Mercurial > repos > galaxyp > openms_fidoadapter
changeset 4:935188b9c911 draft
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 1e51bed3a1c10c67ef0404216608e9333db04c64
| author | galaxyp |
|---|---|
| date | Wed, 18 Oct 2017 15:11:18 -0400 |
| parents | abd0666c9bf2 |
| children | 17e115ff19cf |
| files | FidoAdapter.xml macros.xml readme.md repository_dependencies.xml |
| diffstat | 4 files changed, 15 insertions(+), 9 deletions(-) [+] |
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--- a/FidoAdapter.xml Wed Aug 09 09:00:19 2017 -0400 +++ b/FidoAdapter.xml Wed Oct 18 15:11:18 2017 -0400 @@ -1,7 +1,7 @@ <?xml version='1.0' encoding='UTF-8'?> <!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTD2Galaxy.--> <!--Proposed Tool Section: [ID Processing]--> -<tool id="FidoAdapter" name="FidoAdapter" version="2.2.0"> +<tool id="FidoAdapter" name="FidoAdapter" version="2.2.0.1"> <description>Runs the protein inference engine Fido.</description> <macros> <token name="@EXECUTABLE@">FidoAdapter</token> @@ -11,8 +11,8 @@ <expand macro="stdio"/> <expand macro="requirements"/> <command>FidoAdapter --fidocp_executable fido_choose_parameters --fido_executable fido +-fidocp_executable FidoChooseParameters +-fido_executable Fido #if $param_in: -in $param_in
--- a/macros.xml Wed Aug 09 09:00:19 2017 -0400 +++ b/macros.xml Wed Oct 18 15:11:18 2017 -0400 @@ -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">
--- a/readme.md Wed Aug 09 09:00:19 2017 -0400 +++ b/readme.md Wed Oct 18 15:11:18 2017 -0400 @@ -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): ```
--- a/repository_dependencies.xml Wed Aug 09 09:00:19 2017 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -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>