Mercurial > repos > eschen42 > mqppep_preproc
diff mqppep_preproc.xml @ 16:d9906288cc6a draft
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 7127d1511d45a8b22d4f50eee6db24d844371227"
| author | eschen42 |
|---|---|
| date | Tue, 05 Apr 2022 01:47:37 +0000 |
| parents | 28a126da9b28 |
| children | 43f1fd0ff86b |
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--- a/mqppep_preproc.xml Sat Mar 26 02:26:38 2022 +0000 +++ b/mqppep_preproc.xml Tue Apr 05 01:47:37 2022 +0000 @@ -1,4 +1,10 @@ -<tool id="mqppep_preproc" name="MaxQuant Phosphopeptide Preprocessing" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" python_template_version="3.5"> +<tool + id="mqppep_preproc" + name="MaxQuant Phosphopeptide Preprocessing" + version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" + python_template_version="3.5" + profile="21.05" + > <description> Transform the output of MaxQuant for phosphoproteome-enriched samples to prepare it for statistical anlaysis. </description> @@ -10,7 +16,7 @@ ( echo '--- localization-filter step:' ) && ( - \$CONDA_PREFIX/bin/Rscript '$__tool_directory__/MaxQuantProcessingScript.R' + Rscript '$__tool_directory__/MaxQuantProcessingScript.R' -i '$phosphoSites' #if $pst_py_selector == "y" --enriched Y @@ -34,7 +40,7 @@ ) && ( echo '--- kinase-mapping step:' ) && ( - \$CONDA_PREFIX/bin/perl '$__tool_directory__/PhosphoPeptide_Upstream_Kinase_Mapping.pl' + perl '$__tool_directory__/PhosphoPeptide_Upstream_Kinase_Mapping.pl' -i '$phosphoPepIntensities' -f '$protein_fasta' -n '$networkin' @@ -56,7 +62,7 @@ ) && ( echo '--- merge-and-filter step:' ) && ( - \$CONDA_PREFIX/bin/python '$__tool_directory__/mqppep_mrgfltr.py' + python '$__tool_directory__/mqppep_mrgfltr.py' --phosphopeptides='$mapped_phophopeptides' --ppep_mapping_db='$mqppep_output_sqlite' --species='$species' @@ -368,7 +374,8 @@ *To generate this file:* - **(1)** Download the "precomputed data for all available kinase predictors against ENSEMBL" [available at the NetworkKIN predictions link on the downloads page at `https://networkin.info/download.shtml <https://networkin.info/download.shtml>`_] (N.B.: "Commercial users are requested to contact the authors before using the data on this website"); + **(1)** Download the "precomputed data for all available kinase predictors against ENSEMBL" + (Available at the NetworkKIN predictions link on the downloads page at https://web.archive.org/web/20200208000403/http://networkin.info/download/networkin_human_predictions_3.1.tsv.xz; N.B.: "Commercial users are requested to contact the authors before using the data on the networkin.info website"); **(2)** Decompress the .tsv.xz with file with "unxz" (from XZ Utils `https://tukaani.org/xz/ <https://tukaani.org/xz/>`_);