| Previous changeset 45:5fa8b409599e (2018-04-30) Next changeset 47:44ca2967218c (2018-09-15) |
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Commit message:
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 57426db0c017009ac7ab0498f8580efc453398c8 |
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modified:
macros.xml peptide_shaker.xml searchgui.xml test-data/tiny_searchgui_result1.zip test-data/tiny_searchgui_result_amandaonly.zip |
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added:
test-data/peptide_shaker_modifications_result1.cpsx test-data/peptide_shaker_modifications_result1.zip test-data/tiny_searchgui_modifications_result1.zip test-data/tiny_searchgui_modifications_result_amandaonly.zip |
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removed:
test-data/peptide_shaker_result1.cpsx test-data/peptide_shaker_result1.zip |
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| diff -r 5fa8b409599e -r baeced706dbc macros.xml --- a/macros.xml Mon Apr 30 04:41:50 2018 -0400 +++ b/macros.xml Wed Jul 11 08:14:23 2018 -0400 |
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| @@ -49,7 +49,7 @@ </token> <token name="@SEARCHGUI_MAJOR_VERSION@">3</token> - <token name="@SEARCHGUI_VERSION@">3.2.24</token> + <token name="@SEARCHGUI_VERSION@">3.3.3</token> <xml name="general_options"> <section name="protein_digest_options" expanded="false" title="Protein Digestion Options"> |
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| diff -r 5fa8b409599e -r baeced706dbc peptide_shaker.xml --- a/peptide_shaker.xml Mon Apr 30 04:41:50 2018 -0400 +++ b/peptide_shaker.xml Wed Jul 11 08:14:23 2018 -0400 |
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| @@ -1,4 +1,4 @@ -<tool id="peptide_shaker" name="Peptide Shaker" version="1.16.20"> +<tool id="peptide_shaker" name="Peptide Shaker" version="1.16.26"> <description> Perform protein identification using various search engines based on results from SearchGUI </description> @@ -6,7 +6,7 @@ <import>macros.xml</import> </macros> <requirements> - <requirement type="package" version="1.16.20">peptide-shaker</requirement> + <requirement type="package" version="1.16.26">peptide-shaker</requirement> </requirements> <expand macro="stdio" /> <command> @@ -355,11 +355,11 @@ </outputs> <tests> <test> - <param name="searchgui_input" value="tiny_searchgui_result1.zip" ftype="searchgui_archive"/> + <param name="searchgui_input" value="tiny_searchgui_modifications_result1.zip" ftype="searchgui_archive"/> <param name="processing_options_selector" value="no"/> <param name="filtering_options_selector" value="no"/> <param name="outputs" value="zip,3"/> - <output name="output_zip" file="peptide_shaker_result1.zip" ftype="zip" compare="sim_size" delta="3000" /> + <output name="output_zip" file="peptide_shaker_modifications_result1.zip" ftype="zip" compare="sim_size" delta="3000" /> <output name="output_psm"> <assert_contents> <has_text text="cds.comp41779_c0_seq1" /> @@ -367,7 +367,7 @@ </output> </test> <test> - <param name="searchgui_input" value="tiny_searchgui_result1.zip" ftype="searchgui_archive"/> + <param name="searchgui_input" value="tiny_searchgui_modifications_result1.zip" ftype="searchgui_archive"/> <param name="processing_options_selector" value="no"/> <param name="filtering_options_selector" value="yes"/> <param name="min_peptide_length" value="1"/> @@ -421,11 +421,11 @@ </output> </test> <test> - <param name="searchgui_input" value="tiny_searchgui_result1.zip" ftype="searchgui_archive"/> + <param name="searchgui_input" value="tiny_searchgui_modifications_result1.zip" ftype="searchgui_archive"/> <param name="processing_options_selector" value="no"/> <param name="filtering_options_selector" value="no"/> <param name="outputs" value="3,cps"/> - <output name="output_cps" file="peptide_shaker_result1.cpsx" ftype="peptideshaker_archive" compare="sim_size" delta="3000"/> + <output name="output_cps" file="peptide_shaker_modifications_result1.cpsx" ftype="peptideshaker_archive" compare="sim_size" delta="3000"/> <output name="output_psm"> <assert_contents> <has_text text="cds.comp41779_c0_seq1" /> |
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| diff -r 5fa8b409599e -r baeced706dbc searchgui.xml --- a/searchgui.xml Mon Apr 30 04:41:50 2018 -0400 +++ b/searchgui.xml Wed Jul 11 08:14:23 2018 -0400 |
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| @@ -1092,8 +1092,6 @@ <param name="peak_lists" value="searchgui_tinyspectra1.mgf"/> <param name="input_database" value="searchgui_tinydb1.fasta" ftype="fasta"/> <param name="precursor_ion_tol" value="100"/> - <param name="fixed_modifications" value="carbamidomethyl c"/> - <param name="variable_modifications" value="oxidation of m"/> <param name="min_charge" value="1"/> <param name="max_charge" value="3"/> <param name="engines" value="X!Tandem,MSGF,MyriMatch,OMSSA,Comet"/> @@ -1106,13 +1104,42 @@ <param name="peak_lists" value="searchgui_tinyspectra1.mgf"/> <param name="input_database" value="searchgui_tinydb1.fasta" ftype="fasta"/> <param name="precursor_ion_tol" value="100"/> + <param name="min_charge" value="1"/> + <param name="max_charge" value="3"/> + <param name="engines" value="MS_Amanda"/> + <output name="output" file="tiny_searchgui_result_amandaonly.zip" ftype="searchgui_archive" compare="sim_size" delta="5000" /> + </test> + + <!-- Test that specifying non-default search engines works using modifications --> + <!-- + <test> + <param name="peak_lists" value="searchgui_tinyspectra1.mgf"/> + <param name="input_database" value="searchgui_tinydb1.fasta" ftype="fasta"/> + <param name="precursor_ion_tol" value="100"/> + <param name="fixed_modifications" value="carbamidomethyl c"/> + <param name="variable_modifications" value="oxidation of m"/> + <param name="min_charge" value="1"/> + <param name="max_charge" value="3"/> + <param name="engines" value="X!Tandem,MSGF,MyriMatch,OMSSA,Comet"/> + <param name="xtandem.xtandem_advanced" value="yes"/> + <param name="xtandem_advanced.xtandem_refine_selector" value="yes"/> + <output name="output" file="tiny_searchgui_modifications_result1.zip" ftype="searchgui_archive" compare="sim_size" delta="30000" /> + </test> + --> + <!-- Test that search works with MSAmanda - with modifications --> + <!-- + <test> + <param name="peak_lists" value="searchgui_tinyspectra1.mgf"/> + <param name="input_database" value="searchgui_tinydb1.fasta" ftype="fasta"/> + <param name="precursor_ion_tol" value="100"/> <param name="fixed_modifications" value="carbamidomethyl c"/> <param name="variable_modifications" value="oxidation of m"/> <param name="min_charge" value="1"/> <param name="max_charge" value="3"/> <param name="engines" value="MS_Amanda"/> - <output name="output" file="tiny_searchgui_result_amandaonly.zip" ftype="searchgui_archive" compare="sim_size" delta="5000" /> + <output name="output" file="tiny_searchgui_modifications_result_amandaonly.zip" ftype="searchgui_archive" compare="sim_size" delta="5000" /> </test> + --> </tests> <help> **What it does** |
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