pepquery2: pepquery2.xml annotate

annotate pepquery2.xml @ 0:3c45645197f6 draft

planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d

author	galaxyp
date	Wed, 28 Sep 2022 13:56:01 +0000
parents
children	6b5ce9e2b0d0

rev	line source
0 3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	1 <tool id="pepquery2" name="PepQuery2" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	2 <description>Peptide-centric search engine for novel peptide identification and validation.</description>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	3 <macros>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	4 <import>macros.xml</import>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	5 </macros>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	6 <requirements>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	7 <requirement type="package" version="@TOOL_VERSION@">pepquery</requirement>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	8 </requirements>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	9 <stdio>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	10 <exit_code range="1:" level="fatal" description="Failed" />
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	11 <regex match="Exception"
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	12 source="stderr"
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	13 level="fatal"
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	14 description="java Exception" />
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	15 </stdio>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	16 <command><![CDATA[
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	17 @CMD_IMPORTS@
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	18 #if $req_inputs.db_type.db_type_selector == 'history'
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	19 #set $db_file = $re.sub('\s','_',$re.sub('[.][^.]*$','',$req_inputs.db_type.db_file.display_name.split('/')[-1])) + ".fa"
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	20 ln -s '$req_inputs.db_type.db_file' '$db_file' &&
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	21 #end if
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	22 #if $req_inputs.ms_dataset.ms_dataset_type == 'history'
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	23 @INDEX_SPECTRUM_FILES@
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	24 $index_spectrum_files($ms_index.files_path, $req_inputs.ms_dataset.spectrum_files) &&
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	25 #elif $req_inputs.ms_dataset.ms_dataset_type == 'indexed'
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	26 #if $os.path.exists($os.path.join($req_inputs.ms_dataset.index.extra_files_path, 'summary.txt'))
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	27 #set $index_dir = 'index_dir'
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	28 ln -s '$req_inputs.ms_dataset.index.extra_files_path' index_dir &&
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	29 #else
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	30 #raise ValueError
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	31 #end if
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	32 #end if
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	33 ## PepQuery command
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	34 pepquery
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	35 #if $validation.task_type == "known"
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	36 -s 2 $validation.decoy
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	37 #else
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	38 -s 1
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	39 #end if
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	40 #if $req_inputs.ms_dataset.ms_dataset_type in ['history', 'indexed']
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	41 -ms '$index_dir'
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	42 #elif $req_inputs.ms_dataset.ms_dataset_type in ['PepQueryDB', 'public']
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	43 -b '$req_inputs.ms_dataset.dataset'
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	44 #end if
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	45
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	46 #if $req_inputs.db_type.db_type_selector == 'history'
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	47 -db '$db_file'
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	48 #else
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	49 -db '$req_inputs.db_type.db_id'
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	50 #end if
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	51 #if $req_inputs.input_type.input_type_selector == 'peptide'
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	52 -t '$req_inputs.input_type.input_type_selector'
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	53 -i '$req_inputs.input_type.multiple.input'
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	54 #else
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	55 -t '$req_inputs.input_type.input_type_selector'
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	56 #if int(str($req_inputs.input_type.input_type_selector)) == 1
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	57 -i '$req_inputs.input_type.multiple.input'
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	58 #else
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	59 -i '$req_inputs.input_type.input'
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	60 #if int(str($req_inputs.input_type.input_type_selector)) == 2
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	61 #if $req_inputs.input_type.frame == 'None'
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	62 -f '0'
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	63 #else
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	64 -f '$req_inputs.input_type.frame'
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	65 #end if
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	66 #else
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	67 -anno '$req_inputs.input_type.anno'
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	68 #end if
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	69 #end if
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	70 #end if
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	71 -indexType $req_inputs.indexType
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	72
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	73 #if $modifications.fixed_mod
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	74 -fixMod '$modifications.fixed_mod'
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	75 #end if
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	76 #if $modifications.var_mod
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	77 -varMod '$modifications.var_mod'
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	78 #end if
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	79 #if $digestion.enzyme
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	80 -e '$digestion.enzyme'
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	81 #end if
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	82 #if $digestion.max_missed_cleavages
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	83 -c '$digestion.max_missed_cleavages'
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	84 #end if
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	85
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	86 #if $modifications.max_mods
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	87 -maxVar '$modifications.max_mods'
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	88 #end if
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	89 $modifications.unmodified
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	90 $modifications.aa
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	91 #if $ms_params.tolerance_params.precursor_tolerance
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	92 -tol '$ms_params.tolerance_params.precursor_tolerance'
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	93 #end if
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	94
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	95 #if $ms_params.tolerance_params.precursor_unit
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	96 -tolu '$ms_params.tolerance_params.precursor_unit'
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	97 #end if
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	98 #if $ms_params.tolerance_params.tolerance
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	99 -itol '$ms_params.tolerance_params.tolerance'
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	100 #end if
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	101 #if $ms_params.search.frag_method
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	102 -fragmentMethod '$ms_params.search.frag_method'
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	103 #end if
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	104 #if $ms_params.search.scoring_method
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	105 -m '$ms_params.search.scoring_method'
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	106 #end if
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	107 $ms_params.search.extra_score_validation
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	108 #if $ms_params.search.max_charge
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	109 -maxCharge '$ms_params.search.max_charge'
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	110 #end if
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	111 #if $ms_params.search.min_charge
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	112 -minCharge '$ms_params.search.min_charge'
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	113 #end if
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	114 #if $ms_params.search.min_peaks
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	115 -minPeaks '$ms_params.search.min_peaks'
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	116 #end if
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	117 #if $ms_params.search.isotope_error
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	118 -ti '$ms_params.search.isotope_error'
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	119 #end if
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	120 #if $ms_params.search.min_score
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	121 -minScore '$ms_params.search.min_score'
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	122 #end if
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	123 #if $ms_params.search.min_length
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	124 -minLength '$ms_params.search.min_length'
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	125 #end if
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	126 #if $ms_params.search.max_length
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	127 -maxLength '$ms_params.search.max_length'
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	128 #end if
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	129 #if $ms_params.search.num_random_peptides
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	130 -n '$ms_params.search.num_random_peptides'
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	131 #end if
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	132 #if 'psm_annotation.txt' in $outputs_selected
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	133 -plot
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	134 #end if
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	135 $fast
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	136 -o pepquery_output
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	137 \| sed 's/No valid peptide/Error: No valid peptide/' \| tee >(cat 1>&2)
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	138 ]]>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	139 </command>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	140 <inputs>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	141 <conditional name="validation">
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	142 <param name="task_type" argument="-s" type="select" label="Validation Task Type">
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	143 <option value="novel" selected="true">novel peptide/protein validation</option>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	144 <option value="known">known peptide/protein validation</option>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	145 </param>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	146 <when value="novel"/>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	147 <when value="known">
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	148 <param name="decoy" argument="-decoy" type="boolean" truevalue="-decoy" falsevalue="" checked="false" label="Identity the decoy version of the selected target protein"/>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	149 </when>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	150 </conditional>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	151 <section name="req_inputs" title="Input Data" expanded="true">
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	152 <conditional name="input_type">
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	153 <param name="input_type_selector" argument="-t" type="select" label="Input Type" help="" >
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	154 <option value="peptide">peptide</option>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	155 <option value="1">protein</option>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	156 <option value="2">DNA (translate to protein sequences)</option>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	157 <!-- these are not working with pepquery version 1.6
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	158 <option value="3">VCF (translate to protein sequences)</option>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	159 <option value="4">BED (translate to protein sequences)</option>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	160 <option value="5">GTF (translate to protein sequences)</option>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	161 -->
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	162 </param>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	163 <when value="peptide">
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	164 <conditional name="multiple">
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	165 <param name="peptide_input_selector" type="select" label="Peptides?">
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	166 <option value="multiple">Peptide list from your history</option>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	167 <option value="single">Single peptide entered as text</option>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	168 </param>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	169 <when value="multiple">
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	170 <param name="input" argument="-i" type="data" format="txt" label="Peptide Sequences (.txt)" help="Peptide sequence file containing peptides which you want to search (no column header, 1 peptide per line)." />
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	171 </when>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	172 <when value="single">
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	173 <param name="input" argument="-i" type="text" label="Peptide Sequence" help="Peptide sequence(s) which you want to search">
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	174 <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>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	175 </param>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	176 </when>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	177 </conditional>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	178 </when>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	179 <when value="1">
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	180 <conditional name="multiple">
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	181 <param name="protein_input_selector" type="select" label="Proteins?">
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	182 <option value="multiple">Protein fasta from your history</option>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	183 <option value="single">Single protein entered as text</option>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	184 </param>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	185 <when value="multiple">
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	186 <param name="input" argument="-i" type="data" format="fasta" label="Protein Sequences (.txt)" help="Protein fasta file containing proteins which you want to search." />
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	187 </when>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	188 <when value="single">
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	189 <param name="input" argument="-i" type="text" label="Protein Sequence" help="Protein sequence which you want to search">
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	190 <validator type="regex" message="Must be AA letters">^[AC-IK-NP-TV-Yac-ik-np-tv-y]+$</validator>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	191 </param>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	192 </when>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	193 </conditional>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	194 </when>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	195 <when value="2">
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	196 <param name="input" argument="-i" type="text" label="DNA Sequence (at least 60 bp)" help="DNA sequence which you want to search">
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	197 <validator type="regex" message="Must be at least 60bp">^[acgtuAGCTU]{60}[acgtuAGCTU]*$</validator>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	198 </param>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	199 <param name="frame" argument="-f" type="select" label="Frame(s) for DNA translation" multiple="true" help="The frame(s) to translate DNA sequence to protein. Selecting nothing (default) keeps the longest frame">
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	200 <option value="1">1</option>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	201 <option value="2">2</option>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	202 <option value="3">3</option>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	203 <option value="4">4</option>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	204 <option value="5">5</option>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	205 <option value="6">6</option>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	206 </param>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	207 </when>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	208 <!-- these are not working with pepquery version 1.6
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	209 <when value="3">
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	210 <param name="input" type="data" format="vcf" label="VCF File" argument="-i" help="" />
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	211 <param name="anno" type="data_collection" label="Annotation Files" argument="-anno" help="Annotation files for the VCF file. Please follow preparation instructions here: http://bioconductor.org/packages/devel/bioc/html/PGA.html" />
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	212 </when>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	213 <when value="4">
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	214 <param name="input" type="data" format="bed" label="BED File" argument="-i" help="" />
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	215 <param name="anno" type="data_collection" label="Annotation Files" argument="-anno" help="Annotation files for the BED file. Please follow preparation instructions here: http://bioconductor.org/packages/devel/bioc/html/PGA.html" />
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	216 </when>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	217 <when value="5">
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	218 <param name="input" type="data" format="gtf" label="GTF File" argument="-i" help="" />
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	219 <param name="anno" type="data_collection" label="Annotation Files" argument="-anno" help="Annotation files for the GTF file. Please follow preparation instructions here: http://bioconductor.org/packages/devel/bioc/html/PGA.html" />
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	220 </when>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	221 -->
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	222 </conditional>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	223 <conditional name="db_type">
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	224 <param name="db_type_selector" type="select" label="Protein Reference Database from" help="" >
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	225 <option value="history">history</option>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	226 <option value="download">download</option>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	227 </param>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	228 <when value="history">
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	229 <param name="db_file" argument="-db" type="data" format="fasta" label="Protein Reference Database File" help="an input sequence that matches a reference will be ignored." />
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	230 </when>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	231 <when value="download">
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	232 <param name="db_id" type="text" value="" label="Public protein sequence database">
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	233 <help>Currently supported dowloads: gencode:human, swissprot:human, refseq:human</help>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	234 <option value="gencode:human">gencode:human</option>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	235 <option value="swissprot:human">swissprot:human</option>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	236 <option value="refseq:human">refseq:human</option>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	237 <validator type="regex" message="">^(swissprot\|refseq\|gencode):(human)$</validator>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	238 </param>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	239 </when>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	240 </conditional>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	241 <conditional name="ms_dataset">
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	242 <param name="ms_dataset_type" type="select" label="MS/MS dataset to search" help="" >
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	243 <option value="history"> Spectrum Datasets from history</option>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	244 <option value="indexed">Indexed MS/MS spectrums</option>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	245 <option value="PepQueryDB">PepQueryDB</option>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	246 <option value="public">public proteomics data repositories</option>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	247 </param>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	248 <when value="history">
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	249 <param name="spectrum_files" argument="-ms" type="data" format="mgf,mzml,mzxml,thermo.raw" label="Spectrum File" help="Spectrum file used for identification, formats: MGF,mzML,mzXML,Thermo RAW" />
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	250 </when>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	251 <when value="indexed">
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	252 <param name="index" argument="-ms" type="data" format="txt" label="PepQuery Index" help="" />
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	253 </when>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	254 <when value="PepQueryDB">
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	255 <param name="dataset" argument="-b" type="text" value="" label="PepQueryDB dataset">
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	256 <option value="all">all</option>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	257 <option value="w">w:global proteome</option>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	258 <option value="p">p:phosphorylation</option>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	259 <option value="a">a:acetylation</option>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	260 <option value="u">u:ubiquitination</option>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	261 <option value="g">g:glycosylation</option>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	262 <option value="Academia_Sinica_LUAD100_Phosphoproteome_PDC000220">Academia_Sinica_LUAD100_Phosphoproteome_PDC000220</option>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	263 <option value="Academia_Sinica_LUAD100_Proteome_PDC000219">Academia_Sinica_LUAD100_Proteome_PDC000219</option>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	264 <option value="CCLE_proteome_MSV000085836">CCLE_proteome_MSV000085836</option>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	265 <option value="CPTAC">CPTAC</option>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	266 <option value="CPTAC_CCRCC_Discovery_Study_Phosphoproteme_PDC000128">CPTAC_CCRCC_Discovery_Study_Phosphoproteme_PDC000128</option>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	267 <option value="CPTAC_CCRCC_Discovery_Study_Proteome_PDC000127">CPTAC_CCRCC_Discovery_Study_Proteome_PDC000127</option>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	268 <option value="CPTAC_GBM_Discovery_Study_Acetylome_PDC000245">CPTAC_GBM_Discovery_Study_Acetylome_PDC000245</option>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	269 <option value="CPTAC_GBM_Discovery_Study_Phosphoproteome_PDC000205">CPTAC_GBM_Discovery_Study_Phosphoproteome_PDC000205</option>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	270 <option value="CPTAC_GBM_Discovery_Study_Proteome_PDC000204">CPTAC_GBM_Discovery_Study_Proteome_PDC000204</option>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	271 <option value="CPTAC_HNSCC_Discovery_Study_Phosphoproteome_PDC000222">CPTAC_HNSCC_Discovery_Study_Phosphoproteome_PDC000222</option>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	272 <option value="CPTAC_HNSCC_Discovery_Study_Proteome_PDC000221">CPTAC_HNSCC_Discovery_Study_Proteome_PDC000221</option>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	273 <option value="CPTAC_LSCC_Discovery_Study_Acetylome_PDC000233">CPTAC_LSCC_Discovery_Study_Acetylome_PDC000233</option>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	274 <option value="CPTAC_LSCC_Discovery_Study_Phosphoproteome_PDC000232">CPTAC_LSCC_Discovery_Study_Phosphoproteome_PDC000232</option>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	275 <option value="CPTAC_LSCC_Discovery_Study_Proteome_PDC000234">CPTAC_LSCC_Discovery_Study_Proteome_PDC000234</option>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	276 <option value="CPTAC_LSCC_Discovery_Study_Ubiquitylome_PDC000237">CPTAC_LSCC_Discovery_Study_Ubiquitylome_PDC000237</option>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	277 <option value="CPTAC_LUAD_Discovery_Study_Acetylome_PDC000224">CPTAC_LUAD_Discovery_Study_Acetylome_PDC000224</option>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	278 <option value="CPTAC_LUAD_Discovery_Study_Phosphoproteome_PDC000149">CPTAC_LUAD_Discovery_Study_Phosphoproteome_PDC000149</option>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	279 <option value="CPTAC_LUAD_Discovery_Study_Proteome_PDC000153">CPTAC_LUAD_Discovery_Study_Proteome_PDC000153</option>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	280 <option value="CPTAC_PDA_Discovery_Study_Phosphoproteome_PDC000271">CPTAC_PDA_Discovery_Study_Phosphoproteome_PDC000271</option>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	281 <option value="CPTAC_PDA_Discovery_Study_Proteome_PDC000270">CPTAC_PDA_Discovery_Study_Proteome_PDC000270</option>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	282 <option value="CPTAC_Pediatric_Brain_Cancer_Pilot_Study_Phosphoproteome_PDC000176">CPTAC_Pediatric_Brain_Cancer_Pilot_Study_Phosphoproteome_PDC000176</option>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	283 <option value="CPTAC_Pediatric_Brain_Cancer_Pilot_Study_Proteome_PDC000180">CPTAC_Pediatric_Brain_Cancer_Pilot_Study_Proteome_PDC000180</option>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	284 <option value="CPTAC_Prospective_Breast_BI_Acetylome_PDC000239">CPTAC_Prospective_Breast_BI_Acetylome_PDC000239</option>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	285 <option value="CPTAC_Prospective_Breast_BI_Phosphoproteome_PDC000121">CPTAC_Prospective_Breast_BI_Phosphoproteome_PDC000121</option>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	286 <option value="CPTAC_Prospective_Breast_BI_Proteome_PDC000120">CPTAC_Prospective_Breast_BI_Proteome_PDC000120</option>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	287 <option value="CPTAC_Prospective_Colon_PNNL_Phosphoproteome_PDC000117">CPTAC_Prospective_Colon_PNNL_Phosphoproteome_PDC000117</option>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	288 <option value="CPTAC_Prospective_Colon_PNNL_Proteome_PDC000116">CPTAC_Prospective_Colon_PNNL_Proteome_PDC000116</option>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	289 <option value="CPTAC_Prospective_Colon_VU_Proteome_PDC000109">CPTAC_Prospective_Colon_VU_Proteome_PDC000109</option>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	290 <option value="CPTAC_Prospective_Ovarian_JHU_Glycoproteome_PDC000251">CPTAC_Prospective_Ovarian_JHU_Glycoproteome_PDC000251</option>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	291 <option value="CPTAC_Prospective_Ovarian_JHU_Proteome_PDC000110">CPTAC_Prospective_Ovarian_JHU_Proteome_PDC000110</option>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	292 <option value="CPTAC_Prospective_Ovarian_PNNL_Phosphoproteome_PDC000119">CPTAC_Prospective_Ovarian_PNNL_Phosphoproteome_PDC000119</option>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	293 <option value="CPTAC_Prospective_Ovarian_PNNL_Proteome_Qeplus_PDC000118">CPTAC_Prospective_Ovarian_PNNL_Proteome_Qeplus_PDC000118</option>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	294 <option value="CPTAC_TCGA_Breast_Cancer_Phosphoproteome_PDC000174">CPTAC_TCGA_Breast_Cancer_Phosphoproteome_PDC000174</option>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	295 <option value="CPTAC_TCGA_Breast_Cancer_Proteome_PDC000173">CPTAC_TCGA_Breast_Cancer_Proteome_PDC000173</option>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	296 <option value="CPTAC_TCGA_Colon_Cancer_Proteome_PDC000111">CPTAC_TCGA_Colon_Cancer_Proteome_PDC000111</option>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	297 <option value="CPTAC_TCGA_Ovarian_Glycoproteome_PDC000112">CPTAC_TCGA_Ovarian_Glycoproteome_PDC000112</option>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	298 <option value="CPTAC_TCGA_Ovarian_Phosphoproteome_PDC000115">CPTAC_TCGA_Ovarian_Phosphoproteome_PDC000115</option>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	299 <option value="CPTAC_TCGA_Ovarian_Proteome_PDC000113_PDC000114">CPTAC_TCGA_Ovarian_Proteome_PDC000113_PDC000114</option>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	300 <option value="CPTAC_UCEC_Discovery_Study_Acetylome_PDC000226">CPTAC_UCEC_Discovery_Study_Acetylome_PDC000226</option>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	301 <option value="CPTAC_UCEC_Discovery_Study_Phosphoproteome_PDC000126">CPTAC_UCEC_Discovery_Study_Phosphoproteome_PDC000126</option>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	302 <option value="CPTAC_UCEC_Discovery_Study_Proteome_PDC000125">CPTAC_UCEC_Discovery_Study_Proteome_PDC000125</option>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	303 <option value="Deep_29_healthy_human_tissues_PXD010154">Deep_29_healthy_human_tissues_PXD010154</option>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	304 <option value="GTEx_32_Tissues_Proteome_PXD016999">GTEx_32_Tissues_Proteome_PXD016999</option>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	305 <option value="HBV_Related_Hepatocellular_Carcinoma_Phosphoproteome_PDC000199">HBV_Related_Hepatocellular_Carcinoma_Phosphoproteome_PDC000199</option>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	306 <option value="HBV_Related_Hepatocellular_Carcinoma_Proteome_PDC000198">HBV_Related_Hepatocellular_Carcinoma_Proteome_PDC000198</option>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	307 <option value="Oral_Squamous_Cell_Carcinoma_Study_Proteome_PDC000262">Oral_Squamous_Cell_Carcinoma_Study_Proteome_PDC000262</option>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	308 <option value="Proteogenomics_of_Gastric_Cancer_Glycoproteome_PDC000216">Proteogenomics_of_Gastric_Cancer_Glycoproteome_PDC000216</option>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	309 <option value="Proteogenomics_of_Gastric_Cancer_Phosphoproteome_PDC000215">Proteogenomics_of_Gastric_Cancer_Phosphoproteome_PDC000215</option>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	310 <option value="Proteogenomics_of_Gastric_Cancer_Proteome_PDC000214">Proteogenomics_of_Gastric_Cancer_Proteome_PDC000214</option>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	311 </param>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	312 </when>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	313 <when value="public">
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	314 <param name="dataset" type="text" value="" label="Public dataset">
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	315 <validator type="regex" message="An identifier strating with PXD or MSV or JPST">^(PXD\|MSV\|JPST).*$</validator>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	316 </param>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	317 </when>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	318 </conditional>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	319
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	320 <param name="indexType" argument="-indexType" type="select" label="Report Spectrum Scan as" help="" >
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	321 <option value="1" selected="true">index (1-based) in MGF</option>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	322 <option value="2">spectrum title in MGF</option>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	323 </param>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	324 </section>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	325
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	326 <param name="parameter_set" argument="-p" type="text" value="" optional="true" label="MS/MS searching parameter set name">
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	327 <help>Currently supported set names start with: MS1 or TMT</help>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	328 <option value="MS1_H_MS2_H_LF">MS1_H_MS2_H_LF</option>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	329 <option value="MS1_H_MS2_L_LF">MS1_H_MS2_L_LF</option>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	330 <option value="TMT10_11">TMT10_11</option>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	331 <option value="TMT10_11_MS2_L">TMT10_11_MS2_L</option>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	332 <option value="TMT10_11_MS2_L_phosphorylation">TMT10_11_MS2_L_phosphorylation</option>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	333 <option value="TMT10_11_acetylation">TMT10_11_acetylation</option>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	334 <option value="TMT10_11_glycosylation">TMT10_11_glycosylation</option>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	335 <option value="TMT10_11_phosphorylation">TMT10_11_phosphorylation</option>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	336 <option value="TMT10_11_ubiquitination">TMT10_11_ubiquitination</option>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	337 </param>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	338
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	339 <!--
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	340 TMT10_11_MS2_L_phosphorylation
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	341 Fixed modification: 1,11,12 = Carbamidomethylation of C,TMT 10-plex of K,TMT 10-plex of peptide N-term
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	342 Variable modification: 2,7,8,9 = Oxidation of M,Phosphorylation of S,Phosphorylation of T,Phosphorylation of Y
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	343 Enzyme: 1
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	344 Max Missed cleavages: 1
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	345 Precursor mass tolerance: 20.0
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	346 Precursor ion mass tolerance unit: ppm
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	347 Fragment ion mass tolerance: 0.6
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	348 Fragment ion mass tolerance unit: Da
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	349 -->
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	350
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	351 <section name="modifications" title="Modifications" expanded="false">
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	352 <param name="fixed_mod" argument="-fixMod" type="select" label="Fixed modification(s)" multiple="true" optional="true">
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	353 <help>default: 1: Carbamidomethylation of C [57.02146372057]</help>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	354 <expand macro="modifications" />
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	355 </param>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	356 <param name="var_mod" argument="-varMod" type="select" label="Variable modification(s)" multiple="true" optional="true">
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	357 <help>default: 2: Oxidation of M [15.99491461956]</help>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	358 <expand macro="modifications" />
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	359 </param>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	360
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	361 <param name="max_mods" argument="-maxVar" type="integer" label="Max Modifications" value="" min="0" max="10" optional="true" help="Max number of variable modifications Default: 3" />
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	362 <param name="unmodified" argument="-hc" type="boolean" truevalue="-hc" falsevalue="" checked="false" label="Use more stringent criterion for unrestricted modification searching" help="TRUE: score(UMS)>=score(targetPSM); FALSE: score(UMS)>score(targetPSM)" />
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	363 <param name="aa" argument="-aa" type="boolean" truevalue="-aa" falsevalue="" checked="false" label="Consider amino acid substitution modifications?" help="Whether or not to consider aa substitution modifications when perform modification filtering." />
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	364 </section>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	365
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	366 <section name="digestion" title="Digestion" expanded="false">
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	367 <param name="enzyme" argument="-e" type="select" optional="true" label="Enzyme" help="Enzyme used for protein digestion" >
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	368 <option value="0">Non enzyme</option>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	369 <option value="1" selected="true">Trypsin</option>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	370 <option value="2">Trypsin (no P rule)</option>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	371 <option value="3">Arg-C</option>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	372 <option value="4">Arg-C (no P rule)</option>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	373 <option value="5">Arg-N</option>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	374 <option value="6">Glu-C</option>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	375 <option value="7">Lys-C</option>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	376 </param>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	377 <param name="max_missed_cleavages" argument="-c" type="integer" value="" optional="true" label="Max Missed Cleavages" help="The max missed cleavages" />
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	378 </section>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	379
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	380 <section name="ms_params" title="Mass spectrometer" expanded="false">
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	381 <section name="tolerance_params" title="Tolerance" expanded="true">
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	382 <param name="precursor_tolerance" argument="-tol" type="integer" value="" optional="true" label="Precursor Tolerance" help="The error window on experimental peptide mass values. This parameter is usually set according to the mass spectrometer which was used to generate the MS/MS data. Default: 10" />
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	383 <param name="precursor_unit" argument="-tolu" type="select" optional="true" label="Precursor Unit" help="The unit of precursor ion m/z tolerance">
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	384 <option value="ppm" selected="true">ppm</option>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	385 <option value="Da">Da</option>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	386 </param>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	387 <param name="tolerance" argument="-itol" type="float" value="0.6" optional="true" label="Tolerance" help="Error window for MS/MS fragment ion mass values in Da unit. Default: 0.6 Da" />
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	388 </section>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	389
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	390 <section name="search" title="PSM" expanded="false">
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	391 <param name="frag_method" argument="-fragmentMethod" type="select" optional="true" label="Fragmentation Method">
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	392 <option value="1" selected="true">CID/HCD</option>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	393 <option value="2">ETD</option>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	394 </param>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	395 <param name="scoring_method" argument="-m" type="select" optional="true" label="Scoring Method">
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	396 <option value="1" selected="true">HyperScore</option>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	397 <option value="2">MVH</option>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	398 </param>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	399 <param name="extra_score_validation" argument="-x" type="boolean" truevalue="-x" falsevalue="" checked="false" label="Add extra score validation" help="use two scoring algorithms for peptide identification" />
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	400 <param name="min_charge" argument="-minCharge" type="integer" value="" optional="true" label="Minimum Charge" help="The minimum charge to consider if the charge state is not available. Default: 2"/>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	401 <param name="max_charge" argument="-maxCharge" type="integer" value="" optional="true" label="Maximum Charge" help="The maximum charge to consider if the charge state is not available. Default: 2" />
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	402 <param name="min_peaks" argument="-minPeaks" type="integer" value="" optional="true" label="Minimum Peaks" help="Min peaks in spectrum. Default: 10" />
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	403 <param name="isotope_error" argument="-ti" type="text" value="" optional="true" label="Isotope peak error range">
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	404 <help>A comma-sepated range of integers from -2 to 2, e.g. '-1,0,1,2' Default: 0</help>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	405 <validator type="regex" message="">^((-2,)?-1,)?0(,1(,2)?)?$</validator>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	406 </param>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	407 <param name="min_score" argument="-minScore" type="integer" value="" min="0" optional="true" label="Minimum Score" help="Minimum score to consider for peptide searching. Default: 12" />
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	408 <param name="min_length" argument="-minLength" type="integer" value="" min="0" optional="true" label="Minimum length of peptide" help="The maximum length of peptide to consider. Default: 7" />
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	409 <param name="max_length" argument="-maxLength" type="integer" value="" min="0" optional="true" label="Maximum length of peptide" help="The maximum length of peptide to consider. Default: 45" />
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	410 <param name="num_random_peptides" argument="-n" type="integer" value="" min="0" optional="true" label="Number of Random Peptides" help="The number of random peptides. Default: 1000" />
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	411 </section>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	412 </section>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	413
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	414 <param name="outputs_selected" type="select" multiple="true" optional="false" label="Select outputs">
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	415 <option value="parameter.txt" selected="true">parameter.txt</option>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	416 <option value="psm.txt" selected="true">psm.txt</option>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	417 <option value="psm_rank.txt" selected="true">psm_rank.txt</option>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	418 <option value="psm_rank.mgf" selected="true">psm_rank.mgf</option>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	419 <option value="psm_annotation.txt" selected="true">psm_annotation.txt</option>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	420 <option value="psm_type.txt" selected="false">psm_type.txt</option>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	421 <option value="detail.txt" selected="true">detail.txt</option>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	422 <option value="ptm.txt" selected="true">ptm.txt</option>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	423 <option value="ptm_detail.txt" selected="true">ptm_detail.txt</option>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	424 <option value="ptm_detail.txt" selected="true">ptm_detail.txt</option>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	425 <option value="ms_index" selected="true">MS/MS Index</option>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	426 </param>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	427 <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." />
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	428 </inputs>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	429 <outputs>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	430 <data name="ms_index" format="txt" label="${tool.name} on ${on_string}: index summary.txt" from_work_dir="index_dir/summary.txt">
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	431 <filter>'ms_index' in outputs_selected and req_inputs['ms_dataset']['ms_dataset_type'] == 'history'</filter>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	432 </data>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	433 <data name="parameter_txt" format="txt" from_work_dir="pepquery_output/parameter.txt" label="${tool.name} on ${on_string}: parameter.txt">
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	434 <filter>'parameter.txt' in outputs_selected</filter>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	435 </data>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	436
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	437 <data name="psm_txt" format="tabular" from_work_dir="pepquery_output/psm.txt" label="${tool.name} on ${on_string}: psm.txt">
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	438 <filter>'psm.txt' in outputs_selected</filter>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	439 <actions>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	440 <action name="comment_lines" type="metadata" default="1" />
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	441 <action name="column_names" type="metadata" default="peptide,modification,n,spectrum_title,charge,exp_mass,tol_ppm,tol_da,isotope_error,pep_mass,mz,score,n_db,total_db,n_random,total_random,pvalue" />
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	442 </actions>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	443 </data>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	444
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	445 <data name="psm_rank_txt" format="tabular" from_work_dir="pepquery_output/psm_rank.txt" label="${tool.name} on ${on_string}: psm_rank.txt">
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	446 <filter>'psm_rank.txt' in outputs_selected</filter>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	447 <actions>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	448 <action name="comment_lines" type="metadata" default="1" />
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	449 <action name="column_names" type="metadata" default="peptide,modification,n,spectrum_title,charge,exp_mass,tol_ppm,tol_da,isotope_error,pep_mass,mz,score,n_db,total_db,n_random,total_random,pvalue,rank,n_ptm,confident,ref_delta_score,mod_delta_score" />
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	450 </actions>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	451 </data>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	452
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	453 <data name="psm_rank_mgf" format="mgf" from_work_dir="pepquery_output/psm_rank.mgf" label="${tool.name} on ${on_string}: psm_rank.mgf">
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	454 <filter>'psm_rank.mgf' in outputs_selected</filter>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	455 </data>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	456 <data name="psm_type_txt" format="tabular" from_work_dir="pepquery_output/psmi_type.txt" label="${tool.name} on ${on_string}: psm_type.txt">
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	457 <filter>'psm_type.txt' in outputs_selected</filter>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	458 <actions>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	459 <action name="comment_lines" type="metadata" default="1" />
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	460 <action name="column_names" type="metadata" default="peptide,spectrum_title,type" />
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	461 </actions>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	462 </data>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	463 <data name="psm_annotation_txt" format="tabular" from_work_dir="pepquery_output/psm_annotation.txt" label="${tool.name} on ${on_string}: psm_annotation.txt">
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	464 <filter>'psm_annotation.txt' in outputs_selected</filter>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	465 <actions>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	466 <action name="comment_lines" type="metadata" default="1" />
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	467 <action name="column_names" type="metadata" default="peptide,modification,Query,calc_mr,observed_mz,charge,pepSeq,m_label,m_mz,m_intensity,mz,intensity" />
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	468 </actions>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	469 </data>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	470 <data name="detail_txt" format="tabular" from_work_dir="pepquery_output/detail.txt" label="${tool.name} on ${on_string}: detail.txt">
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	471 <filter>'detail.txt' in outputs_selected</filter>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	472 <actions>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	473 <action name="comment_lines" type="metadata" default="1" />
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	474 <action name="column_names" type="metadata" default="spectrum_title,peptide,modification,exp_mass,pep_mass,tol_ppm,tol_da,isotope_error,score" />
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	475 </actions>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	476 </data>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	477
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	478 <data name="ptm_txt" format="tabular" from_work_dir="pepquery_output/ptm.txt" label="${tool.name} on ${on_string}: ptm.txt">
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	479 <filter>'ptm.txt' in outputs_selected</filter>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	480 <actions>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	481 <action name="comment_lines" type="metadata" default="1" />
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	482 <action name="column_names" type="metadata" default="spectrum_title,peptide,charge,exp_mass,pep_mass,tol_ppm,tol_da,isotope_error,modification,score" />
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	483 </actions>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	484 </data>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	485 <data name="ptm_detail_txt" format="tabular" from_work_dir="pepquery_output/ptm_detail.txt" label="${tool.name} on ${on_string}: ptm_detail.txt">
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	486 <filter>'ptm_detail.txt' in outputs_selected</filter>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	487 <actions>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	488 <action name="comment_lines" type="metadata" default="1" />
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	489 <action name="column_names" type="metadata" default="peptide,modification,n,spectrum_title,charge,exp_mass,tol_ppm,tol_da,isotope_error,pep_mass,mz,score,n_db,total_db,n_random,total_random,pvalue,rank,ptm_spectrum_title,ptm_peptide,ptm_charge,ptm_exp_mass,ptm_pep_mass,ptm_tol_ppm,ptm_tol_da,ptm_isotope_error,ptm_modification,ptm_score" />
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	490 </actions>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	491 </data>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	492
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	493 </outputs>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	494 <tests>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	495 <!-- Test-1 -->
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	496 <!--
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	497 <test>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	498 <section name="req_inputs">
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	499 <conditional name="input_type">
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	500 <param name="input_type_selector" value="peptide"/>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	501 <conditional name="multiple">
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	502 <param name="peptide_input_selector" value="single" />
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	503 <param name="input" value="ELGSSDLTAR"/>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	504 </conditional>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	505 </conditional>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	506 <param name="db_file" ftype="fasta" value="Uniprot.fasta"/>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	507 <param name="spectrum_file" ftype="mgf" value="iTRAQ_f4.mgf"/>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	508 </section>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	509 <section name="modifications">
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	510 <param name="fixed_mod" value="6,103,157"/>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	511 <param name="var_mod" value="117"/>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	512 <param name="max_mods" value="3"/>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	513 <param name="unmodified" value="False"/>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	514 <param name="aa" value="True"/>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	515 </section>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	516 <section name="ms_params">
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	517 <section name="tolerance_params">
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	518 <param name="precursor_tolerance" value="10"/>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	519 <param name="precursor_unit" value="ppm"/>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	520 <param name="tolerance" value="0.6"/>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	521 </section>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	522 <section name="digestion">
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	523 <param name="enzyme" value="0"/>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	524 <param name="max_missed_cleavages" value="2"/>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	525 </section>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	526 <section name="search">
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	527 <param name="frag_method" value="1"/>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	528 <param name="scoring_method" value="1"/>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	529 <param name="max_charge" value="3"/>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	530 <param name="min_charge" value="2"/>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	531 <param name="min_peaks" value="10"/>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	532 <param name="min_score" value="12"/>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	533 <param name="max_length" value="45"/>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	534 <param name="num_random_peptides" value="1000"/>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	535 </section>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	536 </section>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	537 <output name="psm_rank_txt">
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	538 <assert_contents>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	539 <has_text text="ELGSSDLTAR" />
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	540 <has_line_matching expression="ELGSSDLTAR\tiTRAQ 4-plex of peptide N-term@0\S+\t2\tiTRAQ_f4.mgf\t2\t2\t1191.6\d+\t2.0\d+\t1191.62\d+\t596.81\d+\t18.68\d+\t0\t20\t5\t995\t0.006\d+\t1"/>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	541 </assert_contents>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	542 </output>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	543 </test>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	544 -->
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	545
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	546 <!-- Test-2 -->
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	547 <!--
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	548 <test>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	549 <section name="req_inputs">
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	550 <conditional name="input_type">
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	551 <param name="input_type_selector" value="peptide"/>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	552 <conditional name="multiple">
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	553 <param name="peptide_input_selector" value="multiple" />
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	554 <param name="input" ftype="tabular" value="novel_peptides"/>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	555 </conditional>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	556 </conditional>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	557 <param name="db_file" ftype="fasta" value="Uniprot.fasta"/>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	558 <param name="spectrum_file" ftype="mgf" value="iTRAQ_f4.mgf"/>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	559 </section>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	560 <section name="modifications">
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	561 <param name="fixed_mod" value="6,103,157"/>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	562 <param name="var_mod" value="117"/>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	563 <param name="max_mods" value="3"/>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	564 <param name="unmodified" value="False"/>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	565 <param name="aa" value="True"/>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	566 </section>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	567 <section name="ms_params">
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	568 <section name="tolerance_params">
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	569 <param name="precursor_tolerance" value="10"/>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	570 <param name="precursor_unit" value="ppm"/>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	571 <param name="tolerance" value="0.6"/>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	572 </section>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	573 <section name="digestion">
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	574 <param name="enzyme" value="0"/>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	575 <param name="max_missed_cleavages" value="2"/>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	576 </section>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	577 <section name="search">
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	578 <param name="frag_method" value="1"/>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	579 <param name="scoring_method" value="1"/>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	580 <param name="max_charge" value="3"/>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	581 <param name="min_charge" value="2"/>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	582 <param name="min_peaks" value="10"/>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	583 <param name="min_score" value="12"/>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	584 <param name="max_length" value="45"/>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	585 <param name="num_random_peptides" value="1000"/>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	586 </section>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	587 </section>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	588 <output name="psm_rank_txt">
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	589 <assert_contents>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	590 <has_text text="ELGSSDLTAR" />
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	591 <has_text text="SPYREFTDHLVK" />
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	592 <has_line_matching expression="SPYREFTDHLVK\tiTRAQ 4-plex of K@12\S+;iTRAQ 4-plex of peptide N-term@0\S+\t1\tiTRAQ_f4.mgf\t4\t3\t1778.\d+\t3.02\d+\t1778.95\d+\t593.99\d+\t12.17\d+\t2\t14\t-1\t-1\t100.0\t1"/>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	593 </assert_contents>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	594 </output>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	595 </test>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	596 -->
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	597
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	598 <!-- Test-3 -->
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	599 <!--
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	600 <test>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	601 <section name="req_inputs">
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	602 <conditional name="input_type">
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	603 <param name="input_type_selector" value="peptide"/>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	604 <conditional name="multiple">
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	605 <param name="peptide_input_selector" value="multiple" />
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	606 <param name="input" ftype="tabular" value="novel_peptides"/>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	607 </conditional>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	608 </conditional>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	609 <param name="db_file" ftype="fasta" value="Uniprot.fasta"/>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	610 <param name="spectrum_file" ftype="mgf" value="iTRAQ_f4.mgf"/>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	611 </section>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	612 <section name="modifications">
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	613 <param name="fixed_mod" value="6,103,157"/>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	614 <param name="var_mod" value="117"/>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	615 <param name="max_mods" value="3"/>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	616 <param name="unmodified" value="True"/>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	617 <param name="aa" value="True"/>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	618 </section>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	619 <section name="ms_params">
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	620 <section name="tolerance_params">
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	621 <param name="precursor_tolerance" value="10"/>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	622 <param name="precursor_unit" value="ppm"/>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	623 <param name="tolerance" value="0.6"/>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	624 </section>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	625 <section name="digestion">
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	626 <param name="enzyme" value="0"/>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	627 <param name="max_missed_cleavages" value="1"/>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	628 </section>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	629 <section name="search">
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	630 <param name="frag_method" value="1"/>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	631 <param name="scoring_method" value="1"/>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	632 <param name="max_charge" value="3"/>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	633 <param name="min_charge" value="2"/>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	634 <param name="min_peaks" value="7"/>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	635 <param name="min_score" value="10"/>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	636 <param name="max_length" value="45"/>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	637 <param name="num_random_peptides" value="1000"/>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	638 </section>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	639 </section>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	640 <output name="psm_rank_txt">
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	641 <assert_contents>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	642 <has_text text="ELGSSDLTAR" />
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	643 <has_text text="SPYREFTDHLVK" />
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	644 <has_line_matching expression="ELGSSDLTAR\tiTRAQ 4-plex of peptide N-term@0\S+\t2\t3\t2\t1191.6\d+\t-3.04\d+\t1191.62\d+\t596.8\d+\t24.18\d+\t0\t22\t1\t995\t0.002\d+\t1\t0\tYes" />
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	645 </assert_contents>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	646 </output>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	647 </test>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	648 -->
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	649
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	650 <!-- Test-4 -->
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	651 <!--
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	652 <test>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	653 <section name="req_inputs">
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	654 <conditional name="input_type">
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	655 <param name="input_type_selector" value="1"/>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	656 <conditional name="multiple">
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	657 <param name="protein_input_selector" value="multiple" />
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	658 <param name="input" ftype="fasta" value="novel_proteins.fa"/>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	659 </conditional>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	660 </conditional>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	661 <param name="db_file" ftype="fasta" value="Uniprot.fasta"/>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	662 <param name="spectrum_file" ftype="mgf" value="iTRAQ_f4.mgf"/>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	663 </section>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	664 <section name="modifications">
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	665 <param name="fixed_mod" value="6,103,157"/>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	666 <param name="var_mod" value="117"/>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	667 <param name="max_mods" value="3"/>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	668 <param name="unmodified" value="False"/>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	669 <param name="aa" value="True"/>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	670 </section>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	671 <section name="ms_params">
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	672 <section name="tolerance_params">
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	673 <param name="precursor_tolerance" value="10"/>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	674 <param name="precursor_unit" value="ppm"/>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	675 <param name="tolerance" value="0.6"/>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	676 </section>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	677 <section name="digestion">
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	678 <param name="enzyme" value="0"/>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	679 <param name="max_missed_cleavages" value="2"/>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	680 </section>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	681 <section name="search">
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	682 <param name="frag_method" value="1"/>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	683 <param name="scoring_method" value="1"/>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	684 <param name="max_charge" value="3"/>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	685 <param name="min_charge" value="2"/>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	686 <param name="min_peaks" value="10"/>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	687 <param name="min_score" value="12"/>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	688 <param name="max_length" value="45"/>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	689 <param name="num_random_peptides" value="1000"/>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	690 </section>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	691 </section>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	692 <output name="psm_rank_txt">
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	693 <assert_contents>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	694 <has_text text="ELGSSDLTAR" />
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	695 <has_text text="SPYREFTDHLVK" />
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	696 </assert_contents>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	697 </output>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	698 </test>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	699 -->
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	700
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	701 <!-- Test-5 -->
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	702 <!--
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	703 <test>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	704 <section name="req_inputs">
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	705 <conditional name="input_type">
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	706 <param name="input_type_selector" value="2"/>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	707 <param name="input" value="gaactgggcagcagcgatctgaccgcgcgcagcccgtatcgcgaatttaccgatcatctggtgaaa"/>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	708 </conditional>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	709 <param name="db_file" ftype="fasta" value="Uniprot.fasta"/>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	710 <param name="spectrum_file" ftype="mgf" value="iTRAQ_f4.mgf"/>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	711 </section>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	712 <section name="modifications">
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	713 <param name="fixed_mod" value="6,103,157"/>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	714 <param name="var_mod" value="117"/>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	715 <param name="max_mods" value="3"/>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	716 <param name="unmodified" value="False"/>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	717 <param name="aa" value="True"/>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	718 </section>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	719 <section name="ms_params">
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	720 <section name="tolerance_params">
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	721 <param name="precursor_tolerance" value="10"/>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	722 <param name="precursor_unit" value="ppm"/>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	723 <param name="tolerance" value="0.6"/>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	724 </section>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	725 <section name="digestion">
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	726 <param name="enzyme" value="0"/>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	727 <param name="max_missed_cleavages" value="2"/>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	728 </section>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	729 <section name="search">
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	730 <param name="frag_method" value="1"/>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	731 <param name="scoring_method" value="1"/>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	732 <param name="max_charge" value="3"/>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	733 <param name="min_charge" value="2"/>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	734 <param name="min_peaks" value="10"/>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	735 <param name="min_score" value="12"/>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	736 <param name="max_length" value="45"/>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	737 <param name="num_random_peptides" value="1000"/>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	738 </section>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	739 </section>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	740 <output name="psm_rank_txt">
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	741 <assert_contents>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	742 <has_text text="ELGSSDLTAR" />
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	743 </assert_contents>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	744 </output>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	745 </test>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	746 -->
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	747
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	748 <!-- Test-6 -->
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	749 <!--
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	750 <test>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	751 <section name="req_inputs">
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	752 <conditional name="input_type">
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	753 <param name="input_type_selector" value="peptide"/>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	754 <conditional name="multiple">
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	755 <param name="peptide_input_selector" value="multiple" />
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	756 <param name="input" ftype="tabular" value="novel_peptides"/>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	757 </conditional>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	758 </conditional>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	759 <param name="db_file" ftype="fasta" value="Uniprot.fasta"/>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	760 <param name="spectrum_file" ftype="mgf" value="immunopeptidomics.mgf"/>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	761 <param name="indexType" value="2"/>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	762 <conditional name="tags">
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	763 <param name="tagType" value="PepQuery"/>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	764 <param name="tag_file" ftype="tabular" value="test.tags"/>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	765 <param name="tagIndexType" value="2"/>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	766 </conditional>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	767 </section>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	768 <section name="modifications">
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	769 <param name="fixed_mod" value=""/>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	770 <param name="var_mod" value="117,114,118,128"/>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	771 <param name="max_mods" value="3"/>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	772 <param name="unmodified" value="True"/>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	773 <param name="aa" value="True"/>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	774 </section>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	775 <section name="ms_params">
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	776 <section name="tolerance_params">
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	777 <param name="precursor_tolerance" value="20"/>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	778 <param name="precursor_unit" value="ppm"/>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	779 <param name="tolerance" value="0.02"/>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	780 </section>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	781 <section name="digestion">
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	782 <param name="enzyme" value="0"/>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	783 <param name="max_missed_cleavages" value="0"/>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	784 </section>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	785 <section name="search">
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	786 <param name="frag_method" value="1"/>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	787 <param name="scoring_method" value="1"/>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	788 <param name="max_charge" value="3"/>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	789 <param name="min_charge" value="2"/>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	790 <param name="min_peaks" value="10"/>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	791 <param name="min_score" value="12"/>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	792 <param name="max_length" value="25"/>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	793 <param name="num_random_peptides" value="1000"/>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	794 </section>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	795 </section>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	796 <output name="psm_rank_txt">
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	797 <assert_contents>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	798 <has_text text="MTDRHAGTY" />
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	799 <has_text text="controllerType=0 controllerNumber=1 scan=19905" />
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	800 </assert_contents>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	801 </output>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	802 </test>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	803 -->
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	804
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	805 <!-- Test-7 -->
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	806 <!--
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	807 <test>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	808 <section name="req_inputs">
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	809 <conditional name="input_type">
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	810 <param name="input_type_selector" value="peptide"/>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	811 <conditional name="multiple">
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	812 <param name="peptide_input_selector" value="multiple" />
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	813 <param name="input" ftype="tabular" value="novel_peptides"/>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	814 </conditional>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	815 </conditional>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	816 <param name="db_file" ftype="fasta" value="Uniprot.fasta"/>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	817 <param name="spectrum_file" ftype="mgf" value="immunopeptidomics.mgf"/>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	818 <param name="indexType" value="2"/>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	819 <conditional name="tags">
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	820 <param name="tagType" value="pFind"/>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	821 <param name="qry_res" ftype="txt" value="pFind.qry.res"/>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	822 </conditional>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	823 </section>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	824 <section name="modifications">
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	825 <param name="fixed_mod" value=""/>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	826 <param name="var_mod" value="117,114,118,128"/>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	827 <param name="max_mods" value="3"/>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	828 <param name="unmodified" value="True"/>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	829 <param name="aa" value="True"/>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	830 </section>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	831 <section name="ms_params">
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	832 <section name="tolerance_params">
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	833 <param name="precursor_tolerance" value="20"/>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	834 <param name="precursor_unit" value="ppm"/>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	835 <param name="tolerance" value="0.02"/>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	836 </section>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	837 <section name="digestion">
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	838 <param name="enzyme" value="0"/>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	839 <param name="max_missed_cleavages" value="0"/>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	840 </section>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	841 <section name="search">
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	842 <param name="frag_method" value="1"/>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	843 <param name="scoring_method" value="1"/>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	844 <param name="max_charge" value="3"/>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	845 <param name="min_charge" value="2"/>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	846 <param name="min_peaks" value="10"/>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	847 <param name="min_score" value="12"/>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	848 <param name="max_length" value="25"/>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	849 <param name="num_random_peptides" value="1000"/>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	850 </section>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	851 </section>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	852 <output name="psm_rank_txt">
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	853 <assert_contents>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	854 <has_text text="MTDRHAGTY" />
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	855 <has_text text="controllerType=0 controllerNumber=1 scan=19905" />
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	856 </assert_contents>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	857 </output>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	858 </test>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	859 -->
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	860
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	861 </tests>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	862 <help><![CDATA[
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	863 PepQuery
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	864
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	865 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.
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	866
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	867
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	868 PepQuery_ is a peptide-centric search engine for novel peptide identification and validation. Cancer genomics studies have identified a large number of genomic alterations that may lead to novel, cancer-specific protein sequences. Proteins resulted from these genomic alterations are attractive candidates for cancer biomarkers and therapeutic targets. The leading approach to proteomic validation of genomic alterations is to analyze tandem mass spectrometry (MS/MS) data using customized proteomics databases created from genomics data. Such analysis is time-consuming and requires thorough training and detailed knowledge in proteomics data analysis, leading to a gap between MS/MS data and the cancer genomics community. PepQuery does not require customized databases and allows quick and easy proteomic validation of genomic alterations.
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	869
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	870 PepQuery2 leverages a new MS/MS indexing approach and cloud storage to enable ultrafast, targeted identification of both novel and known peptides. PepQuery2 allows users to search more than one billion MS/MS data indexed in the PepQueryDB from any computers with internet access. It also supports direct analysis of user provided MS/MS data, any public datasets in PRIDE, MassIVE, jPOSTrepo and iProX, or Universal Spectrum Identifiers (USIs) from ProteomeXchange.
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	871
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	872 Inputs
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	873 - A sequence to match, one of the following:
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	874
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	875 - A peptide string or a history dataset with a list of peptides
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	876 - A protein string or a history dataset with a protein fasta
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	877 - A DNA string that is at least 60 base pairs in length
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	878
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	879 - MS/MS data used for identification:
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	880
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	881 - A mass spectrometry history datasets in MGF, mzML, or mzXML format
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	882 - An Indexed MS/MS dataset
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	883 - PepQueryDB dataset IDs
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	884 - Dataset IDs from public proteomics data repositories: PRIDE, MassIVE, jPOSTrepo and iProX
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	885
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	886 - A reference protein fasta database, novel peptides matching a reference sequence will be excluded.
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	887
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	888 - A protein fasta file
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	889 - The ID for a public reference protein database from RefSeq, GENCODE, Ensembl or UniProt.
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	890
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	891
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	892 Outputs
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	893 - Parameters:
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	894
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	895 - parameters used in the search
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	896
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	897 - PSM - tabular with columns:
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	898
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	899 - peptide modification n spectrum_title charge exp_mass ppm pep_mass mz score n_db total_db n_random total_random pvalue
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	900
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	901 - PSM Rank - tabular with columns:
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	902
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	903 - 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
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	904
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	905 - An MGF with the best matching spectrums
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	906
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	907 - Detail - tabular with columns:
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	908
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	909 - spectrum_title peptide modification pep_mass score
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	910
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	911 - PSM annotation - tabular with columns:
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	912
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	913 - peptide Query calc_mr observed_mz charge pepSeq m_label m_mz m_intensity mz intensity
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	914
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	915 - PTM - tabular with columns:
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	916
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	917 - spectrum_title peptide charge exp_mass pep_mass tol_ppm tol_da isotope_error modification score
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	918
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	919 - PTM Detail - tabular with columns:
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	920
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	921 - peptide modification n spectrum_title charge exp_mass tol_ppm tol_da isotope_error pep_mass mz score n_db total_db n_random total_random pvalue rank ptm_spectrum_title ptm_peptide ptm_charge ptm_exp_mass ptm_pep_mass ptm_tol_ppm ptm_tol_da ptm_isotope_error ptm_modification ptm_score
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	922
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	923 - An Indexed MS/MS dataset when MS/MS data is MGF, mzML, or mzXML history datasets
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	924
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	925 The n_ptm field is added when using unrestricted modification searching (-um).
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	926
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	927 .. _PepQuery: http://pepquery.org/document.html
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	928
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	929 ]]></help>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	930 <expand macro="citations" />
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d galaxyp parents: diff changeset	931 </tool>

Mercurial > repos > galaxyp > pepquery2

annotate pepquery2.xml @ 0:3c45645197f6 draft