Mercurial > repos > galaxyp > pepquery2
changeset 4:29e6417b913c draft
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit b7f27d4872020b09656a2f53d667217b762fa202
| author | galaxyp |
|---|---|
| date | Mon, 31 Oct 2022 13:36:14 +0000 |
| parents | d8962e547c9c |
| children | 2045f3b68773 |
| files | pepquery2.xml |
| diffstat | 1 files changed, 22 insertions(+), 11 deletions(-) [+] |
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--- a/pepquery2.xml Tue Oct 25 23:35:01 2022 +0000 +++ b/pepquery2.xml Mon Oct 31 13:36:14 2022 +0000 @@ -374,15 +374,15 @@ </section> <param name="outputs_selected" type="select" multiple="true" optional="false" label="Select outputs"> - <option value="psm.txt" selected="true">psm.txt</option> + <option value="psm.txt">psm.txt</option> <option value="psm_rank.txt" selected="true">psm_rank.txt</option> - <option value="psm_rank.mgf" selected="true">psm_rank.mgf</option> - <option value="psm_annotation.txt" selected="true">psm_annotation.txt</option> - <option value="psm_type.txt" selected="false">psm_type.txt</option> - <option value="detail.txt" selected="true">detail.txt</option> - <option value="ptm.txt" selected="true">ptm.txt</option> - <option value="ptm_detail.txt" selected="true">ptm_detail.txt</option> - <option value="ms_index" selected="true">MS/MS Index</option> + <option value="psm_rank.mgf">psm_rank.mgf</option> + <option value="psm_annotation.txt">psm_annotation.txt</option> + <option value="psm_type.txt">psm_type.txt</option> + <option value="detail.txt">detail.txt</option> + <option value="ptm.txt">ptm.txt</option> + <option value="ptm_detail.txt">ptm_detail.txt</option> + <option value="ms_index">MS/MS Index</option> </param> <param name="fast" argument="-fast" type="boolean" truevalue="-fast" falsevalue="" checked="false" label="Use fast mode for searching" help="In fast mode, only one better match from reference peptide-based competitive filtering steps will be returned. A peptide identified or not is not affected by this setting. For most applications, fast mode will speed up the analysis." /> </inputs> @@ -390,6 +390,7 @@ <data name="log_txt" format="txt" from_work_dir="log.txt" label="${tool.name} on ${on_string}: log.txt"> </data> <data name="parameter_txt" format="txt" from_work_dir="pepquery_output/parameter.txt" label="${tool.name} on ${on_string}: parameter.txt"> + <filter>'parameter.txt' in outputs_selected and req_inputs['ms_dataset']['ms_dataset_type'] == 'history'</filter> </data> <data name="ms_index" format="txt" label="${tool.name} on ${on_string}: index summary.txt" from_work_dir="index_dir/summary.txt"> <filter>'ms_index' in outputs_selected and req_inputs['ms_dataset']['ms_dataset_type'] == 'history'</filter> @@ -757,6 +758,17 @@ The **PepQuery2 Show Sets** tool *PepQuery Modifications* lists all available modifications. **Outputs** + - Log.txt: + + - Logging output from PepQuery2 + - When searching for *novel* peptides ignored peptide have a log message similar to: + + - Ignore peptide (reason: exist in reference database): *PEPTIDE* + + - When searching for *known* proteins, ignored protein have a log message similar to: + + - Target protein is not present in database *DATABASE_NAME*: *PROTEIN_NAME*, ignored! + - Parameters: - parameters used in the search @@ -767,7 +779,7 @@ - PSM Rank - tabular with columns: - - peptide modification n spectrum_title charge exp_mass ppm pep_mass mz score n_db total_db n_random total_random pvalue rank *n_ptm* + - peptide mo/dification n spectrum_title charge exp_mass ppm pep_mass mz score n_db total_db n_random total_random pvalue rank n_ptm - An MGF with the best matching spectrums @@ -789,8 +801,7 @@ - An Indexed MS/MS dataset *when MS/MS data is MGF, mzML, or mzXML history datasets* - The *n_ptm* field is added when using unrestricted modification searching (-um). - + .. _PepQuery: http://pepquery.org/document.html ]]></help>