Mercurial > repos > galaxyp > psm_validation
changeset 0:ddcab0f11473 draft
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/psm_validation commit 896365c9d6b9fcdcbb9c36e0c81db78c8a4e8dab"
| author | galaxyp |
|---|---|
| date | Thu, 15 Oct 2020 07:45:17 +0000 |
| parents | |
| children | b71c651e7950 |
| files | application.py macros.xml psm_validation.xml test-data/test-peptides.txt test-data/test.db |
| diffstat | 5 files changed, 139 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/application.py Thu Oct 15 07:45:17 2020 +0000 @@ -0,0 +1,66 @@ +import argparse + +import psmfragmentation.psmfragmentation as pf + + +if __name__ == "__main__": + parser = argparse.ArgumentParser(description="Run PSM Validator") + parser.add_argument( + "-d", + "--dbname", + help="Path to mzsqlite db", + ) + parser.add_argument( + "-p", + "--peptides", + help="Path to peptide sequence file", + ) + parser.add_argument( + "-n", + "--neutral", + action="store_true", + default=False, + help="Calculate netutral loss", + ) + parser.add_argument( + "-i", + "--internal", + action="store_true", + default=False, + help="Calculate internals", + ) + parser.add_argument( + "-e", "--epsilon", type=float + ) + parser.add_argument( + "-b", + "--b_run", + type=int, + default=2, + help="Number of consecutive b-ions" + ) + parser.add_argument( + "-y", + "--y_run", + type=int, + default=2, + help="Number of consecutive y-ions" + ) + + parser.add_argument( + "-t", + "--test", + action="store_true", + default=False + ) + + args = parser.parse_args() + + itypes = ['b', 'y'] + if args.neutral: + itypes.extend(['b-H2O', 'b-NH3', 'y-H2O', 'y-NH3']) + + if args.internal: + itypes.append('M') + + pf.score_psms(args.dbname, args.peptides, ion_types=itypes, epsilon=args.epsilon, maxcharge=1, b_run=args.b_run, y_run=args.y_run, a_test=args.test)
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros.xml Thu Oct 15 07:45:17 2020 +0000 @@ -0,0 +1,15 @@ +<macros> + <token name="@VERSION@">1.0.3</token> + <xml name="help-text"> + <help> + <![CDATA[ + PSMValidator filters and validates PSMs against a supplied list of peptide sequences. + ]]> + </help> + </xml> + <xml name="pkg_requirement"> + <requirements> + <requirement type="package" version="@VERSION@">psm_fragments</requirement> + </requirements> + </xml> +</macros> \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/psm_validation.xml Thu Oct 15 07:45:17 2020 +0000 @@ -0,0 +1,56 @@ + <tool id="psmvalidator" name="PSM-Fragment Validator" version="@VERSION@"> + <macros> + <import>macros.xml</import> + </macros> + <description>Validate PSMs against Ion Fragmentation</description> + <expand macro="pkg_requirement" /> + <command detect_errors="exit_code"> + <![CDATA[ + python '$__tool_directory__/application.py' + -d '$mz_db_name' + -p '$peptide_sequences' + #if $neutral_loss_ions: + -n + #end if + #if $internal_ions: + -i + #end if + -b $b_ion_run + -y $y_ion_run + -e $epsilon + #if $b_ion_run < 0: + --test + #end if + ]]> + </command> + <inputs> + <param name="mz_db_name" type="data" format="mz.sqlite" label="MZSQLite DB" /> + <param name="peptide_sequences" type="data" format="tabular" label="Peptide Sequence List" /> + <param name="b_ion_run" type="integer" value="2" label="Consecutive B-Ions" /> + <param name="y_ion_run" type="integer" value="2" label="Consecutive Y-Ions" /> + <param name="neutral_loss_ions" type="boolean" checked="True" label="Use Neutral Loss" /> + <param name="internal_ions" type="boolean" checked="True" label="Use Internals" /> + <param name="epsilon" type="float" value="0.5" label="Epsilon" /> + </inputs> + <outputs> + <data name="html_output" format="html" from_work_dir="index.html" label="PSM Ion Fragementation Report" /> + <data name="text_output" format="tabular" from_work_dir="results.tab" label="Tabular Results" /> + </outputs> + <tests> + <test> + <param name="mz_db_name" value="test.db" /> + <param name="peptide_sequences" value="test-peptides.txt" /> + <param name="b_ion_run" value="-99" /> + <param name="y_ion_run" value="-99" /> + <param name="neutral_loss_ions" value="True" /> + <param name="internal_ions" value="True" /> + <param name="epsilon" value="0.5" /> + <output name="html_output"> + <assert_contents> + <has_text text="success" /> + </assert_contents> + </output> + </test> + </tests> + <expand macro="help-text" /> +</tool>