Mercurial > repos > eschen42 > mqppep_preproc
changeset 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 | fd367bb6423d |
| children | ba5f14c2a4af |
| files | macros.xml mqppep_mrgfltr.py mqppep_preproc.xml |
| diffstat | 3 files changed, 21 insertions(+), 21 deletions(-) [+] |
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--- a/macros.xml Sat Mar 26 02:26:38 2022 +0000 +++ b/macros.xml Tue Apr 05 01:47:37 2022 +0000 @@ -1,5 +1,5 @@ <macros> - <token name="@TOOL_VERSION@">0.1.6</token> + <token name="@TOOL_VERSION@">0.1.7</token> <token name="@VERSION_SUFFIX@">0</token> <xml name="requirements"> <requirements> @@ -13,7 +13,6 @@ <requirement type="package" version="1.56.0" >bioconductor-preprocesscore</requirement> <requirement type="package" version="1.64" >perl-dbd-sqlite</requirement> <requirement type="package" version="1.7.1" >r-optparse</requirement> - <requirement type="package" version="1.7.1" >r-optparse</requirement> <requirement type="package" version="2.11" >r-rmarkdown</requirement> <!-- It would be nice to use conda-forge/texlive-core rather than r-tinytex because the
--- a/mqppep_mrgfltr.py Sat Mar 26 02:26:38 2022 +0000 +++ b/mqppep_mrgfltr.py Tue Apr 05 01:47:37 2022 +0000 @@ -707,15 +707,13 @@ "dephosphorylated phosphopeptide not found in DephosphoPep_UniProtSeq_LUT", ) if ( - dephospho_pep - != PhosphoPep_UniProtSeq_LUT[(phospho_pep, DEPHOSPHOPEP)] + dephospho_pep != PhosphoPep_UniProtSeq_LUT[(phospho_pep, DEPHOSPHOPEP)] ): - raise PreconditionError( - dephospho_pep, - "dephosphorylated phosphopeptide does not match " - + "PhosphoPep_UniProtSeq_LUT[(phospho_pep,DEPHOSPHOPEP)] = " - + PhosphoPep_UniProtSeq_LUT[(phospho_pep, DEPHOSPHOPEP)], - ) + my_err_msg = "dephosphorylated phosphopeptide does not match " + my_err_msg += "PhosphoPep_UniProtSeq_LUT[(phospho_pep,DEPHOSPHOPEP)] = " + my_err_msg += PhosphoPep_UniProtSeq_LUT[(phospho_pep, DEPHOSPHOPEP)] + raise PreconditionError(dephospho_pep, my_err_msg) + result[SEQUENCE] = [dephospho_pep] result[UNIPROT_ID] = DephosphoPep_UniProtSeq_LUT[ (dephospho_pep, UNIPROT_ID) @@ -822,17 +820,13 @@ # add Sequence10 if psite < 10: # phospho_pep at N terminus seq10 = ( - str(UniProtSeq)[:psite] - + "p" - + str(UniProtSeq)[psite: psite + 11] + str(UniProtSeq)[:psite] + "p" + str(UniProtSeq)[psite: psite + 11] ) elif ( len(UniProtSeq) - psite < 11 ): # phospho_pep at C terminus seq10 = ( - str(UniProtSeq)[psite - 10: psite] - + "p" - + str(UniProtSeq)[psite:] + str(UniProtSeq)[psite - 10: psite] + "p" + str(UniProtSeq)[psite:] ) else: seq10 = str(UniProtSeq)[psite - 10: psite + 11]
--- 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/>`_);