pepquery2: pepquery2.xml annotate

annotate pepquery2.xml @ 1:b5489f81c2fa draft

planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit fb66172091bb840e4cb673975fd1ebbfd8dcf3f7

author	galaxyp
date	Wed, 18 Oct 2023 06:40:40 +0000
parents	a07976bbc4d9
children	c32806a80862

rev	line source
0 a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	1 <tool id="pepquery2" name="PepQuery2" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	2 <description>Peptide-centric search engine for novel peptide identification and validation.</description>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	3 <macros>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	4 <import>macros.xml</import>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	5 </macros>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	6 <requirements>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	7 <requirement type="package" version="@TOOL_VERSION@">pepquery</requirement>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	8 </requirements>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	9 <stdio>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	10 <exit_code range="1:" level="fatal" description="Failed" />
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	11 <regex match="Exception"
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	12 source="stderr"
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	13 level="fatal"
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	14 description="java Exception" />
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	15 </stdio>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	16 <command><![CDATA[
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	17 @CMD_IMPORTS@
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	18 #if $req_inputs.db_type.db_type_selector == 'history'
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	19 #set $db_file = $re.sub('\s','_',$re.sub('[.][^.]*$','',$req_inputs.db_type.db_file.display_name.split('/')[-1])) + ".fa"
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	20 ln -s '$req_inputs.db_type.db_file' '$db_file' &&
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	21 #end if
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	22 #if $req_inputs.ms_dataset.ms_dataset_type == 'history'
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	23 @INDEX_SPECTRUM_FILES@
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	24 $index_spectrum_files($ms_index.files_path, $req_inputs.ms_dataset.spectrum_files) &&
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	25 #elif $req_inputs.ms_dataset.ms_dataset_type == 'indexed'
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	26 #if $os.path.exists($os.path.join($req_inputs.ms_dataset.index.extra_files_path, 'summary.txt'))
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	27 #set $index_dir = 'index_dir'
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	28 ln -s '$req_inputs.ms_dataset.index.extra_files_path' index_dir &&
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	29 #else
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	30 #raise ValueError
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	31 #end if
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	32 #end if
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	33 ## PepQuery command
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	34 pepquery
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	35 -Xmx\$[ \${GALAXY_MEMORY_MB:-8192} / 1024 ]g
1 b5489f81c2fa planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit fb66172091bb840e4cb673975fd1ebbfd8dcf3f7 galaxyp parents: 0 diff changeset	36 #if $digestion.enzyme == '0'
b5489f81c2fa planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit fb66172091bb840e4cb673975fd1ebbfd8dcf3f7 galaxyp parents: 0 diff changeset	37 -XX:ThreadStackSize=2048
b5489f81c2fa planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit fb66172091bb840e4cb673975fd1ebbfd8dcf3f7 galaxyp parents: 0 diff changeset	38 #end if
0 a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	39 #if $validation.task_type == "known"
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	40 -s 2 $validation.decoy
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	41 #else
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	42 -s 1
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	43 #end if
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	44 #if $req_inputs.ms_dataset.ms_dataset_type in ['history', 'indexed']
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	45 -ms '$index_dir'
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	46 #elif $req_inputs.ms_dataset.ms_dataset_type in ['PepQueryDB', 'public']
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	47 -b '$req_inputs.ms_dataset.dataset'
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	48 #end if
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	49
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	50 #if $req_inputs.db_type.db_type_selector == 'history'
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	51 -db '$db_file'
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	52 #else
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	53 -db '$req_inputs.db_type.db_id'
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	54 #end if
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	55 #if $req_inputs.input_type.input_type_selector == 'peptide'
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	56 -t $req_inputs.input_type.input_type_selector
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	57 -i '$req_inputs.input_type.multiple.input'
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	58 #else
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	59 -t $req_inputs.input_type.input_type_selector
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	60 #if $req_inputs.input_type.input_type_selector == 'protein'
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	61 #if $req_inputs.input_type.multiple.protein_input_selector == 'identifier'
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	62 #set $prot_id = str($req_inputs.input_type.multiple.input).replace('\|','\\|')
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	63 -i '"$prot_id"'
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	64 #else
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	65 -i '$req_inputs.input_type.multiple.input'
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	66 #end if
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	67 #else
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	68 -i '$req_inputs.input_type.input'
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	69 #if $req_inputs.input_type.input_type_selector == 'DNA'
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	70 #if $req_inputs.input_type.frame == 'None'
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	71 -frame '0'
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	72 #else
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	73 -frame '$req_inputs.input_type.frame'
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	74 #end if
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	75 #else
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	76 -anno '$req_inputs.input_type.anno'
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	77 #end if
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	78 #end if
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	79 #end if
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	80 #if $req_inputs.indexType
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	81 -indexType $req_inputs.indexType
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	82 #end if
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	83
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	84 #if $modifications.fixed_mod
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	85 -fixMod '$modifications.fixed_mod'
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	86 #end if
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	87 #if $modifications.var_mod
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	88 -varMod '$modifications.var_mod'
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	89 #end if
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	90 #if $digestion.enzyme
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	91 -e '$digestion.enzyme'
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	92 #end if
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	93 #if $digestion.max_missed_cleavages
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	94 -c '$digestion.max_missed_cleavages'
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	95 #end if
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	96
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	97 #if $modifications.max_mods
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	98 -maxVar '$modifications.max_mods'
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	99 #end if
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	100 $modifications.unmodified
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	101 $modifications.aa
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	102 #if $ms_params.tolerance_params.precursor_tolerance
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	103 -tol '$ms_params.tolerance_params.precursor_tolerance'
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	104 #end if
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	105
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	106 #if $ms_params.tolerance_params.precursor_unit
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	107 -tolu '$ms_params.tolerance_params.precursor_unit'
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	108 #end if
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	109 #if $ms_params.tolerance_params.tolerance
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	110 -itol '$ms_params.tolerance_params.tolerance'
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	111 #end if
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	112 #if $ms_params.search.frag_method
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	113 -fragmentMethod '$ms_params.search.frag_method'
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	114 #end if
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	115 #if $ms_params.search.scoring_method
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	116 -m '$ms_params.search.scoring_method'
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	117 #end if
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	118 $ms_params.search.extra_score_validation
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	119 #if $ms_params.search.max_charge
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	120 -maxCharge '$ms_params.search.max_charge'
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	121 #end if
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	122 #if $ms_params.search.min_charge
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	123 -minCharge '$ms_params.search.min_charge'
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	124 #end if
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	125 #if $ms_params.search.min_peaks
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	126 -minPeaks '$ms_params.search.min_peaks'
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	127 #end if
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	128 #if $ms_params.search.isotope_error
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	129 -ti '$ms_params.search.isotope_error'
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	130 #end if
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	131 #if $ms_params.search.min_score
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	132 -minScore '$ms_params.search.min_score'
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	133 #end if
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	134 #if $ms_params.search.min_length
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	135 -minLength '$ms_params.search.min_length'
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	136 #end if
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	137 #if $ms_params.search.max_length
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	138 -maxLength '$ms_params.search.max_length'
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	139 #end if
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	140 #if $ms_params.search.num_random_peptides
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	141 -n '$ms_params.search.num_random_peptides'
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	142 #end if
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	143 #if 'psm_annotation.txt' in $outputs_selected
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	144 -plot
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	145 #end if
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	146 $fast
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	147 -o pepquery_output
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	148 \| tee >(sed "s/\x1b[^m]*m//g" > log.txt)
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	149 #set $flist = str($outputs_selected).replace(',',' ').replace('ms_index','')
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	150 && for i in $flist; do for f in `find pepquery_output// -name \$i`; do cat \$f >> pepquery_output/\${i}; done; done
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	151 && for f in `find pepquery_output/*/ -name parameter.txt`; do cp \$f pepquery_output/parameter.txt; done
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	152 ]]>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	153 </command>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	154 <inputs>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	155 <conditional name="validation">
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	156 <param name="task_type" argument="-s" type="select" label="Validation Task Type">
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	157 <option value="novel" selected="true">novel peptide/protein validation</option>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	158 <option value="known">known peptide/protein validation</option>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	159 </param>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	160 <when value="novel"/>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	161 <when value="known">
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	162 <param name="decoy" argument="-decoy" type="boolean" truevalue="-decoy" falsevalue="" checked="false" label="Identity the decoy version of the selected target protein"/>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	163 </when>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	164 </conditional>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	165 <section name="req_inputs" title="Input Data" expanded="true">
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	166 <conditional name="input_type">
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	167 <param name="input_type_selector" argument="-t" type="select" label="Input Type" help="" >
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	168 <option value="peptide">peptide</option>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	169 <option value="protein">protein</option>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	170 <option value="DNA">DNA (translate to protein sequences)</option>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	171 <!-- VCF,BED,GTF input options have not been implemented in this tool -->
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	172 </param>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	173 <when value="peptide">
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	174 <conditional name="multiple">
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	175 <param name="peptide_input_selector" type="select" label="Peptides?">
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	176 <option value="multiple">Peptide list from your history</option>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	177 <option value="single">Single peptide entered as text</option>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	178 </param>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	179 <when value="multiple">
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	180 <param name="input" argument="-i" type="data" format="tabular" label="Peptide Sequences (.txt)">
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	181 <help>Peptide sequence file containing peptides which you want to search (no column headers).
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	182 First column is am peptide sequence. Optional second column is spectrum title.
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	183 </help>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	184 </param>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	185 </when>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	186 <when value="single">
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	187 <param name="input" argument="-i" type="text" label="Peptide Sequence" help="Peptide sequence(s) which you want to search">
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	188 <validator type="regex" message="Must be AA letters, multiple peptides separated by commas">^[AC-IK-NP-TV-Yac-ik-np-tv-y]+(,[AC-IK-NP-TV-Yac-ik-np-tv-y]+)*$</validator>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	189 </param>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	190 </when>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	191 </conditional>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	192 </when>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	193 <when value="protein">
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	194 <conditional name="multiple">
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	195 <param name="protein_input_selector" type="select" label="Proteins?">
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	196 <option value="multiple">Protein fasta from your history</option>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	197 <option value="single">Single protein entered as text</option>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	198 <option value="identifier">Protein Identifier from selected Protein Reference Database</option>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	199 </param>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	200 <when value="multiple">
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	201 <param name="input" argument="-i" type="data" format="fasta" label="Protein Sequences (.txt)" help="Protein fasta file containing proteins which you want to search." />
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	202 </when>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	203 <when value="single">
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	204 <param name="input" argument="-i" type="text" label="Protein Sequence" help="Protein sequence which you want to search">
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	205 <validator type="regex" message="Must be AA letters">^[AC-IK-NP-TV-Yac-ik-np-tv-y]+$</validator>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	206 </param>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	207 </when>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	208 <when value="identifier">
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	209 <param name="input" argument="-i" type="text" label="Protein Identifier" help="Protein ID from the selected Protein Reference Database. E.g. sp\|P07205\|PGK2_HUMAN from swissprot:human">
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	210 <sanitizer invalid_char="">
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	211 <valid initial="string.ascii_letters,string.digits">
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	212 <add value="\|" />
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	213 </valid>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	214 </sanitizer>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	215 <validator type="regex" message="Spaces not allowed in ID">^[^ ]+$</validator>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	216 </param>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	217 </when>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	218 </conditional>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	219 </when>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	220 <when value="DNA">
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	221 <param name="input" argument="-i" type="text" label="DNA Sequence (at least 60 bp)" help="DNA sequence which you want to search">
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	222 <validator type="regex" message="Must be at least 60bp">^[acgtuAGCTU]{60}[acgtuAGCTU]*$</validator>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	223 </param>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	224 <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">
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	225 <option value="1">1</option>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	226 <option value="2">2</option>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	227 <option value="3">3</option>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	228 <option value="4">4</option>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	229 <option value="5">5</option>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	230 <option value="6">6</option>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	231 </param>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	232 </when>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	233 </conditional>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	234 <conditional name="db_type">
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	235 <param name="db_type_selector" type="select" label="Protein Reference Database from" help="" >
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	236 <option value="history">history</option>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	237 <option value="download">download</option>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	238 </param>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	239 <when value="history">
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	240 <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." />
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	241 </when>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	242 <when value="download">
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	243 <param name="db_id" type="text" value="" label="Public protein sequence database">
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	244 <help>Currently supported dowloads: gencode:human, swissprot:human, refseq:human</help>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	245 <option value="gencode:human">gencode:human</option>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	246 <option value="swissprot:human">swissprot:human</option>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	247 <option value="refseq:human">refseq:human</option>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	248 <validator type="regex" message="">^(swissprot\|refseq\|gencode):(human)$</validator>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	249 </param>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	250 </when>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	251 </conditional>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	252 <conditional name="ms_dataset">
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	253 <param name="ms_dataset_type" type="select" label="MS/MS dataset to search" help="" >
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	254 <option value="history"> Spectrum Datasets from history</option>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	255 <option value="indexed">Indexed MS/MS spectrums</option>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	256 <option value="PepQueryDB">PepQueryDB</option>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	257 <option value="public">public proteomics data repositories</option>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	258 </param>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	259 <when value="history">
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	260 <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" />
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	261 </when>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	262 <when value="indexed">
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	263 <param name="index" argument="-ms" type="data" format="txt" label="PepQuery Index" help="" />
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	264 </when>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	265 <when value="PepQueryDB">
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	266 <param name="dataset" argument="-b" type="text" value="" label="PepQueryDB dataset">
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	267 <help>PepQueryDB dataset IDs (separated by commas).</help>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	268 <expand macro="pepquerydb_options" />
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	269 <validator type="regex" message="PepQueryDB dataset_name(,dataset_name)">^[a-zA-Z][^,](,[a-zA-Z][^,])*$</validator>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	270 </param>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	271 </when>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	272 <when value="public">
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	273 <param name="dataset" type="text" value="" label="Public dataset">
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	274 <validator type="regex" message="An identifier strating with PXD or MSV or JPST">^(PXD\|MSV\|JPST).*$</validator>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	275 </param>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	276 </when>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	277 </conditional>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	278
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	279 <param name="indexType" argument="-indexType" type="select" optional="true" label="Report Spectrum Scan as" help="Default: index" >
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	280 <option value="1">index (1-based) in MGF</option>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	281 <option value="2">spectrum title in MGF</option>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	282 </param>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	283 </section>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	284
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	285 <param name="parameter_set" argument="-p" type="text" value="" optional="true" label="MS/MS searching parameter set name">
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	286 <help>Currently supported set names start with: MS1 or TMT</help>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	287 <option value="MS1_H_MS2_H_LF">MS1_H_MS2_H_LF</option>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	288 <option value="MS1_H_MS2_L_LF">MS1_H_MS2_L_LF</option>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	289 <option value="TMT10_11">TMT10_11</option>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	290 <option value="TMT10_11_MS2_L">TMT10_11_MS2_L</option>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	291 <option value="TMT10_11_MS2_L_phosphorylation">TMT10_11_MS2_L_phosphorylation</option>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	292 <option value="TMT10_11_acetylation">TMT10_11_acetylation</option>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	293 <option value="TMT10_11_glycosylation">TMT10_11_glycosylation</option>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	294 <option value="TMT10_11_phosphorylation">TMT10_11_phosphorylation</option>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	295 <option value="TMT10_11_ubiquitination">TMT10_11_ubiquitination</option>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	296 </param>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	297
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	298 <section name="modifications" title="Modifications" expanded="false">
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	299 <param name="fixed_mod" argument="-fixMod" type="select" label="Fixed modification(s)" multiple="true" optional="true">
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	300 <help>Default: 1: Carbamidomethylation of C [57.02146372057]</help>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	301 <expand macro="modifications" />
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	302 </param>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	303 <param name="var_mod" argument="-varMod" type="select" label="Variable modification(s)" multiple="true" optional="true">
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	304 <help>Default: 2: Oxidation of M [15.99491461956]</help>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	305 <expand macro="modifications" />
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	306 </param>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	307
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	308 <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" />
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	309 <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)" />
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	310 <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." />
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	311 </section>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	312
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	313 <section name="digestion" title="Digestion" expanded="false">
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	314 <param name="enzyme" argument="-e" type="select" optional="true" label="Enzyme" help="Enzyme used for protein digestion. Default: Trypsin" >
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	315 <option value="0">Non enzyme</option>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	316 <option value="1">Trypsin</option>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	317 <option value="2">Trypsin (no P rule)</option>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	318 <option value="3">Arg-C</option>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	319 <option value="4">Arg-C (no P rule)</option>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	320 <option value="5">Arg-N</option>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	321 <option value="6">Glu-C</option>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	322 <option value="7">Lys-C</option>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	323 </param>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	324 <param name="max_missed_cleavages" argument="-c" type="integer" value="" optional="true" label="Max Missed Cleavages" help="The max missed cleavages" />
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	325 </section>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	326
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	327 <section name="ms_params" title="Mass spectrometer" expanded="false">
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	328 <section name="tolerance_params" title="Tolerance" expanded="true">
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	329 <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" />
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	330 <param name="precursor_unit" argument="-tolu" type="select" optional="true" label="Precursor Unit" help="The unit of precursor ion m/z tolerance. Default: ppm">
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	331 <option value="ppm">ppm</option>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	332 <option value="Da">Da</option>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	333 </param>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	334 <param name="tolerance" argument="-itol" type="float" value="" optional="true" label="Tolerance" help="Error window for MS/MS fragment ion mass values in Da unit. Default: 0.6 Da" />
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	335 </section>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	336
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	337 <section name="search" title="PSM" expanded="false">
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	338 <param name="frag_method" argument="-fragmentMethod" type="select" optional="true" label="Fragmentation Method" help="Default: CID/HCD">
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	339 <option value="1">CID/HCD</option>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	340 <option value="2">ETD</option>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	341 </param>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	342 <param name="scoring_method" argument="-m" type="select" optional="true" label="Scoring Method" help="Default: HyperScore">
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	343 <option value="1">HyperScore</option>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	344 <option value="2">MVH</option>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	345 </param>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	346 <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" />
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	347 <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"/>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	348 <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: 3" />
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	349 <param name="min_peaks" argument="-minPeaks" type="integer" value="" optional="true" label="Minimum Peaks" help="Min peaks in spectrum. Default: 10" />
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	350 <param name="isotope_error" argument="-ti" type="text" value="" optional="true" label="Isotope peak error range">
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	351 <help>A comma-sepated range of integers from -2 to 2, e.g. '-1,0,1,2' Default: 0</help>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	352 <validator type="regex" message="">^((-2,)?-1,)?0(,1(,2)?)?$</validator>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	353 </param>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	354 <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" />
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	355 <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" />
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	356 <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" />
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	357 <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" />
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	358 </section>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	359 </section>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	360
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	361 <param name="outputs_selected" type="select" multiple="true" optional="false" label="Select outputs">
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	362 <option value="psm.txt">psm.txt</option>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	363 <option value="psm_rank.txt" selected="true">psm_rank.txt</option>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	364 <option value="psm_rank.mgf">psm_rank.mgf</option>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	365 <option value="psm_annotation.txt">psm_annotation.txt</option>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	366 <option value="psm_type.txt">psm_type.txt</option>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	367 <option value="detail.txt">detail.txt</option>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	368 <option value="ptm.txt">ptm.txt</option>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	369 <option value="ptm_detail.txt">ptm_detail.txt</option>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	370 <option value="ms_index">MS/MS Index</option>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	371 </param>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	372 <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." />
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	373 </inputs>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	374 <outputs>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	375 <data name="log_txt" format="txt" from_work_dir="log.txt" label="${tool.name} on ${on_string}: log.txt">
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	376 </data>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	377 <data name="parameter_txt" format="txt" from_work_dir="pepquery_output/parameter.txt" label="${tool.name} on ${on_string}: parameter.txt">
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	378 <filter>'parameter.txt' in outputs_selected and req_inputs['ms_dataset']['ms_dataset_type'] == 'history'</filter>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	379 </data>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	380 <data name="ms_index" format="txt" label="${tool.name} on ${on_string}: index summary.txt" from_work_dir="index_dir/summary.txt">
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	381 <filter>'ms_index' in outputs_selected and req_inputs['ms_dataset']['ms_dataset_type'] == 'history'</filter>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	382 </data>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	383 <data name="psm_txt" format="tabular" from_work_dir="pepquery_output/psm.txt" label="${tool.name} on ${on_string}: psm.txt">
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	384 <filter>'psm.txt' in outputs_selected</filter>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	385 <actions>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	386 <action name="comment_lines" type="metadata" default="1" />
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	387 <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" />
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	388 </actions>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	389 </data>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	390
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	391 <data name="psm_rank_txt" format="tabular" from_work_dir="pepquery_output/psm_rank.txt" label="${tool.name} on ${on_string}: psm_rank.txt">
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	392 <filter>'psm_rank.txt' in outputs_selected</filter>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	393 <actions>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	394 <action name="comment_lines" type="metadata" default="1" />
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	395 <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" />
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	396 </actions>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	397 </data>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	398
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	399 <data name="psm_rank_mgf" format="mgf" from_work_dir="pepquery_output/psm_rank.mgf" label="${tool.name} on ${on_string}: psm_rank.mgf">
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	400 <filter>'psm_rank.mgf' in outputs_selected</filter>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	401 </data>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	402 <data name="psm_type_txt" format="tabular" from_work_dir="pepquery_output/psmi_type.txt" label="${tool.name} on ${on_string}: psm_type.txt">
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	403 <filter>'psm_type.txt' in outputs_selected</filter>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	404 <actions>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	405 <action name="comment_lines" type="metadata" default="1" />
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	406 <action name="column_names" type="metadata" default="peptide,spectrum_title,type" />
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	407 </actions>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	408 </data>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	409 <data name="psm_annotation_txt" format="tabular" from_work_dir="pepquery_output/psm_annotation.txt" label="${tool.name} on ${on_string}: psm_annotation.txt">
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	410 <filter>'psm_annotation.txt' in outputs_selected</filter>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	411 <actions>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	412 <action name="comment_lines" type="metadata" default="1" />
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	413 <action name="column_names" type="metadata" default="peptide,modification,Query,calc_mr,observed_mz,charge,pepSeq,m_label,m_mz,m_intensity,mz,intensity" />
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	414 </actions>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	415 </data>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	416 <data name="detail_txt" format="tabular" from_work_dir="pepquery_output/detail.txt" label="${tool.name} on ${on_string}: detail.txt">
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	417 <filter>'detail.txt' in outputs_selected</filter>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	418 <actions>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	419 <action name="comment_lines" type="metadata" default="1" />
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	420 <action name="column_names" type="metadata" default="spectrum_title,peptide,modification,exp_mass,pep_mass,tol_ppm,tol_da,isotope_error,score" />
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	421 </actions>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	422 </data>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	423
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	424 <data name="ptm_txt" format="tabular" from_work_dir="pepquery_output/ptm.txt" label="${tool.name} on ${on_string}: ptm.txt">
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	425 <filter>'ptm.txt' in outputs_selected</filter>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	426 <actions>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	427 <action name="comment_lines" type="metadata" default="1" />
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	428 <action name="column_names" type="metadata" default="spectrum_title,peptide,charge,exp_mass,pep_mass,tol_ppm,tol_da,isotope_error,modification,score" />
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	429 </actions>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	430 </data>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	431 <data name="ptm_detail_txt" format="tabular" from_work_dir="pepquery_output/ptm_detail.txt" label="${tool.name} on ${on_string}: ptm_detail.txt">
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	432 <filter>'ptm_detail.txt' in outputs_selected</filter>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	433 <actions>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	434 <action name="comment_lines" type="metadata" default="1" />
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	435 <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" />
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	436 </actions>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	437 </data>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	438
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	439 </outputs>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	440 <tests>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	441 <!-- Test-1 PepQueryDB peptide gencode:human -->
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	442 <test expect_num_outputs="2">
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	443 <conditional name="validation">
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	444 <param name="task_type" value="novel"/>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	445 </conditional>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	446 <section name="req_inputs">
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	447 <conditional name="input_type">
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	448 <param name="input_type_selector" value="peptide"/>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	449 <conditional name="multiple">
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	450 <param name="peptide_input_selector" value="single" />
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	451 <param name="input" value="LVVVGADGVGK,AHSSMVGVNLPQK"/>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	452 </conditional>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	453 </conditional>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	454 <conditional name="db_type">
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	455 <param name="db_type_selector" value="download" />
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	456 <param name="db_id" value="gencode:human"/>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	457 </conditional>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	458 <conditional name="ms_dataset">
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	459 <param name="ms_dataset_type" value="PepQueryDB"/>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	460 <param name="dataset" value="CPTAC_LUAD_Discovery_Study_Proteome_PDC000153" />
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	461 </conditional>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	462 <param name="indexType" value="1"/>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	463 </section>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	464 <param name="parameter_set" value=""/>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	465 <section name="modifications">
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	466 <param name="fixed_mod" value="1"/>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	467 <param name="var_mod" value="2"/>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	468 <param name="max_mods" value="3"/>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	469 <param name="unmodified" value="True"/>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	470 <param name="aa" value="False"/>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	471 </section>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	472 <section name="digestion">
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	473 <param name="enzyme" value="1"/>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	474 <param name="max_missed_cleavages" value="2"/>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	475 </section>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	476 <section name="ms_params">
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	477 <section name="tolerance_params">
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	478 <param name="precursor_tolerance" value="10"/>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	479 <param name="precursor_unit" value="ppm"/>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	480 <param name="tolerance" value="0.6"/>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	481 </section>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	482 <section name="search">
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	483 <param name="frag_method" value="1"/>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	484 <param name="scoring_method" value="1"/>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	485 <param name="extra_score_validation" value="False"/>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	486 <param name="min_charge" value="2"/>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	487 <param name="max_charge" value="3"/>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	488 <param name="min_peaks" value="10"/>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	489 <param name="isotope_error" value="0"/>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	490 <param name="min_score" value="12"/>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	491 <param name="min_length" value="7"/>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	492 <param name="max_length" value="45"/>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	493 <param name="num_random_peptides" value="1000"/>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	494 </section>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	495 </section>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	496 <output name="psm_rank_txt">
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	497 <assert_contents>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	498 <has_text text="LVVVGADGVGK" />
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	499 <not_has_text text="AHSSMVGVNLPQK" />
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	500 <has_text text="02CPTAC_LUAD_W_BI_20180518_KR_f15:25149:2" />
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	501 <has_n_columns n="22" />
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	502 </assert_contents>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	503 </output>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	504 <output name="log_txt">
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	505 <assert_contents>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	506 <has_text text="Ignore peptide (reason: exist in reference database): AHSSMVGVNLPQK" />
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	507 </assert_contents>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	508 </output>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	509 </test>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	510
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	511 <!-- Test-2 PepQueryDB peptide gencode:human pep.txt -->
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	512 <test expect_num_outputs="2">
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	513 <conditional name="validation">
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	514 <param name="task_type" value="novel"/>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	515 </conditional>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	516 <section name="req_inputs">
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	517 <conditional name="input_type">
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	518 <param name="input_type_selector" value="peptide"/>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	519 <conditional name="multiple">
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	520 <param name="peptide_input_selector" value="multiple" />
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	521 <param name="input" ftype="tabular" value="pep.txt"/>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	522 </conditional>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	523 </conditional>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	524 <conditional name="db_type">
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	525 <param name="db_type_selector" value="download" />
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	526 <param name="db_id" value="gencode:human"/>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	527 </conditional>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	528 <conditional name="ms_dataset">
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	529 <param name="ms_dataset_type" value="PepQueryDB"/>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	530 <param name="dataset" value="CPTAC_LUAD_Discovery_Study_Proteome_PDC000153" />
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	531 </conditional>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	532 <param name="indexType" value="1"/>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	533 </section>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	534 <param name="parameter_set" value=""/>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	535 <section name="modifications">
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	536 <param name="fixed_mod" value="1"/>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	537 <param name="var_mod" value="2"/>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	538 <param name="max_mods" value="3"/>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	539 <param name="unmodified" value="True"/>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	540 <param name="aa" value="False"/>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	541 </section>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	542 <section name="digestion">
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	543 <param name="enzyme" value="1"/>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	544 <param name="max_missed_cleavages" value="2"/>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	545 </section>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	546 <section name="ms_params">
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	547 <section name="tolerance_params">
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	548 <param name="precursor_tolerance" value="10"/>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	549 <param name="precursor_unit" value="ppm"/>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	550 <param name="tolerance" value="0.6"/>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	551 </section>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	552 <section name="search">
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	553 <param name="frag_method" value="1"/>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	554 <param name="scoring_method" value="1"/>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	555 <param name="extra_score_validation" value="False"/>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	556 <param name="min_charge" value="2"/>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	557 <param name="max_charge" value="3"/>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	558 <param name="min_peaks" value="10"/>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	559 <param name="isotope_error" value="0"/>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	560 <param name="min_score" value="12"/>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	561 <param name="min_length" value="7"/>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	562 <param name="max_length" value="45"/>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	563 <param name="num_random_peptides" value="1000"/>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	564 </section>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	565 </section>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	566 <output name="psm_rank_txt">
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	567 <assert_contents>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	568 <has_text text="LVVVGADGVGK" />
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	569 <not_has_text text="AHSSMVGVNLPQK" />
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	570 <has_text text="02CPTAC_LUAD_W_BI_20180518_KR_f15:25149:2" />
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	571 <has_n_columns n="22" />
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	572 </assert_contents>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	573 </output>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	574 <output name="log_txt">
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	575 <assert_contents>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	576 <has_text text="Ignore peptide (reason: exist in reference database): AHSSMVGVNLPQK" />
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	577 </assert_contents>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	578 </output>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	579 </test>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	580
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	581 <!-- Test-3 MGF peptide Uniprot.fasta -->
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	582 <test expect_num_outputs="2">
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	583 <conditional name="validation">
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	584 <param name="task_type" value="novel"/>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	585 </conditional>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	586 <section name="req_inputs">
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	587 <conditional name="input_type">
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	588 <param name="input_type_selector" value="peptide"/>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	589 <conditional name="multiple">
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	590 <param name="peptide_input_selector" value="single" />
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	591 <param name="input" value="ELGSSDLTAR"/>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	592 </conditional>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	593 </conditional>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	594 <conditional name="db_type">
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	595 <param name="db_type_selector" value="history" />
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	596 <param name="db_file" ftype="fasta" value="Uniprot.fasta"/>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	597 </conditional>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	598 <conditional name="ms_dataset">
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	599 <param name="ms_dataset_type" value="history"/>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	600 <param name="spectrum_files" ftype="mgf" value="iTRAQ_f4.mgf"/>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	601 </conditional>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	602 <param name="indexType" value="1"/>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	603 </section>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	604 <param name="parameter_set" value=""/>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	605 <section name="modifications">
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	606 <!-- 21: iTRAQ 4-plex of K [144.1020624208] -->
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	607 <!-- 22: iTRAQ 4-plex of peptide N-term [144.1020624208] -->
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	608 <param name="fixed_mod" value="1,21,22"/>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	609 <!-- 2: Oxidation of M [15.99491461956] -->
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	610 <param name="var_mod" value="2"/>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	611 <param name="max_mods" value="3"/>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	612 <param name="unmodified" value="True"/>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	613 <param name="aa" value="False"/>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	614 </section>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	615 <section name="digestion">
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	616 <param name="enzyme" value="1"/>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	617 <param name="max_missed_cleavages" value="2"/>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	618 </section>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	619 <section name="ms_params">
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	620 <section name="tolerance_params">
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	621 <param name="precursor_tolerance" value="10"/>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	622 <param name="precursor_unit" value="ppm"/>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	623 <param name="tolerance" value="0.6"/>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	624 </section>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	625 <section name="search">
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	626 <param name="frag_method" value="1"/>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	627 <param name="scoring_method" value="1"/>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	628 <param name="extra_score_validation" value="False"/>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	629 <param name="min_charge" value="2"/>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	630 <param name="max_charge" value="3"/>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	631 <param name="min_peaks" value="10"/>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	632 <param name="isotope_error" value="0"/>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	633 <param name="min_score" value="12"/>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	634 <param name="min_length" value="7"/>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	635 <param name="max_length" value="45"/>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	636 <param name="num_random_peptides" value="1000"/>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	637 </section>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	638 </section>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	639 <output name="psm_rank_txt">
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	640 <assert_contents>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	641 <has_text text="ELGSSDLTAR" />
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	642 <has_line_matching expression="ELGSSDLTAR\tiTRAQ 4-plex of peptide N-term@0\[144.1\d+\]\t2\tiTRAQ_f4:3:2\t2\t1191.62\d+\t-3.04\d+\t-0.003\d+\t0.0\t1191.6\d+\t596.8\d+\t24.1\d+\t0\t0\t1\t995\t0.002\d+\t1\t0\tYes\t24.1\d+\t24.1\d+"/>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	643 <has_n_columns n="22" />
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	644 </assert_contents>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	645 </output>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	646 </test>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	647
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	648 <!-- Test-4 PepQueryDB known peptide gencode:human pep.txt -->
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	649 <test expect_num_outputs="2">
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	650 <conditional name="validation">
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	651 <param name="task_type" value="known"/>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	652 </conditional>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	653 <section name="req_inputs">
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	654 <conditional name="input_type">
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	655 <param name="input_type_selector" value="peptide"/>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	656 <conditional name="multiple">
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	657 <param name="peptide_input_selector" value="single" />
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	658 <param name="input" value="AHSSMVGVNLPQK"/>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	659 </conditional>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	660 </conditional>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	661 <conditional name="db_type">
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	662 <param name="db_type_selector" value="download" />
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	663 <param name="db_id" value="gencode:human"/>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	664 </conditional>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	665 <conditional name="ms_dataset">
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	666 <param name="ms_dataset_type" value="PepQueryDB"/>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	667 <param name="dataset" value="CPTAC_LUAD_Discovery_Study_Proteome_PDC000153" />
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	668 </conditional>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	669 <param name="indexType" value="1"/>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	670 </section>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	671 <section name="modifications">
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	672 <param name="unmodified" value="True"/>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	673 </section>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	674 <output name="psm_rank_txt">
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	675 <assert_contents>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	676 <has_text text="AHSSMVGVNLPQK" />
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	677 <has_text text="6CPTAC_LUAD_W_BI_20180718_KL_f12:20286:3" />
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	678 <has_n_columns n="22" />
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	679 </assert_contents>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	680 </output>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	681 </test>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	682
1 b5489f81c2fa planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit fb66172091bb840e4cb673975fd1ebbfd8dcf3f7 galaxyp parents: 0 diff changeset	683 <!-- Test-5 Non-enzyme search -->
b5489f81c2fa planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit fb66172091bb840e4cb673975fd1ebbfd8dcf3f7 galaxyp parents: 0 diff changeset	684 <test expect_num_outputs="2">
b5489f81c2fa planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit fb66172091bb840e4cb673975fd1ebbfd8dcf3f7 galaxyp parents: 0 diff changeset	685 <conditional name="validation">
b5489f81c2fa planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit fb66172091bb840e4cb673975fd1ebbfd8dcf3f7 galaxyp parents: 0 diff changeset	686 <param name="task_type" value="novel"/>
b5489f81c2fa planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit fb66172091bb840e4cb673975fd1ebbfd8dcf3f7 galaxyp parents: 0 diff changeset	687 </conditional>
b5489f81c2fa planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit fb66172091bb840e4cb673975fd1ebbfd8dcf3f7 galaxyp parents: 0 diff changeset	688 <section name="req_inputs">
b5489f81c2fa planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit fb66172091bb840e4cb673975fd1ebbfd8dcf3f7 galaxyp parents: 0 diff changeset	689 <conditional name="input_type">
b5489f81c2fa planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit fb66172091bb840e4cb673975fd1ebbfd8dcf3f7 galaxyp parents: 0 diff changeset	690 <param name="input_type_selector" value="peptide"/>
b5489f81c2fa planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit fb66172091bb840e4cb673975fd1ebbfd8dcf3f7 galaxyp parents: 0 diff changeset	691 <conditional name="multiple">
b5489f81c2fa planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit fb66172091bb840e4cb673975fd1ebbfd8dcf3f7 galaxyp parents: 0 diff changeset	692 <param name="peptide_input_selector" value="single" />
b5489f81c2fa planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit fb66172091bb840e4cb673975fd1ebbfd8dcf3f7 galaxyp parents: 0 diff changeset	693 <param name="input" value="ELGSSDLTAR"/>
b5489f81c2fa planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit fb66172091bb840e4cb673975fd1ebbfd8dcf3f7 galaxyp parents: 0 diff changeset	694 </conditional>
b5489f81c2fa planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit fb66172091bb840e4cb673975fd1ebbfd8dcf3f7 galaxyp parents: 0 diff changeset	695 </conditional>
b5489f81c2fa planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit fb66172091bb840e4cb673975fd1ebbfd8dcf3f7 galaxyp parents: 0 diff changeset	696 <conditional name="db_type">
b5489f81c2fa planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit fb66172091bb840e4cb673975fd1ebbfd8dcf3f7 galaxyp parents: 0 diff changeset	697 <param name="db_type_selector" value="history" />
b5489f81c2fa planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit fb66172091bb840e4cb673975fd1ebbfd8dcf3f7 galaxyp parents: 0 diff changeset	698 <param name="db_file" ftype="fasta" value="Uniprot.fasta"/>
b5489f81c2fa planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit fb66172091bb840e4cb673975fd1ebbfd8dcf3f7 galaxyp parents: 0 diff changeset	699 </conditional>
b5489f81c2fa planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit fb66172091bb840e4cb673975fd1ebbfd8dcf3f7 galaxyp parents: 0 diff changeset	700 <conditional name="ms_dataset">
b5489f81c2fa planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit fb66172091bb840e4cb673975fd1ebbfd8dcf3f7 galaxyp parents: 0 diff changeset	701 <param name="ms_dataset_type" value="history"/>
b5489f81c2fa planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit fb66172091bb840e4cb673975fd1ebbfd8dcf3f7 galaxyp parents: 0 diff changeset	702 <param name="spectrum_files" ftype="mgf" value="iTRAQ_f4.mgf"/>
b5489f81c2fa planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit fb66172091bb840e4cb673975fd1ebbfd8dcf3f7 galaxyp parents: 0 diff changeset	703 </conditional>
b5489f81c2fa planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit fb66172091bb840e4cb673975fd1ebbfd8dcf3f7 galaxyp parents: 0 diff changeset	704 <param name="indexType" value="1"/>
b5489f81c2fa planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit fb66172091bb840e4cb673975fd1ebbfd8dcf3f7 galaxyp parents: 0 diff changeset	705 </section>
b5489f81c2fa planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit fb66172091bb840e4cb673975fd1ebbfd8dcf3f7 galaxyp parents: 0 diff changeset	706 <param name="parameter_set" value=""/>
b5489f81c2fa planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit fb66172091bb840e4cb673975fd1ebbfd8dcf3f7 galaxyp parents: 0 diff changeset	707 <section name="modifications">
b5489f81c2fa planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit fb66172091bb840e4cb673975fd1ebbfd8dcf3f7 galaxyp parents: 0 diff changeset	708 <!-- 21: iTRAQ 4-plex of K [144.1020624208] -->
b5489f81c2fa planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit fb66172091bb840e4cb673975fd1ebbfd8dcf3f7 galaxyp parents: 0 diff changeset	709 <!-- 22: iTRAQ 4-plex of peptide N-term [144.1020624208] -->
b5489f81c2fa planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit fb66172091bb840e4cb673975fd1ebbfd8dcf3f7 galaxyp parents: 0 diff changeset	710 <param name="fixed_mod" value="1,21,22"/>
b5489f81c2fa planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit fb66172091bb840e4cb673975fd1ebbfd8dcf3f7 galaxyp parents: 0 diff changeset	711 <!-- 2: Oxidation of M [15.99491461956] -->
b5489f81c2fa planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit fb66172091bb840e4cb673975fd1ebbfd8dcf3f7 galaxyp parents: 0 diff changeset	712 <param name="var_mod" value="2"/>
b5489f81c2fa planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit fb66172091bb840e4cb673975fd1ebbfd8dcf3f7 galaxyp parents: 0 diff changeset	713 <param name="max_mods" value="3"/>
b5489f81c2fa planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit fb66172091bb840e4cb673975fd1ebbfd8dcf3f7 galaxyp parents: 0 diff changeset	714 <param name="unmodified" value="True"/>
b5489f81c2fa planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit fb66172091bb840e4cb673975fd1ebbfd8dcf3f7 galaxyp parents: 0 diff changeset	715 <param name="aa" value="False"/>
b5489f81c2fa planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit fb66172091bb840e4cb673975fd1ebbfd8dcf3f7 galaxyp parents: 0 diff changeset	716 </section>
b5489f81c2fa planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit fb66172091bb840e4cb673975fd1ebbfd8dcf3f7 galaxyp parents: 0 diff changeset	717 <section name="digestion">
b5489f81c2fa planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit fb66172091bb840e4cb673975fd1ebbfd8dcf3f7 galaxyp parents: 0 diff changeset	718 <param name="enzyme" value="0"/>
b5489f81c2fa planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit fb66172091bb840e4cb673975fd1ebbfd8dcf3f7 galaxyp parents: 0 diff changeset	719 </section>
b5489f81c2fa planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit fb66172091bb840e4cb673975fd1ebbfd8dcf3f7 galaxyp parents: 0 diff changeset	720 <section name="ms_params">
b5489f81c2fa planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit fb66172091bb840e4cb673975fd1ebbfd8dcf3f7 galaxyp parents: 0 diff changeset	721 <section name="tolerance_params">
b5489f81c2fa planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit fb66172091bb840e4cb673975fd1ebbfd8dcf3f7 galaxyp parents: 0 diff changeset	722 <param name="precursor_tolerance" value="10"/>
b5489f81c2fa planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit fb66172091bb840e4cb673975fd1ebbfd8dcf3f7 galaxyp parents: 0 diff changeset	723 <param name="precursor_unit" value="ppm"/>
b5489f81c2fa planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit fb66172091bb840e4cb673975fd1ebbfd8dcf3f7 galaxyp parents: 0 diff changeset	724 <param name="tolerance" value="0.6"/>
b5489f81c2fa planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit fb66172091bb840e4cb673975fd1ebbfd8dcf3f7 galaxyp parents: 0 diff changeset	725 </section>
b5489f81c2fa planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit fb66172091bb840e4cb673975fd1ebbfd8dcf3f7 galaxyp parents: 0 diff changeset	726 <section name="search">
b5489f81c2fa planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit fb66172091bb840e4cb673975fd1ebbfd8dcf3f7 galaxyp parents: 0 diff changeset	727 <param name="frag_method" value="1"/>
b5489f81c2fa planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit fb66172091bb840e4cb673975fd1ebbfd8dcf3f7 galaxyp parents: 0 diff changeset	728 <param name="scoring_method" value="1"/>
b5489f81c2fa planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit fb66172091bb840e4cb673975fd1ebbfd8dcf3f7 galaxyp parents: 0 diff changeset	729 <param name="extra_score_validation" value="False"/>
b5489f81c2fa planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit fb66172091bb840e4cb673975fd1ebbfd8dcf3f7 galaxyp parents: 0 diff changeset	730 <param name="min_charge" value="2"/>
b5489f81c2fa planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit fb66172091bb840e4cb673975fd1ebbfd8dcf3f7 galaxyp parents: 0 diff changeset	731 <param name="max_charge" value="3"/>
b5489f81c2fa planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit fb66172091bb840e4cb673975fd1ebbfd8dcf3f7 galaxyp parents: 0 diff changeset	732 <param name="min_peaks" value="10"/>
b5489f81c2fa planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit fb66172091bb840e4cb673975fd1ebbfd8dcf3f7 galaxyp parents: 0 diff changeset	733 <param name="isotope_error" value="0"/>
b5489f81c2fa planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit fb66172091bb840e4cb673975fd1ebbfd8dcf3f7 galaxyp parents: 0 diff changeset	734 <param name="min_score" value="12"/>
b5489f81c2fa planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit fb66172091bb840e4cb673975fd1ebbfd8dcf3f7 galaxyp parents: 0 diff changeset	735 <param name="min_length" value="7"/>
b5489f81c2fa planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit fb66172091bb840e4cb673975fd1ebbfd8dcf3f7 galaxyp parents: 0 diff changeset	736 <param name="max_length" value="45"/>
b5489f81c2fa planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit fb66172091bb840e4cb673975fd1ebbfd8dcf3f7 galaxyp parents: 0 diff changeset	737 <param name="num_random_peptides" value="1000"/>
b5489f81c2fa planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit fb66172091bb840e4cb673975fd1ebbfd8dcf3f7 galaxyp parents: 0 diff changeset	738 </section>
b5489f81c2fa planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit fb66172091bb840e4cb673975fd1ebbfd8dcf3f7 galaxyp parents: 0 diff changeset	739 </section>
b5489f81c2fa planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit fb66172091bb840e4cb673975fd1ebbfd8dcf3f7 galaxyp parents: 0 diff changeset	740 <output name="psm_rank_txt">
b5489f81c2fa planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit fb66172091bb840e4cb673975fd1ebbfd8dcf3f7 galaxyp parents: 0 diff changeset	741 <assert_contents>
b5489f81c2fa planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit fb66172091bb840e4cb673975fd1ebbfd8dcf3f7 galaxyp parents: 0 diff changeset	742 <has_text text="ELGSSDLTAR" />
b5489f81c2fa planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit fb66172091bb840e4cb673975fd1ebbfd8dcf3f7 galaxyp parents: 0 diff changeset	743 <has_line_matching expression="ELGSSDLTAR\tiTRAQ 4-plex of peptide N-term@0\[144.1\d+\]\t2\tiTRAQ_f4:3:2\t2\t1191.62\d+\t-3.04\d+\t-0.003\d+\t0.0\t1191.6\d+\t596.8\d+\t24.1\d+\t0\t13\t1\t995\t0.002\d+\t1\t0\tYes\t10.3\d+\t8.23\d+"/>
b5489f81c2fa planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit fb66172091bb840e4cb673975fd1ebbfd8dcf3f7 galaxyp parents: 0 diff changeset	744 <has_n_columns n="22" />
b5489f81c2fa planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit fb66172091bb840e4cb673975fd1ebbfd8dcf3f7 galaxyp parents: 0 diff changeset	745 </assert_contents>
b5489f81c2fa planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit fb66172091bb840e4cb673975fd1ebbfd8dcf3f7 galaxyp parents: 0 diff changeset	746 </output>
b5489f81c2fa planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit fb66172091bb840e4cb673975fd1ebbfd8dcf3f7 galaxyp parents: 0 diff changeset	747 </test>
b5489f81c2fa planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit fb66172091bb840e4cb673975fd1ebbfd8dcf3f7 galaxyp parents: 0 diff changeset	748
0 a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	749 </tests>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	750 <help><![CDATA[
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	751 PepQuery2
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	752
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	753 PepQuery_ is a universal targeted peptide search engine for identifying or validating known and novel peptides of interest in any local or publicly available mass spectrometry-based proteomics datasets.
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	754
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	755
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	756 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.
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	757
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	758 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.
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	759
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	760 Inputs
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	761 - A sequence to match, one of the following:
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	762
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	763 - A peptide string (or strings separated by commas)
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	764 - A history dataset with a list of peptides
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	765 - A protein string or a history dataset with a protein fasta
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	766 - A DNA string that is at least 60 base pairs in length
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	767
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	768
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	769 - MS/MS data used for identification, one of the following:
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	770
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	771 - Mass Spectrometry history datasets in MGF, mzML, or mzXML format
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	772 - An Indexed MS/MS dataset (from previous PepQuery2 run or from PepQuery2 index tool.)
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	773 - PepQueryDB dataset IDs
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	774
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	775 ..
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	776
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	777 Multiple datasets from PepQueryDB must be separated by comma. A pattern to match datasets in PepQueryDB is also supported, for example, use 'CPTAC' to search all datasets contain 'CPTAC'. In addition, dataset selection from PepQueryDB based on data type (w:global proteome, p:phosphorylation, a:acetylation, u:ubiquitination, g:glycosylation) is also supported. For example, use 'p' to search all phosphoproteomics datasets in PepQueryDB. The PepQuery2 Show Sets tool will list available PepQueryDB datasets.
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	778
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	779
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	780 - Dataset IDs from public proteomics data repositories: PRIDE, MassIVE, jPOSTrepo and iProX
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	781
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	782 ..
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	783
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	784 Dataset ID from public proteomics data repositories, one dataset is supported for each analysis. For example, use 'PXD000529' to use all MS/MS data from dataset PXD000529 or use 'PXD000529:LM3' to use data files containing LM3 from dataset PXD000529
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	785
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	786 - A reference protein fasta database, novel peptides matching a reference sequence will be excluded.
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	787
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	788 - A protein fasta file
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	789 - The ID for a public reference protein database from RefSeq, GENCODE, Ensembl or UniProt.
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	790
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	791
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	792 Options
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	793
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	794 - MS/MS searching parameter set name
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	795
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	796 ..
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	797
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	798 Setting a parameter set name will change defaults for various options, These may be overridden by manually setting the option.
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	799 The PepQuery2 Show Sets tool PepQuery Predefined Parameter Sets will list those available along with the option values that will be set.
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	800 The PepQuery2 Show Sets tool PepQuery Datasets column parameter_set column for each PepQueryDB dataset.
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	801
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	802
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	803 - Override default options
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	804
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	805 ..
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	806
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	807 Values for modifications are provided in a select list.
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	808 The PepQuery2 Show Sets tool PepQuery Modifications lists all available modifications.
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	809
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	810 Outputs
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	811 - Log.txt:
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	812
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	813 - Logging output from PepQuery2
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	814 - When searching for novel peptides ignored peptide have a log message similar to:
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	815
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	816 - Ignore peptide (reason: exist in reference database): PEPTIDE
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	817
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	818 - When searching for known proteins, ignored protein have a log message similar to:
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	819
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	820 - Target protein is not present in database DATABASE_NAME: PROTEIN_NAME, ignored!
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	821
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	822 - Parameters:
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	823
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	824 - parameters used in the search
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	825
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	826 - PSM - tabular with columns:
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	827
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	828 - peptide modification n spectrum_title charge exp_mass ppm pep_mass mz score n_db total_db n_random total_random pvalue
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	829
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	830 - PSM Rank - tabular with columns:
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	831
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	832 - peptide mo/dification n spectrum_title charge exp_mass ppm pep_mass mz score n_db total_db n_random total_random pvalue rank n_ptm
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	833
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	834 - An MGF with the best matching spectrums
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	835
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	836 - Detail - tabular with columns:
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	837
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	838 - spectrum_title peptide modification pep_mass score
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	839
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	840 - PSM annotation - tabular with columns:
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	841
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	842 - peptide Query calc_mr observed_mz charge pepSeq m_label m_mz m_intensity mz intensity
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	843
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	844 - PTM - tabular with columns:
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	845
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	846 - spectrum_title peptide charge exp_mass pep_mass tol_ppm tol_da isotope_error modification score
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	847
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	848 - PTM Detail - tabular with columns:
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	849
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	850 - 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
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	851
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	852 - An Indexed MS/MS dataset when MS/MS data is MGF, mzML, or mzXML history datasets
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	853
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	854
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	855 .. _PepQuery: http://pepquery.org/document.html
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	856
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	857 ]]></help>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	858 <expand macro="citations" />
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597 galaxyp parents: diff changeset	859 </tool>

Mercurial > repos > galaxyp > pepquery2

annotate pepquery2.xml @ 1:b5489f81c2fa draft