Mercurial > repos > galaxyp > pepquery2
changeset 1:b5489f81c2fa draft default tip
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit fb66172091bb840e4cb673975fd1ebbfd8dcf3f7
| author | galaxyp |
|---|---|
| date | Wed, 18 Oct 2023 06:40:40 +0000 |
| parents | a07976bbc4d9 |
| children | |
| files | macros.xml pepquery2.xml |
| diffstat | 2 files changed, 70 insertions(+), 1 deletions(-) [+] |
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--- a/macros.xml Sun Nov 06 16:25:25 2022 +0000 +++ b/macros.xml Wed Oct 18 06:40:40 2023 +0000 @@ -1,6 +1,6 @@ <macros> <token name="@TOOL_VERSION@">2.0.2</token> - <token name="@VERSION_SUFFIX@">0</token> + <token name="@VERSION_SUFFIX@">1</token> <xml name="citations"> <citations> <citation type="doi">10.1101/gr.235028.118</citation>
--- a/pepquery2.xml Sun Nov 06 16:25:25 2022 +0000 +++ b/pepquery2.xml Wed Oct 18 06:40:40 2023 +0000 @@ -33,6 +33,9 @@ ## PepQuery command pepquery -Xmx\$[ \${GALAXY_MEMORY_MB:-8192} / 1024 ]g +#if $digestion.enzyme == '0' + -XX:ThreadStackSize=2048 +#end if #if $validation.task_type == "known" -s 2 $validation.decoy #else @@ -677,6 +680,72 @@ </output> </test> + <!-- Test-5 Non-enzyme search --> + <test expect_num_outputs="2"> + <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="single" /> + <param name="input" value="ELGSSDLTAR"/> + </conditional> + </conditional> + <conditional name="db_type"> + <param name="db_type_selector" value="history" /> + <param name="db_file" ftype="fasta" value="Uniprot.fasta"/> + </conditional> + <conditional name="ms_dataset"> + <param name="ms_dataset_type" value="history"/> + <param name="spectrum_files" ftype="mgf" value="iTRAQ_f4.mgf"/> + </conditional> + <param name="indexType" value="1"/> + </section> + <param name="parameter_set" value=""/> + <section name="modifications"> + <!-- 21: iTRAQ 4-plex of K [144.1020624208] --> + <!-- 22: iTRAQ 4-plex of peptide N-term [144.1020624208] --> + <param name="fixed_mod" value="1,21,22"/> + <!-- 2: Oxidation of M [15.99491461956] --> + <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="0"/> + </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_rank_txt"> + <assert_contents> + <has_text text="ELGSSDLTAR" /> + <has_line_matching expression="ELGSSDLTAR\tiTRAQ 4-plex of peptide N-term@0\[144.1\d+\]\t2\tiTRAQ_f4:3:2\t2\t1191.62\d+\t-3.04\d+\t-0.003\d+\t0.0\t1191.6\d+\t596.8\d+\t24.1\d+\t0\t13\t1\t995\t0.002\d+\t1\t0\tYes\t10.3\d+\t8.23\d+"/> + <has_n_columns n="22" /> + </assert_contents> + </output> + </test> + </tests> <help><![CDATA[ **PepQuery2**