| Previous changeset 1:a25d96e0d837 (2017-08-09) Next changeset 3:e2b35770f86d (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:
MetaProSIP.xml macros.xml readme.md |
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removed:
repository_dependencies.xml |
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| diff -r a25d96e0d837 -r 21644dec106d MetaProSIP.xml --- a/MetaProSIP.xml Wed Aug 09 09:29:30 2017 -0400 +++ b/MetaProSIP.xml Wed Oct 18 15:29:01 2017 -0400 |
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| @@ -9,7 +9,9 @@ </macros> <expand macro="references"/> <expand macro="stdio"/> - <expand macro="requirements"/> + <expand macro="requirements"> + <requirement type="package" version="3.3.1">r-base</requirement> + </expand> <command>MetaProSIP #if $param_in_mzML: @@ -27,9 +29,9 @@ #if $param_in_featureXML: -in_featureXML $param_in_featureXML #end if -#if $param_r_executable: - -r_executable $param_r_executable -#end if + +-r_executable 'R' + #if $param_mz_tolerance_ppm: -mz_tolerance_ppm $param_mz_tolerance_ppm #end if @@ -133,7 +135,6 @@ <param name="param_in_mzML" type="data" format="mzml" optional="False" label="Centroided MS1 data" help="(-in_mzML) "/> <param name="param_in_fasta" type="data" format="fasta" optional="False" label="Protein sequence database" help="(-in_fasta) "/> <param name="param_in_featureXML" type="data" format="featurexml" optional="False" label="Feature data annotated with identifications (IDMapper)" help="(-in_featureXML) "/> - <param name="param_r_executable" type="data" format="txt" value="R" label="Path to the R executable (default: 'R')" help="(-r_executable) "/> <param name="param_mz_tolerance_ppm" type="float" value="10.0" label="Tolerance in ppm" help="(-mz_tolerance_ppm) "/> <param name="param_rt_tolerance_s" type="float" value="30.0" label="Rolerance window around feature rt for XIC extraction" help="(-rt_tolerance_s) "/> <param name="param_intensity_threshold" type="float" value="10.0" label="Intensity threshold to collect peaks in the MS1 spectrum" help="(-intensity_threshold) "/> |
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| diff -r a25d96e0d837 -r 21644dec106d macros.xml --- a/macros.xml Wed Aug 09 09:29:30 2017 -0400 +++ b/macros.xml Wed Oct 18 15:29:01 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 a25d96e0d837 -r 21644dec106d readme.md --- a/readme.md Wed Aug 09 09:29:30 2017 -0400 +++ b/readme.md Wed Oct 18 15:29:01 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 a25d96e0d837 -r 21644dec106d repository_dependencies.xml --- a/repository_dependencies.xml Wed Aug 09 09:29:30 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> |