Mercurial > repos > galaxyp > pepquery2
changeset 3:d8962e547c9c draft
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit ea7f4bae8a2ae72470b895476faf9a368496aa8d
| author | galaxyp |
|---|---|
| date | Tue, 25 Oct 2022 23:35:01 +0000 |
| parents | 3b2874c58bcd |
| children | 29e6417b913c |
| files | pepquery2.xml test-data/pep.txt |
| diffstat | 2 files changed, 116 insertions(+), 5 deletions(-) [+] |
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--- a/pepquery2.xml Tue Oct 25 16:06:20 2022 +0000 +++ b/pepquery2.xml Tue Oct 25 23:35:01 2022 +0000 @@ -178,7 +178,7 @@ <option value="single">Single peptide entered as text</option> </param> <when value="multiple"> - <param name="input" argument="-i" type="data" format="txt" label="Peptide Sequences (.txt)"> + <param name="input" argument="-i" type="data" format="tabular" label="Peptide Sequences (.txt)"> <help>Peptide sequence file containing peptides which you want to search (no column headers). First column is am peptide sequence. Optional second column is spectrum title. </help> @@ -186,7 +186,7 @@ </when> <when value="single"> <param name="input" argument="-i" type="text" label="Peptide Sequence" help="Peptide sequence(s) which you want to search"> - <validator type="regex" message="Must be AA letters">^[AC-IK-NP-TV-Yac-ik-np-tv-y]+(,[AC-IK-NP-TV-Yac-ik-np-tv-y]+)*$</validator> + <validator type="regex" message="Must be AA letters, multiple peptides separated by commas">^[AC-IK-NP-TV-Yac-ik-np-tv-y]+(,[AC-IK-NP-TV-Yac-ik-np-tv-y]+)*$</validator> </param> </when> </conditional> @@ -387,7 +387,7 @@ <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> <outputs> - <data name="log" format="txt" from_work_dir="log.txt" label="${tool.name} on ${on_string}: log.txt"> + <data name="log_txt" format="txt" from_work_dir="log.txt" label="${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"> </data> @@ -462,7 +462,7 @@ <param name="input_type_selector" value="peptide"/> <conditional name="multiple"> <param name="peptide_input_selector" value="single" /> - <param name="input" value="LVVVGADGVGK"/> + <param name="input" value="LVVVGADGVGK,AHSSMVGVNLPQK"/> </conditional> </conditional> <conditional name="db_type"> @@ -510,12 +510,87 @@ <output name="psm_txt"> <assert_contents> <has_text text="LVVVGADGVGK" /> + <not_has_text text="AHSSMVGVNLPQK" /> <has_text text="02CPTAC_LUAD_W_BI_20180518_KR_f15:25149:2" /> </assert_contents> </output> + <output name="log_txt"> + <assert_contents> + <has_text text="Ignore peptide (reason: exist in reference database): AHSSMVGVNLPQK" /> + </assert_contents> + </output> </test> - <!-- Test-2 MGF peptide Uniprot.fasta --> + <!-- Test-2 PepQueryDB peptide gencode:human pep.txt --> + <test> + <conditional name="validation"> + <param name="task_type" value="novel"/> + </conditional> + <section name="req_inputs"> + <conditional name="input_type"> + <param name="input_type_selector" value="peptide"/> + <conditional name="multiple"> + <param name="peptide_input_selector" value="multiple" /> + <param name="input" ftype="tabular" value="pep.txt"/> + </conditional> + </conditional> + <conditional name="db_type"> + <param name="db_type_selector" value="download" /> + <param name="db_id" value="gencode:human"/> + </conditional> + <conditional name="ms_dataset"> + <param name="ms_dataset_type" value="PepQueryDB"/> + <param name="dataset" value="CPTAC_LUAD_Discovery_Study_Proteome_PDC000153" /> + </conditional> + <param name="indexType" value="1"/> + </section> + <param name="parameter_set" value=""/> + <section name="modifications"> + <param name="fixed_mod" value="1"/> + <param name="var_mod" value="2"/> + <param name="max_mods" value="3"/> + <param name="unmodified" value="True"/> + <param name="aa" value="False"/> + </section> + <section name="digestion"> + <param name="enzyme" value="1"/> + <param name="max_missed_cleavages" value="2"/> + </section> + <section name="ms_params"> + <section name="tolerance_params"> + <param name="precursor_tolerance" value="10"/> + <param name="precursor_unit" value="ppm"/> + <param name="tolerance" value="0.6"/> + </section> + <section name="search"> + <param name="frag_method" value="1"/> + <param name="scoring_method" value="1"/> + <param name="extra_score_validation" value="False"/> + <param name="min_charge" value="2"/> + <param name="max_charge" value="3"/> + <param name="min_peaks" value="10"/> + <param name="isotope_error" value="0"/> + <param name="min_score" value="12"/> + <param name="min_length" value="7"/> + <param name="max_length" value="45"/> + <param name="num_random_peptides" value="1000"/> + </section> + </section> + <output name="psm_txt"> + <assert_contents> + <has_text text="LVVVGADGVGK" /> + <not_has_text text="AHSSMVGVNLPQK" /> + <has_text text="02CPTAC_LUAD_W_BI_20180518_KR_f15:25149:2" /> + </assert_contents> + </output> + <output name="log_txt"> + <assert_contents> + <has_text text="Ignore peptide (reason: exist in reference database): AHSSMVGVNLPQK" /> + </assert_contents> + </output> + </test> + + <!-- Test-3 MGF peptide Uniprot.fasta --> <test> <conditional name="validation"> <param name="task_type" value="novel"/> @@ -586,6 +661,40 @@ </output> </test> + <!-- Test-4 PepQueryDB known peptide gencode:human pep.txt --> + <test> + <conditional name="validation"> + <param name="task_type" value="known"/> + </conditional> + <section name="req_inputs"> + <conditional name="input_type"> + <param name="input_type_selector" value="peptide"/> + <conditional name="multiple"> + <param name="peptide_input_selector" value="single" /> + <param name="input" value="AHSSMVGVNLPQK"/> + </conditional> + </conditional> + <conditional name="db_type"> + <param name="db_type_selector" value="download" /> + <param name="db_id" value="gencode:human"/> + </conditional> + <conditional name="ms_dataset"> + <param name="ms_dataset_type" value="PepQueryDB"/> + <param name="dataset" value="CPTAC_LUAD_Discovery_Study_Proteome_PDC000153" /> + </conditional> + <param name="indexType" value="1"/> + </section> + <section name="modifications"> + <param name="unmodified" value="True"/> + </section> + <output name="psm_txt"> + <assert_contents> + <has_text text="AHSSMVGVNLPQK" /> + <has_text text="6CPTAC_LUAD_W_BI_20180718_KL_f12:20286:3" /> + </assert_contents> + </output> + </test> + </tests> <help><![CDATA[ **PepQuery2**