Mercurial > repos > jjohnson > encyclopedia_walnut
changeset 6:0172dfa08216 draft
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 17dcc85ebd7507af5557a1aee4816ac437a3f27b"
| author | jjohnson |
|---|---|
| date | Fri, 21 Aug 2020 16:13:00 -0400 |
| parents | 4936de9f9024 |
| children | 7556b19daa48 |
| files | encyclopedia_walnut.xml macros.xml |
| diffstat | 2 files changed, 18 insertions(+), 11 deletions(-) [+] |
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--- a/encyclopedia_walnut.xml Wed Aug 19 08:39:11 2020 -0400 +++ b/encyclopedia_walnut.xml Fri Aug 21 16:13:00 2020 -0400 @@ -30,9 +30,9 @@ <param name="select_outputs" type="select" label="Select outputs" multiple="true"> <option value="log" selected="true">log</option> <option value="elib" selected="true">elib</option> - <option value="features" selected="true">features.txt</option> + <option value="features" selected="false">features.txt</option> <option value="pecan" selected="true">pecan.txt</option> - <option value="pecan_decoy" selected="true">pecan.decoy.txt</option> + <option value="pecan_decoy" selected="false">pecan.decoy.txt</option> </param> </inputs> <outputs> @@ -65,6 +65,7 @@ <test> <param name="scan_input" ftype="mzml" value="BCS_hela_narrow_3_1.mzML"/> <param name="fasta" ftype="fasta" value="uniprot_tiny_human.fasta"/> + <param name="select_outputs" values="log,features,pecan"/> <output name="features" ftype="tabular"> <assert_contents> <has_text text="LHYNEGLNIK"/> @@ -73,9 +74,6 @@ </test> </tests> <help><![CDATA[ - - <help><![CDATA[ - **Walnut** @ENCYCLOPEDIA_WIKI@ @@ -84,20 +82,29 @@ Walnut uses PeCAn-style scoring to extract peptide fragmentation chromatograms from MZML files, assign peaks, and calculate various peak features. These features are interpreted by Percolator to identify peptides. + **Inputs** - - A spectrum file in mzML format - A protein data base in fasta format - @MSCONVERT_HELP@ **Outputs** - A log file - - The identified features in tabular format - - The identified proteins in tabular format + - A Chromatogram Library (.elib) + - The identified features in tabular format + Feature values of scans that are used by percolator to determine matches. + - The identified Peptide Spectral Match results in tabular format + Columns: PSMId, score, q-value, posterior_error_prob, peptide, proteinIds + - The identified peptides in tabular format + Per peptide: the normalized intensity for each scan file. + Columns: Peptide, Protein, numFragments, intensity_in_file1, intensity_in_file2, ... + - The identified proteins in tabular format + Per protein: the normalized intensity for each scan file. + Columns: Protein, NumPeptides, PeptideSequences, intensity_in_file1, intensity_in_file2, ... + ]]></help> <expand macro="citations" />
--- a/macros.xml Wed Aug 19 08:39:11 2020 -0400 +++ b/macros.xml Fri Aug 21 16:13:00 2020 -0400 @@ -128,7 +128,7 @@ <token name="@LINK_LIB_INPUT@"><![CDATA[ #if $library #set $l_name = $ln_name($library) - cp '$library' $l_name && + cp '$library' '$l_name' && #else #set $l_name = None #end if @@ -494,7 +494,7 @@ </token> <token name="@MSCONVERT_HELP@"><![CDATA[ - The MSConvert command can be used to deconvolute DIA raw files. You need to use these options + The MSConvert command can be used to convert and deconvolute DIA raw files to mzML format. You need to use these options: ::