e9bb7d151a XTandemAdapter.xml --- a/XTandemAdapter.xml Wed Aug 09 09:18:43 2017 -0400 +++ b/XTandemAdapter.xml Wed Oct 18 15:22:33 2017 -0400 |
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| @@ -132,7 +132,7 @@ </param> <param name="param_max_precursor_charge" type="integer" min="0" optional="True" value="4" label="Maximum precursor charge ('0' to use X! Tandem default)" help="(-max_precursor_charge) "/> <param name="param_no_isotope_error" display="radio" type="boolean" truevalue="-no_isotope_error" falsevalue="" checked="false" optional="True" label="By default, misassignment to the first and second isotopic 13C peak are also considered" help="(-no_isotope_error) Set this flag to disable"/> - <repeat name="rep_param_fixed_modifications" min="0" max="1" title="param_fixed_modifications"> + <repeat name="rep_param_fixed_modifications" min="0" title="param_fixed_modifications"> <param name="param_fixed_modifications" type="select" optional="True" label="Fixed modifications, specified using Unimod (www.unimod.org) terms," help="(-fixed_modifications) e.g. 'Carbamidomethyl (C)' or 'Oxidation (M)'"> <option value="15N-oxobutanoic (N-term C)">15N-oxobutanoic (N-term C)</option> <option value="2-dimethylsuccinyl (C)">2-dimethylsuccinyl (C)</option> |
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| diff -r cd0746ee4796 -r 22e9bb7d151a macros.xml --- a/macros.xml Wed Aug 09 09:18:43 2017 -0400 +++ b/macros.xml Wed Oct 18 15:22:33 2017 -0400 |
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| @@ -6,6 +6,7 @@ <requirement type="package" version="15.12.15.2">xtandem</requirement> <requirement type="package" version="1.0">fido</requirement> <requirement type="package" version="2016.10.26">msgf_plus</requirement> + <yield/> </requirements> </xml> <xml name="stdio"> |
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| diff -r cd0746ee4796 -r 22e9bb7d151a readme.md --- a/readme.md Wed Aug 09 09:18:43 2017 -0400 +++ b/readme.md Wed Oct 18 15:22:33 2017 -0400 |
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| @@ -69,6 +69,7 @@ omssa_executable pepnovo_executable \ xtandem_executable param_model_directory \ java_executable java_memory java_permgen \ + r_executable rt_concat_trafo_out \ -f /PATH/TO/filetypes.txt -m /PATH/TO/macros.xml \ -s PATH/TO/SKIP_TOOLS_FILES.txt ``` @@ -77,8 +78,8 @@ * As last step you need to change manually the binary names of all external binaries you want to use in OpenMS. For example: ``` - sed -i '13 a\-fido_executable fido' wrappers/FidoAdapter.xml - sed -i '13 a\-fidocp_executable fido_choose_parameters' wrappers/FidoAdapter.xml + sed -i '13 a\-fido_executable Fido' wrappers/FidoAdapter.xml + sed -i '13 a\-fidocp_executable FidoChooseParameters' wrappers/FidoAdapter.xml sed -i '13 a\-myrimatch_executable myrimatch' wrappers/MyriMatchAdapter.xml sed -i '13 a\-omssa_executable omssa' wrappers/OMSSAAdapter.xml sed -i '13 a\-xtandem_executable xtandem' wrappers/XTandemAdapter.xml @@ -117,6 +118,14 @@ ]]> ``` + * In `MetaProSIP.xml` add `R` as a requirement: + + ``` + <expand macro="requirements"> + <requirement type="package" version="3.3.1">r-base</requirement> + </expand> + ``` + * In `IDFileConverter.xml` the following is needed in the command section at the beginning (check your file to know what to copy where): ``` |
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| diff -r cd0746ee4796 -r 22e9bb7d151a repository_dependencies.xml --- a/repository_dependencies.xml Wed Aug 09 09:18:43 2017 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,4 +0,0 @@ -<?xml version="1.0"?> -<repositories description="Required proteomics dependencies."> - <repository changeset_revision="300fc3aa6954" name="proteomics_datatypes" owner="iracooke" toolshed="https://toolshed.g2.bx.psu.edu" /> -</repositories> |