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comparison pepquery2.xml @ 1:b5489f81c2fa draft

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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 c32806a80862
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0:a07976bbc4d9 1:b5489f81c2fa
31 #end if 31 #end if
32 #end if 32 #end if
33 ## PepQuery command 33 ## PepQuery command
34 pepquery 34 pepquery
35 -Xmx\$[ \${GALAXY_MEMORY_MB:-8192} / 1024 ]g 35 -Xmx\$[ \${GALAXY_MEMORY_MB:-8192} / 1024 ]g
36 #if $digestion.enzyme == '0'
37 -XX:ThreadStackSize=2048
38 #end if
36 #if $validation.task_type == "known" 39 #if $validation.task_type == "known"
37 -s 2 $validation.decoy 40 -s 2 $validation.decoy
38 #else 41 #else
39 -s 1 42 -s 1
40 #end if 43 #end if
675 <has_n_columns n="22" /> 678 <has_n_columns n="22" />
676 </assert_contents> 679 </assert_contents>
677 </output> 680 </output>
678 </test> 681 </test>
679 682
683 <!-- Test-5 Non-enzyme search -->
684 <test expect_num_outputs="2">
685 <conditional name="validation">
686 <param name="task_type" value="novel"/>
687 </conditional>
688 <section name="req_inputs">
689 <conditional name="input_type">
690 <param name="input_type_selector" value="peptide"/>
691 <conditional name="multiple">
692 <param name="peptide_input_selector" value="single" />
693 <param name="input" value="ELGSSDLTAR"/>
694 </conditional>
695 </conditional>
696 <conditional name="db_type">
697 <param name="db_type_selector" value="history" />
698 <param name="db_file" ftype="fasta" value="Uniprot.fasta"/>
699 </conditional>
700 <conditional name="ms_dataset">
701 <param name="ms_dataset_type" value="history"/>
702 <param name="spectrum_files" ftype="mgf" value="iTRAQ_f4.mgf"/>
703 </conditional>
704 <param name="indexType" value="1"/>
705 </section>
706 <param name="parameter_set" value=""/>
707 <section name="modifications">
708 <!-- 21: iTRAQ 4-plex of K [144.1020624208] -->
709 <!-- 22: iTRAQ 4-plex of peptide N-term [144.1020624208] -->
710 <param name="fixed_mod" value="1,21,22"/>
711 <!-- 2: Oxidation of M [15.99491461956] -->
712 <param name="var_mod" value="2"/>
713 <param name="max_mods" value="3"/>
714 <param name="unmodified" value="True"/>
715 <param name="aa" value="False"/>
716 </section>
717 <section name="digestion">
718 <param name="enzyme" value="0"/>
719 </section>
720 <section name="ms_params">
721 <section name="tolerance_params">
722 <param name="precursor_tolerance" value="10"/>
723 <param name="precursor_unit" value="ppm"/>
724 <param name="tolerance" value="0.6"/>
725 </section>
726 <section name="search">
727 <param name="frag_method" value="1"/>
728 <param name="scoring_method" value="1"/>
729 <param name="extra_score_validation" value="False"/>
730 <param name="min_charge" value="2"/>
731 <param name="max_charge" value="3"/>
732 <param name="min_peaks" value="10"/>
733 <param name="isotope_error" value="0"/>
734 <param name="min_score" value="12"/>
735 <param name="min_length" value="7"/>
736 <param name="max_length" value="45"/>
737 <param name="num_random_peptides" value="1000"/>
738 </section>
739 </section>
740 <output name="psm_rank_txt">
741 <assert_contents>
742 <has_text text="ELGSSDLTAR" />
743 <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+"/>
744 <has_n_columns n="22" />
745 </assert_contents>
746 </output>
747 </test>
748
680 </tests> 749 </tests>
681 <help><![CDATA[ 750 <help><![CDATA[
682 **PepQuery2** 751 **PepQuery2**
683 752
684 PepQuery_ is a universal targeted peptide search engine for identifying or validating known and novel peptides of interest in any local or publicly available mass spectrometry-based proteomics datasets. 753 PepQuery_ is a universal targeted peptide search engine for identifying or validating known and novel peptides of interest in any local or publicly available mass spectrometry-based proteomics datasets.