| Previous changeset 3:1dc8550349dd (2017-08-09) Next changeset 5:b60d678ffefb (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:
FileMerger.xml macros.xml readme.md |
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removed:
repository_dependencies.xml |
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| diff -r 1dc8550349dd -r 55344a50655c FileMerger.xml --- a/FileMerger.xml Wed Aug 09 09:07:38 2017 -0400 +++ b/FileMerger.xml Wed Oct 18 15:15:50 2017 -0400 |
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| @@ -26,16 +26,6 @@ -rt_concat:gap $param_rt_concat_gap #end if -#if $rep_param_rt_concat_trafo_out: --rt_concat:trafo_out - #for token in $rep_param_rt_concat_trafo_out: - #if " " in str(token): - "$token.param_rt_concat_trafo_out" - #else - $token.param_rt_concat_trafo_out - #end if - #end for -#end if #if $param_raw_rt_auto: -raw:rt_auto #end if @@ -74,8 +64,8 @@ <param name="param_annotate_file_origin" display="radio" type="boolean" truevalue="-annotate_file_origin" falsevalue="" checked="false" optional="True" label="Store the original filename in each feature using meta value "file_origin" (for featureXML and consensusXML only)" help="(-annotate_file_origin) "/> <param name="param_rt_concat_gap" type="float" value="0.0" label="The amount of gap (in seconds) to insert between the RT ranges of different input files" help="(-gap) RT concatenation is enabled if a value > 0 is set"/> <param name="param_raw_rt_auto" display="radio" type="boolean" truevalue="-raw:rt_auto" falsevalue="" checked="false" optional="True" label="Assign retention times automatically (integers starting at 1)" help="(-rt_auto) "/> - <repeat name="rep_param_raw_rt_custom" min="0" max="1" title="param_raw_rt_custom"> - <param name="param_raw_rt_custom" type="text" size="30" value="0" label="List of custom retention times that are assigned to the files" help="(-rt_custom) The number of given retention times must be equal to the number of input files"> + <repeat name="rep_param_raw_rt_custom" min="0" title="param_raw_rt_custom"> + <param name="param_raw_rt_custom" type="text" size="30" value="0" label="Custom retention times that are assigned to the files" help="(-rt_custom) The number of given retention times must be equal to the number of input files"> <sanitizer> <valid initial="string.printable"> <remove value="'"/> @@ -91,8 +81,7 @@ </expand> </inputs> <outputs> - <data name="param_out" format="featurexml"/> - <data name="param_rt_concat_trafo_out" format="trafoxml"/> + <data name="param_out" format="mzml"/> </outputs> <help>Merges several MS files into one file. |
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| diff -r 1dc8550349dd -r 55344a50655c macros.xml --- a/macros.xml Wed Aug 09 09:07:38 2017 -0400 +++ b/macros.xml Wed Oct 18 15:15:50 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 1dc8550349dd -r 55344a50655c readme.md --- a/readme.md Wed Aug 09 09:07:38 2017 -0400 +++ b/readme.md Wed Oct 18 15:15:50 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 1dc8550349dd -r 55344a50655c repository_dependencies.xml --- a/repository_dependencies.xml Wed Aug 09 09:07:38 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> |