Mercurial > repos > galaxyp > pepquery2

annotate pepquery2.xml @ 6:01fd80b15053 draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
author galaxyp
date Sun, 06 Nov 2022 16:23:05 +0000
parents 2045f3b68773
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
parents:
diff changeset
1 <tool id="pepquery2" name="PepQuery2" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
parents:
diff changeset
2 <description>Peptide-centric search engine for novel peptide identification and validation.</description>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
parents:
diff changeset
3 <macros>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
parents:
diff changeset
4 <import>macros.xml</import>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
parents:
diff changeset
5 </macros>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
parents:
diff changeset
6 <requirements>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
parents:
diff changeset
7 <requirement type="package" version="@TOOL_VERSION@">pepquery</requirement>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
parents:
diff changeset
8 </requirements>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
parents:
diff changeset
9 <stdio>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
parents:
diff changeset
10 <exit_code range="1:" level="fatal" description="Failed" />
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
parents:
diff changeset
11 <regex match="Exception"
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
parents:
diff changeset
12 source="stderr"
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
parents:
diff changeset
13 level="fatal"
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
parents:
diff changeset
14 description="java Exception" />
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
parents:
diff changeset
15 </stdio>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
parents:
diff changeset
16 <command><![CDATA[
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
parents:
diff changeset
17 @CMD_IMPORTS@
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
parents:
diff changeset
18 #if $req_inputs.db_type.db_type_selector == 'history'
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
parents:
diff changeset
19 #set $db_file = $re.sub('\s','_',$re.sub('[.][^.]*$','',$req_inputs.db_type.db_file.display_name.split('/')[-1])) + ".fa"
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
parents:
diff changeset
20 ln -s '$req_inputs.db_type.db_file' '$db_file' &&
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
parents:
diff changeset
21 #end if
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
parents:
diff changeset
22 #if $req_inputs.ms_dataset.ms_dataset_type == 'history'
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
parents:
diff changeset
23 @INDEX_SPECTRUM_FILES@
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
parents:
diff changeset
24 $index_spectrum_files($ms_index.files_path, $req_inputs.ms_dataset.spectrum_files) &&
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
parents:
diff changeset
25 #elif $req_inputs.ms_dataset.ms_dataset_type == 'indexed'
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
parents:
diff changeset
26 #if $os.path.exists($os.path.join($req_inputs.ms_dataset.index.extra_files_path, 'summary.txt'))
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
parents:
diff changeset
27 #set $index_dir = 'index_dir'
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
parents:
diff changeset
28 ln -s '$req_inputs.ms_dataset.index.extra_files_path' index_dir &&
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
parents:
diff changeset
29 #else
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
parents:
diff changeset
30 #raise ValueError
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
parents:
diff changeset
31 #end if
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
parents:
diff changeset
32 #end if
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
parents:
diff changeset
33 ## PepQuery command
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
parents:
diff changeset
34 pepquery
2
3b2874c58bcd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit b0bcec3ad7b4b4c682cfdf9257fe04f55dda8071
galaxyp
parents: 1
diff changeset
35 -Xmx\$[ \${GALAXY_MEMORY_MB:-8192} / 1024 ]g
0
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
parents:
diff changeset
36 #if $validation.task_type == "known"
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
parents:
diff changeset
37 -s 2 $validation.decoy
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
parents:
diff changeset
38 #else
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
parents:
diff changeset
39 -s 1
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
parents:
diff changeset
40 #end if
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
parents:
diff changeset
41 #if $req_inputs.ms_dataset.ms_dataset_type in ['history', 'indexed']
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
parents:
diff changeset
42 -ms '$index_dir'
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
parents:
diff changeset
43 #elif $req_inputs.ms_dataset.ms_dataset_type in ['PepQueryDB', 'public']
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
parents:
diff changeset
44 -b '$req_inputs.ms_dataset.dataset'
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
parents:
diff changeset
45 #end if
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
parents:
diff changeset
46
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
parents:
diff changeset
47 #if $req_inputs.db_type.db_type_selector == 'history'
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
parents:
diff changeset
48 -db '$db_file'
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
parents:
diff changeset
49 #else
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
parents:
diff changeset
50 -db '$req_inputs.db_type.db_id'
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
parents:
diff changeset
51 #end if
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
parents:
diff changeset
52 #if $req_inputs.input_type.input_type_selector == 'peptide'
2
3b2874c58bcd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit b0bcec3ad7b4b4c682cfdf9257fe04f55dda8071
galaxyp
parents: 1
diff changeset
53 -t $req_inputs.input_type.input_type_selector
0
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
parents:
diff changeset
54 -i '$req_inputs.input_type.multiple.input'
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
parents:
diff changeset
55 #else
2
3b2874c58bcd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit b0bcec3ad7b4b4c682cfdf9257fe04f55dda8071
galaxyp
parents: 1
diff changeset
56 -t $req_inputs.input_type.input_type_selector
3b2874c58bcd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit b0bcec3ad7b4b4c682cfdf9257fe04f55dda8071
galaxyp
parents: 1
diff changeset
57 #if $req_inputs.input_type.input_type_selector == 'protein'
3b2874c58bcd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit b0bcec3ad7b4b4c682cfdf9257fe04f55dda8071
galaxyp
parents: 1
diff changeset
58 #if $req_inputs.input_type.multiple.protein_input_selector == 'identifier'
3b2874c58bcd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit b0bcec3ad7b4b4c682cfdf9257fe04f55dda8071
galaxyp
parents: 1
diff changeset
59 #set $prot_id = str($req_inputs.input_type.multiple.input).replace('|','\|')
3b2874c58bcd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit b0bcec3ad7b4b4c682cfdf9257fe04f55dda8071
galaxyp
parents: 1
diff changeset
60 -i '"$prot_id"'
3b2874c58bcd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit b0bcec3ad7b4b4c682cfdf9257fe04f55dda8071
galaxyp
parents: 1
diff changeset
61 #else
3b2874c58bcd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit b0bcec3ad7b4b4c682cfdf9257fe04f55dda8071
galaxyp
parents: 1
diff changeset
62 -i '$req_inputs.input_type.multiple.input'
3b2874c58bcd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit b0bcec3ad7b4b4c682cfdf9257fe04f55dda8071
galaxyp
parents: 1
diff changeset
63 #end if
0
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
parents:
diff changeset
64 #else
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
parents:
diff changeset
65 -i '$req_inputs.input_type.input'
2
3b2874c58bcd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit b0bcec3ad7b4b4c682cfdf9257fe04f55dda8071
galaxyp
parents: 1
diff changeset
66 #if $req_inputs.input_type.input_type_selector == 'DNA'
0
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
parents:
diff changeset
67 #if $req_inputs.input_type.frame == 'None'
2
3b2874c58bcd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit b0bcec3ad7b4b4c682cfdf9257fe04f55dda8071
galaxyp
parents: 1
diff changeset
68 -frame '0'
0
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
parents:
diff changeset
69 #else
2
3b2874c58bcd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit b0bcec3ad7b4b4c682cfdf9257fe04f55dda8071
galaxyp
parents: 1
diff changeset
70 -frame '$req_inputs.input_type.frame'
0
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
parents:
diff changeset
71 #end if
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
parents:
diff changeset
72 #else
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
parents:
diff changeset
73 -anno '$req_inputs.input_type.anno'
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
parents:
diff changeset
74 #end if
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
parents:
diff changeset
75 #end if
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
parents:
diff changeset
76 #end if
2
3b2874c58bcd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit b0bcec3ad7b4b4c682cfdf9257fe04f55dda8071
galaxyp
parents: 1
diff changeset
77 #if $req_inputs.indexType
0
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
parents:
diff changeset
78 -indexType $req_inputs.indexType
2
3b2874c58bcd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit b0bcec3ad7b4b4c682cfdf9257fe04f55dda8071
galaxyp
parents: 1
diff changeset
79 #end if
0
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
parents:
diff changeset
80
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
parents:
diff changeset
81 #if $modifications.fixed_mod
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
parents:
diff changeset
82 -fixMod '$modifications.fixed_mod'
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
parents:
diff changeset
83 #end if
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
parents:
diff changeset
84 #if $modifications.var_mod
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
parents:
diff changeset
85 -varMod '$modifications.var_mod'
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
parents:
diff changeset
86 #end if
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
parents:
diff changeset
87 #if $digestion.enzyme
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
parents:
diff changeset
88 -e '$digestion.enzyme'
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
parents:
diff changeset
89 #end if
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
parents:
diff changeset
90 #if $digestion.max_missed_cleavages
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
parents:
diff changeset
91 -c '$digestion.max_missed_cleavages'
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
parents:
diff changeset
92 #end if
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
parents:
diff changeset
93
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
parents:
diff changeset
94 #if $modifications.max_mods
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
parents:
diff changeset
95 -maxVar '$modifications.max_mods'
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
parents:
diff changeset
96 #end if
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
parents:
diff changeset
97 $modifications.unmodified
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
parents:
diff changeset
98 $modifications.aa
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
parents:
diff changeset
99 #if $ms_params.tolerance_params.precursor_tolerance
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
parents:
diff changeset
100 -tol '$ms_params.tolerance_params.precursor_tolerance'
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
parents:
diff changeset
101 #end if
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
parents:
diff changeset
102
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
parents:
diff changeset
103 #if $ms_params.tolerance_params.precursor_unit
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
parents:
diff changeset
104 -tolu '$ms_params.tolerance_params.precursor_unit'
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
parents:
diff changeset
105 #end if
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
parents:
diff changeset
106 #if $ms_params.tolerance_params.tolerance
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
parents:
diff changeset
107 -itol '$ms_params.tolerance_params.tolerance'
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
parents:
diff changeset
108 #end if
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
parents:
diff changeset
109 #if $ms_params.search.frag_method
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
parents:
diff changeset
110 -fragmentMethod '$ms_params.search.frag_method'
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
parents:
diff changeset
111 #end if
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
parents:
diff changeset
112 #if $ms_params.search.scoring_method
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
parents:
diff changeset
113 -m '$ms_params.search.scoring_method'
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
parents:
diff changeset
114 #end if
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
parents:
diff changeset
115 $ms_params.search.extra_score_validation
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
parents:
diff changeset
116 #if $ms_params.search.max_charge
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
parents:
diff changeset
117 -maxCharge '$ms_params.search.max_charge'
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
parents:
diff changeset
118 #end if
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
parents:
diff changeset
119 #if $ms_params.search.min_charge
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
parents:
diff changeset
120 -minCharge '$ms_params.search.min_charge'
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
parents:
diff changeset
121 #end if
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
parents:
diff changeset
122 #if $ms_params.search.min_peaks
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
parents:
diff changeset
123 -minPeaks '$ms_params.search.min_peaks'
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
parents:
diff changeset
124 #end if
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
parents:
diff changeset
125 #if $ms_params.search.isotope_error
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
parents:
diff changeset
126 -ti '$ms_params.search.isotope_error'
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
parents:
diff changeset
127 #end if
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
parents:
diff changeset
128 #if $ms_params.search.min_score
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
parents:
diff changeset
129 -minScore '$ms_params.search.min_score'
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
parents:
diff changeset
130 #end if
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
parents:
diff changeset
131 #if $ms_params.search.min_length
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
parents:
diff changeset
132 -minLength '$ms_params.search.min_length'
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
parents:
diff changeset
133 #end if
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
parents:
diff changeset
134 #if $ms_params.search.max_length
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
parents:
diff changeset
135 -maxLength '$ms_params.search.max_length'
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
parents:
diff changeset
136 #end if
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
parents:
diff changeset
137 #if $ms_params.search.num_random_peptides
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
parents:
diff changeset
138 -n '$ms_params.search.num_random_peptides'
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
parents:
diff changeset
139 #end if
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
parents:
diff changeset
140 #if 'psm_annotation.txt' in $outputs_selected
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
parents:
diff changeset
141 -plot
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
parents:
diff changeset
142 #end if
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
parents:
diff changeset
143 $fast
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
parents:
diff changeset
144 -o pepquery_output
2
3b2874c58bcd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit b0bcec3ad7b4b4c682cfdf9257fe04f55dda8071
galaxyp
parents: 1
diff changeset
145 | tee >(sed "s/\x1b[^m]*m//g" > log.txt)
3b2874c58bcd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit b0bcec3ad7b4b4c682cfdf9257fe04f55dda8071
galaxyp
parents: 1
diff changeset
146 #set $flist = str($outputs_selected).replace(',',' ').replace('ms_index','')
1
6b5ce9e2b0d0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 3f50a508dbb9050be48de5685cec9a82683d8457
galaxyp
parents: 0
diff changeset
147 && for i in $flist; do for f in `find pepquery_output/*/* -name \$i`; do cat \$f >> pepquery_output/\${i}; done; done
6b5ce9e2b0d0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 3f50a508dbb9050be48de5685cec9a82683d8457
galaxyp
parents: 0
diff changeset
148 && for f in `find pepquery_output/*/ -name parameter.txt`; do cp \$f pepquery_output/parameter.txt; done
0
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
parents:
diff changeset
149 ]]>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
parents:
diff changeset
150 </command>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
parents:
diff changeset
151 <inputs>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
parents:
diff changeset
152 <conditional name="validation">
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
parents:
diff changeset
153 <param name="task_type" argument="-s" type="select" label="Validation Task Type">
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
parents:
diff changeset
154 <option value="novel" selected="true">novel peptide/protein validation</option>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
parents:
diff changeset
155 <option value="known">known peptide/protein validation</option>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
parents:
diff changeset
156 </param>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
parents:
diff changeset
157 <when value="novel"/>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
parents:
diff changeset
158 <when value="known">
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
parents:
diff changeset
159 <param name="decoy" argument="-decoy" type="boolean" truevalue="-decoy" falsevalue="" checked="false" label="Identity the decoy version of the selected target protein"/>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
parents:
diff changeset
160 </when>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
parents:
diff changeset
161 </conditional>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
parents:
diff changeset
162 <section name="req_inputs" title="Input Data" expanded="true">
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
parents:
diff changeset
163 <conditional name="input_type">
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
parents:
diff changeset
164 <param name="input_type_selector" argument="-t" type="select" label="Input Type" help="" >
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
parents:
diff changeset
165 <option value="peptide">peptide</option>
2
3b2874c58bcd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit b0bcec3ad7b4b4c682cfdf9257fe04f55dda8071
galaxyp
parents: 1
diff changeset
166 <option value="protein">protein</option>
3b2874c58bcd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit b0bcec3ad7b4b4c682cfdf9257fe04f55dda8071
galaxyp
parents: 1
diff changeset
167 <option value="DNA">DNA (translate to protein sequences)</option>
6
01fd80b15053 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
galaxyp
parents: 5
diff changeset
168 <!-- VCF,BED,GTF input options have not been implemented in this tool -->
0
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
parents:
diff changeset
169 </param>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
parents:
diff changeset
170 <when value="peptide">
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
parents:
diff changeset
171 <conditional name="multiple">
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
parents:
diff changeset
172 <param name="peptide_input_selector" type="select" label="Peptides?">
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
parents:
diff changeset
173 <option value="multiple">Peptide list from your history</option>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
parents:
diff changeset
174 <option value="single">Single peptide entered as text</option>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
parents:
diff changeset
175 </param>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
parents:
diff changeset
176 <when value="multiple">
3
d8962e547c9c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit ea7f4bae8a2ae72470b895476faf9a368496aa8d
galaxyp
parents: 2
diff changeset
177 <param name="input" argument="-i" type="data" format="tabular" label="Peptide Sequences (.txt)">
2
3b2874c58bcd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit b0bcec3ad7b4b4c682cfdf9257fe04f55dda8071
galaxyp
parents: 1
diff changeset
178 <help>Peptide sequence file containing peptides which you want to search (no column headers).
3b2874c58bcd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit b0bcec3ad7b4b4c682cfdf9257fe04f55dda8071
galaxyp
parents: 1
diff changeset
179 First column is am peptide sequence. Optional second column is spectrum title.
3b2874c58bcd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit b0bcec3ad7b4b4c682cfdf9257fe04f55dda8071
galaxyp
parents: 1
diff changeset
180 </help>
3b2874c58bcd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit b0bcec3ad7b4b4c682cfdf9257fe04f55dda8071
galaxyp
parents: 1
diff changeset
181 </param>
0
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
parents:
diff changeset
182 </when>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
parents:
diff changeset
183 <when value="single">
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
parents:
diff changeset
184 <param name="input" argument="-i" type="text" label="Peptide Sequence" help="Peptide sequence(s) which you want to search">
3
d8962e547c9c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit ea7f4bae8a2ae72470b895476faf9a368496aa8d
galaxyp
parents: 2
diff changeset
185 <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>
0
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
parents:
diff changeset
186 </param>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
parents:
diff changeset
187 </when>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
parents:
diff changeset
188 </conditional>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
parents:
diff changeset
189 </when>
2
3b2874c58bcd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit b0bcec3ad7b4b4c682cfdf9257fe04f55dda8071
galaxyp
parents: 1
diff changeset
190 <when value="protein">
0
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
parents:
diff changeset
191 <conditional name="multiple">
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
parents:
diff changeset
192 <param name="protein_input_selector" type="select" label="Proteins?">
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
parents:
diff changeset
193 <option value="multiple">Protein fasta from your history</option>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
parents:
diff changeset
194 <option value="single">Single protein entered as text</option>
2
3b2874c58bcd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit b0bcec3ad7b4b4c682cfdf9257fe04f55dda8071
galaxyp
parents: 1
diff changeset
195 <option value="identifier">Protein Identifier from selected Protein Reference Database</option>
0
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
parents:
diff changeset
196 </param>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
parents:
diff changeset
197 <when value="multiple">
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
parents:
diff changeset
198 <param name="input" argument="-i" type="data" format="fasta" label="Protein Sequences (.txt)" help="Protein fasta file containing proteins which you want to search." />
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
parents:
diff changeset
199 </when>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
parents:
diff changeset
200 <when value="single">
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
parents:
diff changeset
201 <param name="input" argument="-i" type="text" label="Protein Sequence" help="Protein sequence which you want to search">
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
parents:
diff changeset
202 <validator type="regex" message="Must be AA letters">^[AC-IK-NP-TV-Yac-ik-np-tv-y]+$</validator>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
parents:
diff changeset
203 </param>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
parents:
diff changeset
204 </when>
2
3b2874c58bcd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit b0bcec3ad7b4b4c682cfdf9257fe04f55dda8071
galaxyp
parents: 1
diff changeset
205 <when value="identifier">
3b2874c58bcd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit b0bcec3ad7b4b4c682cfdf9257fe04f55dda8071
galaxyp
parents: 1
diff changeset
206 <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">
3b2874c58bcd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit b0bcec3ad7b4b4c682cfdf9257fe04f55dda8071
galaxyp
parents: 1
diff changeset
207 <sanitizer invalid_char="">
3b2874c58bcd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit b0bcec3ad7b4b4c682cfdf9257fe04f55dda8071
galaxyp
parents: 1
diff changeset
208 <valid initial="string.ascii_letters,string.digits">
3b2874c58bcd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit b0bcec3ad7b4b4c682cfdf9257fe04f55dda8071
galaxyp
parents: 1
diff changeset
209 <add value="|" />
3b2874c58bcd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit b0bcec3ad7b4b4c682cfdf9257fe04f55dda8071
galaxyp
parents: 1
diff changeset
210 </valid>
3b2874c58bcd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit b0bcec3ad7b4b4c682cfdf9257fe04f55dda8071
galaxyp
parents: 1
diff changeset
211 </sanitizer>
3b2874c58bcd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit b0bcec3ad7b4b4c682cfdf9257fe04f55dda8071
galaxyp
parents: 1
diff changeset
212 <validator type="regex" message="Spaces not allowed in ID">^[^ ]+$</validator>
3b2874c58bcd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit b0bcec3ad7b4b4c682cfdf9257fe04f55dda8071
galaxyp
parents: 1
diff changeset
213 </param>
3b2874c58bcd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit b0bcec3ad7b4b4c682cfdf9257fe04f55dda8071
galaxyp
parents: 1
diff changeset
214 </when>
0
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
parents:
diff changeset
215 </conditional>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
parents:
diff changeset
216 </when>
2
3b2874c58bcd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit b0bcec3ad7b4b4c682cfdf9257fe04f55dda8071
galaxyp
parents: 1
diff changeset
217 <when value="DNA">
0
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
parents:
diff changeset
218 <param name="input" argument="-i" type="text" label="DNA Sequence (at least 60 bp)" help="DNA sequence which you want to search">
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
parents:
diff changeset
219 <validator type="regex" message="Must be at least 60bp">^[acgtuAGCTU]{60}[acgtuAGCTU]*$</validator>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
parents:
diff changeset
220 </param>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
parents:
diff changeset
221 <param name="frame" argument="-f" type="select" label="Frame(s) for DNA translation" multiple="true" help="The frame(s) to translate DNA sequence to protein. Selecting nothing (default) keeps the longest frame">
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
parents:
diff changeset
222 <option value="1">1</option>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
parents:
diff changeset
223 <option value="2">2</option>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
parents:
diff changeset
224 <option value="3">3</option>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
parents:
diff changeset
225 <option value="4">4</option>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
parents:
diff changeset
226 <option value="5">5</option>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
parents:
diff changeset
227 <option value="6">6</option>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
parents:
diff changeset
228 </param>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
parents:
diff changeset
229 </when>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
parents:
diff changeset
230 </conditional>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
parents:
diff changeset
231 <conditional name="db_type">
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
parents:
diff changeset
232 <param name="db_type_selector" type="select" label="Protein Reference Database from" help="" >
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
parents:
diff changeset
233 <option value="history">history</option>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
parents:
diff changeset
234 <option value="download">download</option>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
parents:
diff changeset
235 </param>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
parents:
diff changeset
236 <when value="history">
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
parents:
diff changeset
237 <param name="db_file" argument="-db" type="data" format="fasta" label="Protein Reference Database File" help="an input sequence that matches a reference will be ignored." />
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
parents:
diff changeset
238 </when>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
parents:
diff changeset
239 <when value="download">
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
parents:
diff changeset
240 <param name="db_id" type="text" value="" label="Public protein sequence database">
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
parents:
diff changeset
241 <help>Currently supported dowloads: gencode:human, swissprot:human, refseq:human</help>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
parents:
diff changeset
242 <option value="gencode:human">gencode:human</option>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
parents:
diff changeset
243 <option value="swissprot:human">swissprot:human</option>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
parents:
diff changeset
244 <option value="refseq:human">refseq:human</option>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
parents:
diff changeset
245 <validator type="regex" message="">^(swissprot|refseq|gencode):(human)$</validator>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
parents:
diff changeset
246 </param>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
parents:
diff changeset
247 </when>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
parents:
diff changeset
248 </conditional>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
parents:
diff changeset
249 <conditional name="ms_dataset">
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
parents:
diff changeset
250 <param name="ms_dataset_type" type="select" label="MS/MS dataset to search" help="" >
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
parents:
diff changeset
251 <option value="history"> Spectrum Datasets from history</option>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
parents:
diff changeset
252 <option value="indexed">Indexed MS/MS spectrums</option>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
parents:
diff changeset
253 <option value="PepQueryDB">PepQueryDB</option>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
parents:
diff changeset
254 <option value="public">public proteomics data repositories</option>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
parents:
diff changeset
255 </param>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
parents:
diff changeset
256 <when value="history">
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
parents:
diff changeset
257 <param name="spectrum_files" argument="-ms" type="data" format="mgf,mzml,mzxml,thermo.raw" label="Spectrum File" help="Spectrum file used for identification, formats: MGF,mzML,mzXML,Thermo RAW" />
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
parents:
diff changeset
258 </when>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
parents:
diff changeset
259 <when value="indexed">
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
parents:
diff changeset
260 <param name="index" argument="-ms" type="data" format="txt" label="PepQuery Index" help="" />
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
parents:
diff changeset
261 </when>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
parents:
diff changeset
262 <when value="PepQueryDB">
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
parents:
diff changeset
263 <param name="dataset" argument="-b" type="text" value="" label="PepQueryDB dataset">
1
6b5ce9e2b0d0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 3f50a508dbb9050be48de5685cec9a82683d8457
galaxyp
parents: 0
diff changeset
264 <help>PepQueryDB dataset IDs (separated by commas).</help>
6b5ce9e2b0d0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 3f50a508dbb9050be48de5685cec9a82683d8457
galaxyp
parents: 0
diff changeset
265 <expand macro="pepquerydb_options" />
6b5ce9e2b0d0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 3f50a508dbb9050be48de5685cec9a82683d8457
galaxyp
parents: 0
diff changeset
266 <validator type="regex" message="PepQueryDB dataset_name(,dataset_name)">^[a-zA-Z][^,]*(,[a-zA-Z][^,]*)*$</validator>
0
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
parents:
diff changeset
267 </param>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
parents:
diff changeset
268 </when>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
parents:
diff changeset
269 <when value="public">
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
parents:
diff changeset
270 <param name="dataset" type="text" value="" label="Public dataset">
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
parents:
diff changeset
271 <validator type="regex" message="An identifier strating with PXD or MSV or JPST">^(PXD|MSV|JPST).*$</validator>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
parents:
diff changeset
272 </param>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
parents:
diff changeset
273 </when>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
parents:
diff changeset
274 </conditional>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
parents:
diff changeset
275
2
3b2874c58bcd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit b0bcec3ad7b4b4c682cfdf9257fe04f55dda8071
galaxyp
parents: 1
diff changeset
276 <param name="indexType" argument="-indexType" type="select" optional="true" label="Report Spectrum Scan as" help="Default: index" >
3b2874c58bcd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit b0bcec3ad7b4b4c682cfdf9257fe04f55dda8071
galaxyp
parents: 1
diff changeset
277 <option value="1">index (1-based) in MGF</option>
0
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
parents:
diff changeset
278 <option value="2">spectrum title in MGF</option>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
parents:
diff changeset
279 </param>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
parents:
diff changeset
280 </section>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
parents:
diff changeset
281
1
6b5ce9e2b0d0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 3f50a508dbb9050be48de5685cec9a82683d8457
galaxyp
parents: 0
diff changeset
282 <param name="parameter_set" argument="-p" type="text" value="" optional="true" label="MS/MS searching parameter set name">
6b5ce9e2b0d0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 3f50a508dbb9050be48de5685cec9a82683d8457
galaxyp
parents: 0
diff changeset
283 <help>Currently supported set names start with: MS1 or TMT</help>
6b5ce9e2b0d0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 3f50a508dbb9050be48de5685cec9a82683d8457
galaxyp
parents: 0
diff changeset
284 <option value="MS1_H_MS2_H_LF">MS1_H_MS2_H_LF</option>
6b5ce9e2b0d0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 3f50a508dbb9050be48de5685cec9a82683d8457
galaxyp
parents: 0
diff changeset
285 <option value="MS1_H_MS2_L_LF">MS1_H_MS2_L_LF</option>
6b5ce9e2b0d0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 3f50a508dbb9050be48de5685cec9a82683d8457
galaxyp
parents: 0
diff changeset
286 <option value="TMT10_11">TMT10_11</option>
6b5ce9e2b0d0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 3f50a508dbb9050be48de5685cec9a82683d8457
galaxyp
parents: 0
diff changeset
287 <option value="TMT10_11_MS2_L">TMT10_11_MS2_L</option>
6b5ce9e2b0d0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 3f50a508dbb9050be48de5685cec9a82683d8457
galaxyp
parents: 0
diff changeset
288 <option value="TMT10_11_MS2_L_phosphorylation">TMT10_11_MS2_L_phosphorylation</option>
6b5ce9e2b0d0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 3f50a508dbb9050be48de5685cec9a82683d8457
galaxyp
parents: 0
diff changeset
289 <option value="TMT10_11_acetylation">TMT10_11_acetylation</option>
6b5ce9e2b0d0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 3f50a508dbb9050be48de5685cec9a82683d8457
galaxyp
parents: 0
diff changeset
290 <option value="TMT10_11_glycosylation">TMT10_11_glycosylation</option>
6b5ce9e2b0d0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 3f50a508dbb9050be48de5685cec9a82683d8457
galaxyp
parents: 0
diff changeset
291 <option value="TMT10_11_phosphorylation">TMT10_11_phosphorylation</option>
6b5ce9e2b0d0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 3f50a508dbb9050be48de5685cec9a82683d8457
galaxyp
parents: 0
diff changeset
292 <option value="TMT10_11_ubiquitination">TMT10_11_ubiquitination</option>
6b5ce9e2b0d0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 3f50a508dbb9050be48de5685cec9a82683d8457
galaxyp
parents: 0
diff changeset
293 </param>
0
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
parents:
diff changeset
294
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
parents:
diff changeset
295 <section name="modifications" title="Modifications" expanded="false">
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
parents:
diff changeset
296 <param name="fixed_mod" argument="-fixMod" type="select" label="Fixed modification(s)" multiple="true" optional="true">
2
3b2874c58bcd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit b0bcec3ad7b4b4c682cfdf9257fe04f55dda8071
galaxyp
parents: 1
diff changeset
297 <help>Default: 1: Carbamidomethylation of C [57.02146372057]</help>
0
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
parents:
diff changeset
298 <expand macro="modifications" />
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
parents:
diff changeset
299 </param>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
parents:
diff changeset
300 <param name="var_mod" argument="-varMod" type="select" label="Variable modification(s)" multiple="true" optional="true">
2
3b2874c58bcd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit b0bcec3ad7b4b4c682cfdf9257fe04f55dda8071
galaxyp
parents: 1
diff changeset
301 <help>Default: 2: Oxidation of M [15.99491461956]</help>
0
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
parents:
diff changeset
302 <expand macro="modifications" />
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
parents:
diff changeset
303 </param>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
parents:
diff changeset
304
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
parents:
diff changeset
305 <param name="max_mods" argument="-maxVar" type="integer" label="Max Modifications" value="" min="0" max="10" optional="true" help="Max number of variable modifications Default: 3" />
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
parents:
diff changeset
306 <param name="unmodified" argument="-hc" type="boolean" truevalue="-hc" falsevalue="" checked="false" label="Use more stringent criterion for unrestricted modification searching" help="TRUE: score(UMS)>=score(targetPSM); FALSE: score(UMS)>score(targetPSM)" />
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
parents:
diff changeset
307 <param name="aa" argument="-aa" type="boolean" truevalue="-aa" falsevalue="" checked="false" label="Consider amino acid substitution modifications?" help="Whether or not to consider aa substitution modifications when perform modification filtering." />
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
parents:
diff changeset
308 </section>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
parents:
diff changeset
309
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
parents:
diff changeset
310 <section name="digestion" title="Digestion" expanded="false">
2
3b2874c58bcd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit b0bcec3ad7b4b4c682cfdf9257fe04f55dda8071
galaxyp
parents: 1
diff changeset
311 <param name="enzyme" argument="-e" type="select" optional="true" label="Enzyme" help="Enzyme used for protein digestion. Default: Trypsin" >
0
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
parents:
diff changeset
312 <option value="0">Non enzyme</option>
2
3b2874c58bcd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit b0bcec3ad7b4b4c682cfdf9257fe04f55dda8071
galaxyp
parents: 1
diff changeset
313 <option value="1">Trypsin</option>
0
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
parents:
diff changeset
314 <option value="2">Trypsin (no P rule)</option>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
parents:
diff changeset
315 <option value="3">Arg-C</option>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
parents:
diff changeset
316 <option value="4">Arg-C (no P rule)</option>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
parents:
diff changeset
317 <option value="5">Arg-N</option>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
parents:
diff changeset
318 <option value="6">Glu-C</option>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
parents:
diff changeset
319 <option value="7">Lys-C</option>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
parents:
diff changeset
320 </param>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
parents:
diff changeset
321 <param name="max_missed_cleavages" argument="-c" type="integer" value="" optional="true" label="Max Missed Cleavages" help="The max missed cleavages" />
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
parents:
diff changeset
322 </section>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
parents:
diff changeset
323
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
parents:
diff changeset
324 <section name="ms_params" title="Mass spectrometer" expanded="false">
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
parents:
diff changeset
325 <section name="tolerance_params" title="Tolerance" expanded="true">
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
parents:
diff changeset
326 <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" />
2
3b2874c58bcd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit b0bcec3ad7b4b4c682cfdf9257fe04f55dda8071
galaxyp
parents: 1
diff changeset
327 <param name="precursor_unit" argument="-tolu" type="select" optional="true" label="Precursor Unit" help="The unit of precursor ion m/z tolerance. Default: ppm">
3b2874c58bcd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit b0bcec3ad7b4b4c682cfdf9257fe04f55dda8071
galaxyp
parents: 1
diff changeset
328 <option value="ppm">ppm</option>
0
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
parents:
diff changeset
329 <option value="Da">Da</option>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
parents:
diff changeset
330 </param>
1
6b5ce9e2b0d0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 3f50a508dbb9050be48de5685cec9a82683d8457
galaxyp
parents: 0
diff changeset
331 <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" />
0
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
parents:
diff changeset
332 </section>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
parents:
diff changeset
333
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
parents:
diff changeset
334 <section name="search" title="PSM" expanded="false">
2
3b2874c58bcd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit b0bcec3ad7b4b4c682cfdf9257fe04f55dda8071
galaxyp
parents: 1
diff changeset
335 <param name="frag_method" argument="-fragmentMethod" type="select" optional="true" label="Fragmentation Method" help="Default: CID/HCD">
3b2874c58bcd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit b0bcec3ad7b4b4c682cfdf9257fe04f55dda8071
galaxyp
parents: 1
diff changeset
336 <option value="1">CID/HCD</option>
0
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
parents:
diff changeset
337 <option value="2">ETD</option>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
parents:
diff changeset
338 </param>
2
3b2874c58bcd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit b0bcec3ad7b4b4c682cfdf9257fe04f55dda8071
galaxyp
parents: 1
diff changeset
339 <param name="scoring_method" argument="-m" type="select" optional="true" label="Scoring Method" help="Default: HyperScore">
3b2874c58bcd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit b0bcec3ad7b4b4c682cfdf9257fe04f55dda8071
galaxyp
parents: 1
diff changeset
340 <option value="1">HyperScore</option>
0
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
parents:
diff changeset
341 <option value="2">MVH</option>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
parents:
diff changeset
342 </param>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
parents:
diff changeset
343 <param name="extra_score_validation" argument="-x" type="boolean" truevalue="-x" falsevalue="" checked="false" label="Add extra score validation" help="use two scoring algorithms for peptide identification" />
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
parents:
diff changeset
344 <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"/>
1
6b5ce9e2b0d0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 3f50a508dbb9050be48de5685cec9a82683d8457
galaxyp
parents: 0
diff changeset
345 <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" />
0
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
parents:
diff changeset
346 <param name="min_peaks" argument="-minPeaks" type="integer" value="" optional="true" label="Minimum Peaks" help="Min peaks in spectrum. Default: 10" />
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
parents:
diff changeset
347 <param name="isotope_error" argument="-ti" type="text" value="" optional="true" label="Isotope peak error range">
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
parents:
diff changeset
348 <help>A comma-sepated range of integers from -2 to 2, e.g. '-1,0,1,2' Default: 0</help>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
parents:
diff changeset
349 <validator type="regex" message="">^((-2,)?-1,)?0(,1(,2)?)?$</validator>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
parents:
diff changeset
350 </param>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
parents:
diff changeset
351 <param name="min_score" argument="-minScore" type="integer" value="" min="0" optional="true" label="Minimum Score" help="Minimum score to consider for peptide searching. Default: 12" />
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
parents:
diff changeset
352 <param name="min_length" argument="-minLength" type="integer" value="" min="0" optional="true" label="Minimum length of peptide" help="The maximum length of peptide to consider. Default: 7" />
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
parents:
diff changeset
353 <param name="max_length" argument="-maxLength" type="integer" value="" min="0" optional="true" label="Maximum length of peptide" help="The maximum length of peptide to consider. Default: 45" />
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
parents:
diff changeset
354 <param name="num_random_peptides" argument="-n" type="integer" value="" min="0" optional="true" label="Number of Random Peptides" help="The number of random peptides. Default: 1000" />
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
parents:
diff changeset
355 </section>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
parents:
diff changeset
356 </section>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
parents:
diff changeset
357
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
parents:
diff changeset
358 <param name="outputs_selected" type="select" multiple="true" optional="false" label="Select outputs">
4
29e6417b913c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit b7f27d4872020b09656a2f53d667217b762fa202
galaxyp
parents: 3
diff changeset
359 <option value="psm.txt">psm.txt</option>
0
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
parents:
diff changeset
360 <option value="psm_rank.txt" selected="true">psm_rank.txt</option>
4
29e6417b913c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit b7f27d4872020b09656a2f53d667217b762fa202
galaxyp
parents: 3
diff changeset
361 <option value="psm_rank.mgf">psm_rank.mgf</option>
29e6417b913c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit b7f27d4872020b09656a2f53d667217b762fa202
galaxyp
parents: 3
diff changeset
362 <option value="psm_annotation.txt">psm_annotation.txt</option>
29e6417b913c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit b7f27d4872020b09656a2f53d667217b762fa202
galaxyp
parents: 3
diff changeset
363 <option value="psm_type.txt">psm_type.txt</option>
29e6417b913c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit b7f27d4872020b09656a2f53d667217b762fa202
galaxyp
parents: 3
diff changeset
364 <option value="detail.txt">detail.txt</option>
29e6417b913c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit b7f27d4872020b09656a2f53d667217b762fa202
galaxyp
parents: 3
diff changeset
365 <option value="ptm.txt">ptm.txt</option>
29e6417b913c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit b7f27d4872020b09656a2f53d667217b762fa202
galaxyp
parents: 3
diff changeset
366 <option value="ptm_detail.txt">ptm_detail.txt</option>
29e6417b913c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit b7f27d4872020b09656a2f53d667217b762fa202
galaxyp
parents: 3
diff changeset
367 <option value="ms_index">MS/MS Index</option>
0
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
parents:
diff changeset
368 </param>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
parents:
diff changeset
369 <param name="fast" argument="-fast" type="boolean" truevalue="-fast" falsevalue="" checked="false" label="Use fast mode for searching" help="In fast mode, only one better match from reference peptide-based competitive filtering steps will be returned. A peptide identified or not is not affected by this setting. For most applications, fast mode will speed up the analysis." />
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
parents:
diff changeset
370 </inputs>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
parents:
diff changeset
371 <outputs>
3
d8962e547c9c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit ea7f4bae8a2ae72470b895476faf9a368496aa8d
galaxyp
parents: 2
diff changeset
372 <data name="log_txt" format="txt" from_work_dir="log.txt" label="${tool.name} on ${on_string}: log.txt">
2
3b2874c58bcd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit b0bcec3ad7b4b4c682cfdf9257fe04f55dda8071
galaxyp
parents: 1
diff changeset
373 </data>
1
6b5ce9e2b0d0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 3f50a508dbb9050be48de5685cec9a82683d8457
galaxyp
parents: 0
diff changeset
374 <data name="parameter_txt" format="txt" from_work_dir="pepquery_output/parameter.txt" label="${tool.name} on ${on_string}: parameter.txt">
4
29e6417b913c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit b7f27d4872020b09656a2f53d667217b762fa202
galaxyp
parents: 3
diff changeset
375 <filter>'parameter.txt' in outputs_selected and req_inputs['ms_dataset']['ms_dataset_type'] == 'history'</filter>
1
6b5ce9e2b0d0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 3f50a508dbb9050be48de5685cec9a82683d8457
galaxyp
parents: 0
diff changeset
376 </data>
0
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
parents:
diff changeset
377 <data name="ms_index" format="txt" label="${tool.name} on ${on_string}: index summary.txt" from_work_dir="index_dir/summary.txt">
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
parents:
diff changeset
378 <filter>'ms_index' in outputs_selected and req_inputs['ms_dataset']['ms_dataset_type'] == 'history'</filter>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
parents:
diff changeset
379 </data>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
parents:
diff changeset
380 <data name="psm_txt" format="tabular" from_work_dir="pepquery_output/psm.txt" label="${tool.name} on ${on_string}: psm.txt">
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
parents:
diff changeset
381 <filter>'psm.txt' in outputs_selected</filter>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
parents:
diff changeset
382 <actions>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
parents:
diff changeset
383 <action name="comment_lines" type="metadata" default="1" />
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
parents:
diff changeset
384 <action name="column_names" type="metadata" default="peptide,modification,n,spectrum_title,charge,exp_mass,tol_ppm,tol_da,isotope_error,pep_mass,mz,score,n_db,total_db,n_random,total_random,pvalue" />
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
parents:
diff changeset
385 </actions>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
parents:
diff changeset
386 </data>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
parents:
diff changeset
387
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
parents:
diff changeset
388 <data name="psm_rank_txt" format="tabular" from_work_dir="pepquery_output/psm_rank.txt" label="${tool.name} on ${on_string}: psm_rank.txt">
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
parents:
diff changeset
389 <filter>'psm_rank.txt' in outputs_selected</filter>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
parents:
diff changeset
390 <actions>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
parents:
diff changeset
391 <action name="comment_lines" type="metadata" default="1" />
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
parents:
diff changeset
392 <action name="column_names" type="metadata" default="peptide,modification,n,spectrum_title,charge,exp_mass,tol_ppm,tol_da,isotope_error,pep_mass,mz,score,n_db,total_db,n_random,total_random,pvalue,rank,n_ptm,confident,ref_delta_score,mod_delta_score" />
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
parents:
diff changeset
393 </actions>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
parents:
diff changeset
394 </data>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
parents:
diff changeset
395
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
parents:
diff changeset
396 <data name="psm_rank_mgf" format="mgf" from_work_dir="pepquery_output/psm_rank.mgf" label="${tool.name} on ${on_string}: psm_rank.mgf">
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
parents:
diff changeset
397 <filter>'psm_rank.mgf' in outputs_selected</filter>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
parents:
diff changeset
398 </data>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
parents:
diff changeset
399 <data name="psm_type_txt" format="tabular" from_work_dir="pepquery_output/psmi_type.txt" label="${tool.name} on ${on_string}: psm_type.txt">
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
parents:
diff changeset
400 <filter>'psm_type.txt' in outputs_selected</filter>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
parents:
diff changeset
401 <actions>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
parents:
diff changeset
402 <action name="comment_lines" type="metadata" default="1" />
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
parents:
diff changeset
403 <action name="column_names" type="metadata" default="peptide,spectrum_title,type" />
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
parents:
diff changeset
404 </actions>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
parents:
diff changeset
405 </data>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
parents:
diff changeset
406 <data name="psm_annotation_txt" format="tabular" from_work_dir="pepquery_output/psm_annotation.txt" label="${tool.name} on ${on_string}: psm_annotation.txt">
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
parents:
diff changeset
407 <filter>'psm_annotation.txt' in outputs_selected</filter>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
parents:
diff changeset
408 <actions>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
parents:
diff changeset
409 <action name="comment_lines" type="metadata" default="1" />
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
parents:
diff changeset
410 <action name="column_names" type="metadata" default="peptide,modification,Query,calc_mr,observed_mz,charge,pepSeq,m_label,m_mz,m_intensity,mz,intensity" />
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
parents:
diff changeset
411 </actions>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
parents:
diff changeset
412 </data>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
parents:
diff changeset
413 <data name="detail_txt" format="tabular" from_work_dir="pepquery_output/detail.txt" label="${tool.name} on ${on_string}: detail.txt">
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
parents:
diff changeset
414 <filter>'detail.txt' in outputs_selected</filter>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
parents:
diff changeset
415 <actions>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
parents:
diff changeset
416 <action name="comment_lines" type="metadata" default="1" />
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
parents:
diff changeset
417 <action name="column_names" type="metadata" default="spectrum_title,peptide,modification,exp_mass,pep_mass,tol_ppm,tol_da,isotope_error,score" />
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
parents:
diff changeset
418 </actions>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
parents:
diff changeset
419 </data>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
parents:
diff changeset
420
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
parents:
diff changeset
421 <data name="ptm_txt" format="tabular" from_work_dir="pepquery_output/ptm.txt" label="${tool.name} on ${on_string}: ptm.txt">
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
parents:
diff changeset
422 <filter>'ptm.txt' in outputs_selected</filter>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
parents:
diff changeset
423 <actions>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
parents:
diff changeset
424 <action name="comment_lines" type="metadata" default="1" />
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
parents:
diff changeset
425 <action name="column_names" type="metadata" default="spectrum_title,peptide,charge,exp_mass,pep_mass,tol_ppm,tol_da,isotope_error,modification,score" />
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
parents:
diff changeset
426 </actions>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
parents:
diff changeset
427 </data>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
parents:
diff changeset
428 <data name="ptm_detail_txt" format="tabular" from_work_dir="pepquery_output/ptm_detail.txt" label="${tool.name} on ${on_string}: ptm_detail.txt">
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
parents:
diff changeset
429 <filter>'ptm_detail.txt' in outputs_selected</filter>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
parents:
diff changeset
430 <actions>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
parents:
diff changeset
431 <action name="comment_lines" type="metadata" default="1" />
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
parents:
diff changeset
432 <action name="column_names" type="metadata" default="peptide,modification,n,spectrum_title,charge,exp_mass,tol_ppm,tol_da,isotope_error,pep_mass,mz,score,n_db,total_db,n_random,total_random,pvalue,rank,ptm_spectrum_title,ptm_peptide,ptm_charge,ptm_exp_mass,ptm_pep_mass,ptm_tol_ppm,ptm_tol_da,ptm_isotope_error,ptm_modification,ptm_score" />
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
parents:
diff changeset
433 </actions>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
parents:
diff changeset
434 </data>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
parents:
diff changeset
435
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
parents:
diff changeset
436 </outputs>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
parents:
diff changeset
437 <tests>
1
6b5ce9e2b0d0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 3f50a508dbb9050be48de5685cec9a82683d8457
galaxyp
parents: 0
diff changeset
438 <!-- Test-1 PepQueryDB peptide gencode:human -->
6
01fd80b15053 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
galaxyp
parents: 5
diff changeset
439 <test expect_num_outputs="2">
1
6b5ce9e2b0d0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 3f50a508dbb9050be48de5685cec9a82683d8457
galaxyp
parents: 0
diff changeset
440 <conditional name="validation">
6b5ce9e2b0d0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 3f50a508dbb9050be48de5685cec9a82683d8457
galaxyp
parents: 0
diff changeset
441 <param name="task_type" value="novel"/>
6b5ce9e2b0d0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 3f50a508dbb9050be48de5685cec9a82683d8457
galaxyp
parents: 0
diff changeset
442 </conditional>
6b5ce9e2b0d0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 3f50a508dbb9050be48de5685cec9a82683d8457
galaxyp
parents: 0
diff changeset
443 <section name="req_inputs">
6b5ce9e2b0d0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 3f50a508dbb9050be48de5685cec9a82683d8457
galaxyp
parents: 0
diff changeset
444 <conditional name="input_type">
6b5ce9e2b0d0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 3f50a508dbb9050be48de5685cec9a82683d8457
galaxyp
parents: 0
diff changeset
445 <param name="input_type_selector" value="peptide"/>
6b5ce9e2b0d0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 3f50a508dbb9050be48de5685cec9a82683d8457
galaxyp
parents: 0
diff changeset
446 <conditional name="multiple">
6b5ce9e2b0d0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 3f50a508dbb9050be48de5685cec9a82683d8457
galaxyp
parents: 0
diff changeset
447 <param name="peptide_input_selector" value="single" />
3
d8962e547c9c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit ea7f4bae8a2ae72470b895476faf9a368496aa8d
galaxyp
parents: 2
diff changeset
448 <param name="input" value="LVVVGADGVGK,AHSSMVGVNLPQK"/>
1
6b5ce9e2b0d0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 3f50a508dbb9050be48de5685cec9a82683d8457
galaxyp
parents: 0
diff changeset
449 </conditional>
6b5ce9e2b0d0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 3f50a508dbb9050be48de5685cec9a82683d8457
galaxyp
parents: 0
diff changeset
450 </conditional>
6b5ce9e2b0d0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 3f50a508dbb9050be48de5685cec9a82683d8457
galaxyp
parents: 0
diff changeset
451 <conditional name="db_type">
6b5ce9e2b0d0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 3f50a508dbb9050be48de5685cec9a82683d8457
galaxyp
parents: 0
diff changeset
452 <param name="db_type_selector" value="download" />
6b5ce9e2b0d0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 3f50a508dbb9050be48de5685cec9a82683d8457
galaxyp
parents: 0
diff changeset
453 <param name="db_id" value="gencode:human"/>
6b5ce9e2b0d0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 3f50a508dbb9050be48de5685cec9a82683d8457
galaxyp
parents: 0
diff changeset
454 </conditional>
6b5ce9e2b0d0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 3f50a508dbb9050be48de5685cec9a82683d8457
galaxyp
parents: 0
diff changeset
455 <conditional name="ms_dataset">
6b5ce9e2b0d0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 3f50a508dbb9050be48de5685cec9a82683d8457
galaxyp
parents: 0
diff changeset
456 <param name="ms_dataset_type" value="PepQueryDB"/>
6b5ce9e2b0d0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 3f50a508dbb9050be48de5685cec9a82683d8457
galaxyp
parents: 0
diff changeset
457 <param name="dataset" value="CPTAC_LUAD_Discovery_Study_Proteome_PDC000153" />
6b5ce9e2b0d0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 3f50a508dbb9050be48de5685cec9a82683d8457
galaxyp
parents: 0
diff changeset
458 </conditional>
6b5ce9e2b0d0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 3f50a508dbb9050be48de5685cec9a82683d8457
galaxyp
parents: 0
diff changeset
459 <param name="indexType" value="1"/>
6b5ce9e2b0d0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 3f50a508dbb9050be48de5685cec9a82683d8457
galaxyp
parents: 0
diff changeset
460 </section>
6b5ce9e2b0d0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 3f50a508dbb9050be48de5685cec9a82683d8457
galaxyp
parents: 0
diff changeset
461 <param name="parameter_set" value=""/>
6b5ce9e2b0d0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 3f50a508dbb9050be48de5685cec9a82683d8457
galaxyp
parents: 0
diff changeset
462 <section name="modifications">
6b5ce9e2b0d0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 3f50a508dbb9050be48de5685cec9a82683d8457
galaxyp
parents: 0
diff changeset
463 <param name="fixed_mod" value="1"/>
6b5ce9e2b0d0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 3f50a508dbb9050be48de5685cec9a82683d8457
galaxyp
parents: 0
diff changeset
464 <param name="var_mod" value="2"/>
6b5ce9e2b0d0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 3f50a508dbb9050be48de5685cec9a82683d8457
galaxyp
parents: 0
diff changeset
465 <param name="max_mods" value="3"/>
6b5ce9e2b0d0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 3f50a508dbb9050be48de5685cec9a82683d8457
galaxyp
parents: 0
diff changeset
466 <param name="unmodified" value="True"/>
6b5ce9e2b0d0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 3f50a508dbb9050be48de5685cec9a82683d8457
galaxyp
parents: 0
diff changeset
467 <param name="aa" value="False"/>
6b5ce9e2b0d0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 3f50a508dbb9050be48de5685cec9a82683d8457
galaxyp
parents: 0
diff changeset
468 </section>
6b5ce9e2b0d0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 3f50a508dbb9050be48de5685cec9a82683d8457
galaxyp
parents: 0
diff changeset
469 <section name="digestion">
6b5ce9e2b0d0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 3f50a508dbb9050be48de5685cec9a82683d8457
galaxyp
parents: 0
diff changeset
470 <param name="enzyme" value="1"/>
6b5ce9e2b0d0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 3f50a508dbb9050be48de5685cec9a82683d8457
galaxyp
parents: 0
diff changeset
471 <param name="max_missed_cleavages" value="2"/>
6b5ce9e2b0d0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 3f50a508dbb9050be48de5685cec9a82683d8457
galaxyp
parents: 0
diff changeset
472 </section>
6b5ce9e2b0d0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 3f50a508dbb9050be48de5685cec9a82683d8457
galaxyp
parents: 0
diff changeset
473 <section name="ms_params">
6b5ce9e2b0d0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 3f50a508dbb9050be48de5685cec9a82683d8457
galaxyp
parents: 0
diff changeset
474 <section name="tolerance_params">
6b5ce9e2b0d0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 3f50a508dbb9050be48de5685cec9a82683d8457
galaxyp
parents: 0
diff changeset
475 <param name="precursor_tolerance" value="10"/>
6b5ce9e2b0d0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 3f50a508dbb9050be48de5685cec9a82683d8457
galaxyp
parents: 0
diff changeset
476 <param name="precursor_unit" value="ppm"/>
6b5ce9e2b0d0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 3f50a508dbb9050be48de5685cec9a82683d8457
galaxyp
parents: 0
diff changeset
477 <param name="tolerance" value="0.6"/>
6b5ce9e2b0d0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 3f50a508dbb9050be48de5685cec9a82683d8457
galaxyp
parents: 0
diff changeset
478 </section>
6b5ce9e2b0d0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 3f50a508dbb9050be48de5685cec9a82683d8457
galaxyp
parents: 0
diff changeset
479 <section name="search">
6b5ce9e2b0d0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 3f50a508dbb9050be48de5685cec9a82683d8457
galaxyp
parents: 0
diff changeset
480 <param name="frag_method" value="1"/>
6b5ce9e2b0d0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 3f50a508dbb9050be48de5685cec9a82683d8457
galaxyp
parents: 0
diff changeset
481 <param name="scoring_method" value="1"/>
6b5ce9e2b0d0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 3f50a508dbb9050be48de5685cec9a82683d8457
galaxyp
parents: 0
diff changeset
482 <param name="extra_score_validation" value="False"/>
6b5ce9e2b0d0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 3f50a508dbb9050be48de5685cec9a82683d8457
galaxyp
parents: 0
diff changeset
483 <param name="min_charge" value="2"/>
6b5ce9e2b0d0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 3f50a508dbb9050be48de5685cec9a82683d8457
galaxyp
parents: 0
diff changeset
484 <param name="max_charge" value="3"/>
6b5ce9e2b0d0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 3f50a508dbb9050be48de5685cec9a82683d8457
galaxyp
parents: 0
diff changeset
485 <param name="min_peaks" value="10"/>
6b5ce9e2b0d0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 3f50a508dbb9050be48de5685cec9a82683d8457
galaxyp
parents: 0
diff changeset
486 <param name="isotope_error" value="0"/>
6b5ce9e2b0d0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 3f50a508dbb9050be48de5685cec9a82683d8457
galaxyp
parents: 0
diff changeset
487 <param name="min_score" value="12"/>
6b5ce9e2b0d0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 3f50a508dbb9050be48de5685cec9a82683d8457
galaxyp
parents: 0
diff changeset
488 <param name="min_length" value="7"/>
6b5ce9e2b0d0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 3f50a508dbb9050be48de5685cec9a82683d8457
galaxyp
parents: 0
diff changeset
489 <param name="max_length" value="45"/>
6b5ce9e2b0d0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 3f50a508dbb9050be48de5685cec9a82683d8457
galaxyp
parents: 0
diff changeset
490 <param name="num_random_peptides" value="1000"/>
6b5ce9e2b0d0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 3f50a508dbb9050be48de5685cec9a82683d8457
galaxyp
parents: 0
diff changeset
491 </section>
6b5ce9e2b0d0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 3f50a508dbb9050be48de5685cec9a82683d8457
galaxyp
parents: 0
diff changeset
492 </section>
5
2045f3b68773 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 4b3991069094a9703904b2041d983315bf539aee
galaxyp
parents: 4
diff changeset
493 <output name="psm_rank_txt">
1
6b5ce9e2b0d0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 3f50a508dbb9050be48de5685cec9a82683d8457
galaxyp
parents: 0
diff changeset
494 <assert_contents>
6b5ce9e2b0d0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 3f50a508dbb9050be48de5685cec9a82683d8457
galaxyp
parents: 0
diff changeset
495 <has_text text="LVVVGADGVGK" />
3
d8962e547c9c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit ea7f4bae8a2ae72470b895476faf9a368496aa8d
galaxyp
parents: 2
diff changeset
496 <not_has_text text="AHSSMVGVNLPQK" />
1
6b5ce9e2b0d0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 3f50a508dbb9050be48de5685cec9a82683d8457
galaxyp
parents: 0
diff changeset
497 <has_text text="02CPTAC_LUAD_W_BI_20180518_KR_f15:25149:2" />
6
01fd80b15053 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
galaxyp
parents: 5
diff changeset
498 <has_n_columns n="22" />
1
6b5ce9e2b0d0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 3f50a508dbb9050be48de5685cec9a82683d8457
galaxyp
parents: 0
diff changeset
499 </assert_contents>
6b5ce9e2b0d0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 3f50a508dbb9050be48de5685cec9a82683d8457
galaxyp
parents: 0
diff changeset
500 </output>
3
d8962e547c9c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit ea7f4bae8a2ae72470b895476faf9a368496aa8d
galaxyp
parents: 2
diff changeset
501 <output name="log_txt">
d8962e547c9c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit ea7f4bae8a2ae72470b895476faf9a368496aa8d
galaxyp
parents: 2
diff changeset
502 <assert_contents>
d8962e547c9c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit ea7f4bae8a2ae72470b895476faf9a368496aa8d
galaxyp
parents: 2
diff changeset
503 <has_text text="Ignore peptide (reason: exist in reference database): AHSSMVGVNLPQK" />
d8962e547c9c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit ea7f4bae8a2ae72470b895476faf9a368496aa8d
galaxyp
parents: 2
diff changeset
504 </assert_contents>
d8962e547c9c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit ea7f4bae8a2ae72470b895476faf9a368496aa8d
galaxyp
parents: 2
diff changeset
505 </output>
1
6b5ce9e2b0d0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 3f50a508dbb9050be48de5685cec9a82683d8457
galaxyp
parents: 0
diff changeset
506 </test>
6b5ce9e2b0d0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 3f50a508dbb9050be48de5685cec9a82683d8457
galaxyp
parents: 0
diff changeset
507
3
d8962e547c9c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit ea7f4bae8a2ae72470b895476faf9a368496aa8d
galaxyp
parents: 2
diff changeset
508 <!-- Test-2 PepQueryDB peptide gencode:human pep.txt -->
6
01fd80b15053 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
galaxyp
parents: 5
diff changeset
509 <test expect_num_outputs="2">
3
d8962e547c9c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit ea7f4bae8a2ae72470b895476faf9a368496aa8d
galaxyp
parents: 2
diff changeset
510 <conditional name="validation">
d8962e547c9c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit ea7f4bae8a2ae72470b895476faf9a368496aa8d
galaxyp
parents: 2
diff changeset
511 <param name="task_type" value="novel"/>
d8962e547c9c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit ea7f4bae8a2ae72470b895476faf9a368496aa8d
galaxyp
parents: 2
diff changeset
512 </conditional>
d8962e547c9c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit ea7f4bae8a2ae72470b895476faf9a368496aa8d
galaxyp
parents: 2
diff changeset
513 <section name="req_inputs">
d8962e547c9c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit ea7f4bae8a2ae72470b895476faf9a368496aa8d
galaxyp
parents: 2
diff changeset
514 <conditional name="input_type">
d8962e547c9c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit ea7f4bae8a2ae72470b895476faf9a368496aa8d
galaxyp
parents: 2
diff changeset
515 <param name="input_type_selector" value="peptide"/>
d8962e547c9c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit ea7f4bae8a2ae72470b895476faf9a368496aa8d
galaxyp
parents: 2
diff changeset
516 <conditional name="multiple">
d8962e547c9c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit ea7f4bae8a2ae72470b895476faf9a368496aa8d
galaxyp
parents: 2
diff changeset
517 <param name="peptide_input_selector" value="multiple" />
d8962e547c9c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit ea7f4bae8a2ae72470b895476faf9a368496aa8d
galaxyp
parents: 2
diff changeset
518 <param name="input" ftype="tabular" value="pep.txt"/>
d8962e547c9c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit ea7f4bae8a2ae72470b895476faf9a368496aa8d
galaxyp
parents: 2
diff changeset
519 </conditional>
d8962e547c9c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit ea7f4bae8a2ae72470b895476faf9a368496aa8d
galaxyp
parents: 2
diff changeset
520 </conditional>
d8962e547c9c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit ea7f4bae8a2ae72470b895476faf9a368496aa8d
galaxyp
parents: 2
diff changeset
521 <conditional name="db_type">
d8962e547c9c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit ea7f4bae8a2ae72470b895476faf9a368496aa8d
galaxyp
parents: 2
diff changeset
522 <param name="db_type_selector" value="download" />
d8962e547c9c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit ea7f4bae8a2ae72470b895476faf9a368496aa8d
galaxyp
parents: 2
diff changeset
523 <param name="db_id" value="gencode:human"/>
d8962e547c9c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit ea7f4bae8a2ae72470b895476faf9a368496aa8d
galaxyp
parents: 2
diff changeset
524 </conditional>
d8962e547c9c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit ea7f4bae8a2ae72470b895476faf9a368496aa8d
galaxyp
parents: 2
diff changeset
525 <conditional name="ms_dataset">
d8962e547c9c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit ea7f4bae8a2ae72470b895476faf9a368496aa8d
galaxyp
parents: 2
diff changeset
526 <param name="ms_dataset_type" value="PepQueryDB"/>
d8962e547c9c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit ea7f4bae8a2ae72470b895476faf9a368496aa8d
galaxyp
parents: 2
diff changeset
527 <param name="dataset" value="CPTAC_LUAD_Discovery_Study_Proteome_PDC000153" />
d8962e547c9c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit ea7f4bae8a2ae72470b895476faf9a368496aa8d
galaxyp
parents: 2
diff changeset
528 </conditional>
d8962e547c9c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit ea7f4bae8a2ae72470b895476faf9a368496aa8d
galaxyp
parents: 2
diff changeset
529 <param name="indexType" value="1"/>
d8962e547c9c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit ea7f4bae8a2ae72470b895476faf9a368496aa8d
galaxyp
parents: 2
diff changeset
530 </section>
d8962e547c9c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit ea7f4bae8a2ae72470b895476faf9a368496aa8d
galaxyp
parents: 2
diff changeset
531 <param name="parameter_set" value=""/>
d8962e547c9c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit ea7f4bae8a2ae72470b895476faf9a368496aa8d
galaxyp
parents: 2
diff changeset
532 <section name="modifications">
d8962e547c9c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit ea7f4bae8a2ae72470b895476faf9a368496aa8d
galaxyp
parents: 2
diff changeset
533 <param name="fixed_mod" value="1"/>
d8962e547c9c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit ea7f4bae8a2ae72470b895476faf9a368496aa8d
galaxyp
parents: 2
diff changeset
534 <param name="var_mod" value="2"/>
d8962e547c9c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit ea7f4bae8a2ae72470b895476faf9a368496aa8d
galaxyp
parents: 2
diff changeset
535 <param name="max_mods" value="3"/>
d8962e547c9c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit ea7f4bae8a2ae72470b895476faf9a368496aa8d
galaxyp
parents: 2
diff changeset
536 <param name="unmodified" value="True"/>
d8962e547c9c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit ea7f4bae8a2ae72470b895476faf9a368496aa8d
galaxyp
parents: 2
diff changeset
537 <param name="aa" value="False"/>
d8962e547c9c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit ea7f4bae8a2ae72470b895476faf9a368496aa8d
galaxyp
parents: 2
diff changeset
538 </section>
d8962e547c9c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit ea7f4bae8a2ae72470b895476faf9a368496aa8d
galaxyp
parents: 2
diff changeset
539 <section name="digestion">
d8962e547c9c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit ea7f4bae8a2ae72470b895476faf9a368496aa8d
galaxyp
parents: 2
diff changeset
540 <param name="enzyme" value="1"/>
d8962e547c9c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit ea7f4bae8a2ae72470b895476faf9a368496aa8d
galaxyp
parents: 2
diff changeset
541 <param name="max_missed_cleavages" value="2"/>
d8962e547c9c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit ea7f4bae8a2ae72470b895476faf9a368496aa8d
galaxyp
parents: 2
diff changeset
542 </section>
d8962e547c9c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit ea7f4bae8a2ae72470b895476faf9a368496aa8d
galaxyp
parents: 2
diff changeset
543 <section name="ms_params">
d8962e547c9c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit ea7f4bae8a2ae72470b895476faf9a368496aa8d
galaxyp
parents: 2
diff changeset
544 <section name="tolerance_params">
d8962e547c9c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit ea7f4bae8a2ae72470b895476faf9a368496aa8d
galaxyp
parents: 2
diff changeset
545 <param name="precursor_tolerance" value="10"/>
d8962e547c9c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit ea7f4bae8a2ae72470b895476faf9a368496aa8d
galaxyp
parents: 2
diff changeset
546 <param name="precursor_unit" value="ppm"/>
d8962e547c9c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit ea7f4bae8a2ae72470b895476faf9a368496aa8d
galaxyp
parents: 2
diff changeset
547 <param name="tolerance" value="0.6"/>
d8962e547c9c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit ea7f4bae8a2ae72470b895476faf9a368496aa8d
galaxyp
parents: 2
diff changeset
548 </section>
d8962e547c9c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit ea7f4bae8a2ae72470b895476faf9a368496aa8d
galaxyp
parents: 2
diff changeset
549 <section name="search">
d8962e547c9c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit ea7f4bae8a2ae72470b895476faf9a368496aa8d
galaxyp
parents: 2
diff changeset
550 <param name="frag_method" value="1"/>
d8962e547c9c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit ea7f4bae8a2ae72470b895476faf9a368496aa8d
galaxyp
parents: 2
diff changeset
551 <param name="scoring_method" value="1"/>
d8962e547c9c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit ea7f4bae8a2ae72470b895476faf9a368496aa8d
galaxyp
parents: 2
diff changeset
552 <param name="extra_score_validation" value="False"/>
d8962e547c9c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit ea7f4bae8a2ae72470b895476faf9a368496aa8d
galaxyp
parents: 2
diff changeset
553 <param name="min_charge" value="2"/>
d8962e547c9c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit ea7f4bae8a2ae72470b895476faf9a368496aa8d
galaxyp
parents: 2
diff changeset
554 <param name="max_charge" value="3"/>
d8962e547c9c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit ea7f4bae8a2ae72470b895476faf9a368496aa8d
galaxyp
parents: 2
diff changeset
555 <param name="min_peaks" value="10"/>
d8962e547c9c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit ea7f4bae8a2ae72470b895476faf9a368496aa8d
galaxyp
parents: 2
diff changeset
556 <param name="isotope_error" value="0"/>
d8962e547c9c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit ea7f4bae8a2ae72470b895476faf9a368496aa8d
galaxyp
parents: 2
diff changeset
557 <param name="min_score" value="12"/>
d8962e547c9c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit ea7f4bae8a2ae72470b895476faf9a368496aa8d
galaxyp
parents: 2
diff changeset
558 <param name="min_length" value="7"/>
d8962e547c9c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit ea7f4bae8a2ae72470b895476faf9a368496aa8d
galaxyp
parents: 2
diff changeset
559 <param name="max_length" value="45"/>
d8962e547c9c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit ea7f4bae8a2ae72470b895476faf9a368496aa8d
galaxyp
parents: 2
diff changeset
560 <param name="num_random_peptides" value="1000"/>
d8962e547c9c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit ea7f4bae8a2ae72470b895476faf9a368496aa8d
galaxyp
parents: 2
diff changeset
561 </section>
d8962e547c9c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit ea7f4bae8a2ae72470b895476faf9a368496aa8d
galaxyp
parents: 2
diff changeset
562 </section>
5
2045f3b68773 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 4b3991069094a9703904b2041d983315bf539aee
galaxyp
parents: 4
diff changeset
563 <output name="psm_rank_txt">
3
d8962e547c9c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit ea7f4bae8a2ae72470b895476faf9a368496aa8d
galaxyp
parents: 2
diff changeset
564 <assert_contents>
d8962e547c9c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit ea7f4bae8a2ae72470b895476faf9a368496aa8d
galaxyp
parents: 2
diff changeset
565 <has_text text="LVVVGADGVGK" />
d8962e547c9c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit ea7f4bae8a2ae72470b895476faf9a368496aa8d
galaxyp
parents: 2
diff changeset
566 <not_has_text text="AHSSMVGVNLPQK" />
d8962e547c9c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit ea7f4bae8a2ae72470b895476faf9a368496aa8d
galaxyp
parents: 2
diff changeset
567 <has_text text="02CPTAC_LUAD_W_BI_20180518_KR_f15:25149:2" />
6
01fd80b15053 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
galaxyp
parents: 5
diff changeset
568 <has_n_columns n="22" />
3
d8962e547c9c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit ea7f4bae8a2ae72470b895476faf9a368496aa8d
galaxyp
parents: 2
diff changeset
569 </assert_contents>
d8962e547c9c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit ea7f4bae8a2ae72470b895476faf9a368496aa8d
galaxyp
parents: 2
diff changeset
570 </output>
d8962e547c9c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit ea7f4bae8a2ae72470b895476faf9a368496aa8d
galaxyp
parents: 2
diff changeset
571 <output name="log_txt">
d8962e547c9c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit ea7f4bae8a2ae72470b895476faf9a368496aa8d
galaxyp
parents: 2
diff changeset
572 <assert_contents>
d8962e547c9c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit ea7f4bae8a2ae72470b895476faf9a368496aa8d
galaxyp
parents: 2
diff changeset
573 <has_text text="Ignore peptide (reason: exist in reference database): AHSSMVGVNLPQK" />
d8962e547c9c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit ea7f4bae8a2ae72470b895476faf9a368496aa8d
galaxyp
parents: 2
diff changeset
574 </assert_contents>
d8962e547c9c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit ea7f4bae8a2ae72470b895476faf9a368496aa8d
galaxyp
parents: 2
diff changeset
575 </output>
d8962e547c9c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit ea7f4bae8a2ae72470b895476faf9a368496aa8d
galaxyp
parents: 2
diff changeset
576 </test>
d8962e547c9c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit ea7f4bae8a2ae72470b895476faf9a368496aa8d
galaxyp
parents: 2
diff changeset
577
d8962e547c9c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit ea7f4bae8a2ae72470b895476faf9a368496aa8d
galaxyp
parents: 2
diff changeset
578 <!-- Test-3 MGF peptide Uniprot.fasta -->
6
01fd80b15053 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
galaxyp
parents: 5
diff changeset
579 <test expect_num_outputs="2">
1
6b5ce9e2b0d0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 3f50a508dbb9050be48de5685cec9a82683d8457
galaxyp
parents: 0
diff changeset
580 <conditional name="validation">
6b5ce9e2b0d0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 3f50a508dbb9050be48de5685cec9a82683d8457
galaxyp
parents: 0
diff changeset
581 <param name="task_type" value="novel"/>
6b5ce9e2b0d0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 3f50a508dbb9050be48de5685cec9a82683d8457
galaxyp
parents: 0
diff changeset
582 </conditional>
0
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
parents:
diff changeset
583 <section name="req_inputs">
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
parents:
diff changeset
584 <conditional name="input_type">
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
parents:
diff changeset
585 <param name="input_type_selector" value="peptide"/>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
parents:
diff changeset
586 <conditional name="multiple">
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
parents:
diff changeset
587 <param name="peptide_input_selector" value="single" />
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
parents:
diff changeset
588 <param name="input" value="ELGSSDLTAR"/>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
parents:
diff changeset
589 </conditional>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
parents:
diff changeset
590 </conditional>
1
6b5ce9e2b0d0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 3f50a508dbb9050be48de5685cec9a82683d8457
galaxyp
parents: 0
diff changeset
591 <conditional name="db_type">
6b5ce9e2b0d0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 3f50a508dbb9050be48de5685cec9a82683d8457
galaxyp
parents: 0
diff changeset
592 <param name="db_type_selector" value="history" />
6b5ce9e2b0d0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 3f50a508dbb9050be48de5685cec9a82683d8457
galaxyp
parents: 0
diff changeset
593 <param name="db_file" ftype="fasta" value="Uniprot.fasta"/>
6b5ce9e2b0d0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 3f50a508dbb9050be48de5685cec9a82683d8457
galaxyp
parents: 0
diff changeset
594 </conditional>
6b5ce9e2b0d0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 3f50a508dbb9050be48de5685cec9a82683d8457
galaxyp
parents: 0
diff changeset
595 <conditional name="ms_dataset">
6b5ce9e2b0d0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 3f50a508dbb9050be48de5685cec9a82683d8457
galaxyp
parents: 0
diff changeset
596 <param name="ms_dataset_type" value="history"/>
6b5ce9e2b0d0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 3f50a508dbb9050be48de5685cec9a82683d8457
galaxyp
parents: 0
diff changeset
597 <param name="spectrum_files" ftype="mgf" value="iTRAQ_f4.mgf"/>
6b5ce9e2b0d0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 3f50a508dbb9050be48de5685cec9a82683d8457
galaxyp
parents: 0
diff changeset
598 </conditional>
6b5ce9e2b0d0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 3f50a508dbb9050be48de5685cec9a82683d8457
galaxyp
parents: 0
diff changeset
599 <param name="indexType" value="1"/>
0
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
parents:
diff changeset
600 </section>
1
6b5ce9e2b0d0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 3f50a508dbb9050be48de5685cec9a82683d8457
galaxyp
parents: 0
diff changeset
601 <param name="parameter_set" value=""/>
0
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
parents:
diff changeset
602 <section name="modifications">
1
6b5ce9e2b0d0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 3f50a508dbb9050be48de5685cec9a82683d8457
galaxyp
parents: 0
diff changeset
603 <!-- 21: iTRAQ 4-plex of K [144.1020624208] -->
6b5ce9e2b0d0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 3f50a508dbb9050be48de5685cec9a82683d8457
galaxyp
parents: 0
diff changeset
604 <!-- 22: iTRAQ 4-plex of peptide N-term [144.1020624208] -->
6b5ce9e2b0d0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 3f50a508dbb9050be48de5685cec9a82683d8457
galaxyp
parents: 0
diff changeset
605 <param name="fixed_mod" value="1,21,22"/>
6b5ce9e2b0d0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 3f50a508dbb9050be48de5685cec9a82683d8457
galaxyp
parents: 0
diff changeset
606 <!-- 2: Oxidation of M [15.99491461956] -->
6b5ce9e2b0d0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 3f50a508dbb9050be48de5685cec9a82683d8457
galaxyp
parents: 0
diff changeset
607 <param name="var_mod" value="2"/>
0
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
parents:
diff changeset
608 <param name="max_mods" value="3"/>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
parents:
diff changeset
609 <param name="unmodified" value="True"/>
1
6b5ce9e2b0d0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 3f50a508dbb9050be48de5685cec9a82683d8457
galaxyp
parents: 0
diff changeset
610 <param name="aa" value="False"/>
0
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
parents:
diff changeset
611 </section>
1
6b5ce9e2b0d0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 3f50a508dbb9050be48de5685cec9a82683d8457
galaxyp
parents: 0
diff changeset
612 <section name="digestion">
6b5ce9e2b0d0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 3f50a508dbb9050be48de5685cec9a82683d8457
galaxyp
parents: 0
diff changeset
613 <param name="enzyme" value="1"/>
6b5ce9e2b0d0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 3f50a508dbb9050be48de5685cec9a82683d8457
galaxyp
parents: 0
diff changeset
614 <param name="max_missed_cleavages" value="2"/>
0
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
parents:
diff changeset
615 </section>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
parents:
diff changeset
616 <section name="ms_params">
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
parents:
diff changeset
617 <section name="tolerance_params">
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
parents:
diff changeset
618 <param name="precursor_tolerance" value="10"/>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
parents:
diff changeset
619 <param name="precursor_unit" value="ppm"/>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
parents:
diff changeset
620 <param name="tolerance" value="0.6"/>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
parents:
diff changeset
621 </section>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
parents:
diff changeset
622 <section name="search">
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
parents:
diff changeset
623 <param name="frag_method" value="1"/>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
parents:
diff changeset
624 <param name="scoring_method" value="1"/>
1
6b5ce9e2b0d0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 3f50a508dbb9050be48de5685cec9a82683d8457
galaxyp
parents: 0
diff changeset
625 <param name="extra_score_validation" value="False"/>
0
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
parents:
diff changeset
626 <param name="min_charge" value="2"/>
1
6b5ce9e2b0d0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 3f50a508dbb9050be48de5685cec9a82683d8457
galaxyp
parents: 0
diff changeset
627 <param name="max_charge" value="3"/>
0
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
parents:
diff changeset
628 <param name="min_peaks" value="10"/>
1
6b5ce9e2b0d0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 3f50a508dbb9050be48de5685cec9a82683d8457
galaxyp
parents: 0
diff changeset
629 <param name="isotope_error" value="0"/>
0
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
parents:
diff changeset
630 <param name="min_score" value="12"/>
1
6b5ce9e2b0d0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 3f50a508dbb9050be48de5685cec9a82683d8457
galaxyp
parents: 0
diff changeset
631 <param name="min_length" value="7"/>
0
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
parents:
diff changeset
632 <param name="max_length" value="45"/>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
parents:
diff changeset
633 <param name="num_random_peptides" value="1000"/>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
parents:
diff changeset
634 </section>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
parents:
diff changeset
635 </section>
5
2045f3b68773 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 4b3991069094a9703904b2041d983315bf539aee
galaxyp
parents: 4
diff changeset
636 <output name="psm_rank_txt">
0
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
parents:
diff changeset
637 <assert_contents>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
parents:
diff changeset
638 <has_text text="ELGSSDLTAR" />
1
6b5ce9e2b0d0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 3f50a508dbb9050be48de5685cec9a82683d8457
galaxyp
parents: 0
diff changeset
639 <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+"/>
6
01fd80b15053 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
galaxyp
parents: 5
diff changeset
640 <has_n_columns n="22" />
0
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
parents:
diff changeset
641 </assert_contents>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
parents:
diff changeset
642 </output>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
parents:
diff changeset
643 </test>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
parents:
diff changeset
644
3
d8962e547c9c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit ea7f4bae8a2ae72470b895476faf9a368496aa8d
galaxyp
parents: 2
diff changeset
645 <!-- Test-4 PepQueryDB known peptide gencode:human pep.txt -->
6
01fd80b15053 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
galaxyp
parents: 5
diff changeset
646 <test expect_num_outputs="2">
3
d8962e547c9c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit ea7f4bae8a2ae72470b895476faf9a368496aa8d
galaxyp
parents: 2
diff changeset
647 <conditional name="validation">
d8962e547c9c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit ea7f4bae8a2ae72470b895476faf9a368496aa8d
galaxyp
parents: 2
diff changeset
648 <param name="task_type" value="known"/>
d8962e547c9c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit ea7f4bae8a2ae72470b895476faf9a368496aa8d
galaxyp
parents: 2
diff changeset
649 </conditional>
d8962e547c9c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit ea7f4bae8a2ae72470b895476faf9a368496aa8d
galaxyp
parents: 2
diff changeset
650 <section name="req_inputs">
d8962e547c9c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit ea7f4bae8a2ae72470b895476faf9a368496aa8d
galaxyp
parents: 2
diff changeset
651 <conditional name="input_type">
d8962e547c9c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit ea7f4bae8a2ae72470b895476faf9a368496aa8d
galaxyp
parents: 2
diff changeset
652 <param name="input_type_selector" value="peptide"/>
d8962e547c9c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit ea7f4bae8a2ae72470b895476faf9a368496aa8d
galaxyp
parents: 2
diff changeset
653 <conditional name="multiple">
d8962e547c9c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit ea7f4bae8a2ae72470b895476faf9a368496aa8d
galaxyp
parents: 2
diff changeset
654 <param name="peptide_input_selector" value="single" />
d8962e547c9c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit ea7f4bae8a2ae72470b895476faf9a368496aa8d
galaxyp
parents: 2
diff changeset
655 <param name="input" value="AHSSMVGVNLPQK"/>
d8962e547c9c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit ea7f4bae8a2ae72470b895476faf9a368496aa8d
galaxyp
parents: 2
diff changeset
656 </conditional>
d8962e547c9c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit ea7f4bae8a2ae72470b895476faf9a368496aa8d
galaxyp
parents: 2
diff changeset
657 </conditional>
d8962e547c9c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit ea7f4bae8a2ae72470b895476faf9a368496aa8d
galaxyp
parents: 2
diff changeset
658 <conditional name="db_type">
d8962e547c9c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit ea7f4bae8a2ae72470b895476faf9a368496aa8d
galaxyp
parents: 2
diff changeset
659 <param name="db_type_selector" value="download" />
d8962e547c9c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit ea7f4bae8a2ae72470b895476faf9a368496aa8d
galaxyp
parents: 2
diff changeset
660 <param name="db_id" value="gencode:human"/>
d8962e547c9c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit ea7f4bae8a2ae72470b895476faf9a368496aa8d
galaxyp
parents: 2
diff changeset
661 </conditional>
d8962e547c9c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit ea7f4bae8a2ae72470b895476faf9a368496aa8d
galaxyp
parents: 2
diff changeset
662 <conditional name="ms_dataset">
d8962e547c9c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit ea7f4bae8a2ae72470b895476faf9a368496aa8d
galaxyp
parents: 2
diff changeset
663 <param name="ms_dataset_type" value="PepQueryDB"/>
d8962e547c9c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit ea7f4bae8a2ae72470b895476faf9a368496aa8d
galaxyp
parents: 2
diff changeset
664 <param name="dataset" value="CPTAC_LUAD_Discovery_Study_Proteome_PDC000153" />
d8962e547c9c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit ea7f4bae8a2ae72470b895476faf9a368496aa8d
galaxyp
parents: 2
diff changeset
665 </conditional>
d8962e547c9c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit ea7f4bae8a2ae72470b895476faf9a368496aa8d
galaxyp
parents: 2
diff changeset
666 <param name="indexType" value="1"/>
d8962e547c9c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit ea7f4bae8a2ae72470b895476faf9a368496aa8d
galaxyp
parents: 2
diff changeset
667 </section>
d8962e547c9c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit ea7f4bae8a2ae72470b895476faf9a368496aa8d
galaxyp
parents: 2
diff changeset
668 <section name="modifications">
d8962e547c9c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit ea7f4bae8a2ae72470b895476faf9a368496aa8d
galaxyp
parents: 2
diff changeset
669 <param name="unmodified" value="True"/>
d8962e547c9c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit ea7f4bae8a2ae72470b895476faf9a368496aa8d
galaxyp
parents: 2
diff changeset
670 </section>
5
2045f3b68773 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 4b3991069094a9703904b2041d983315bf539aee
galaxyp
parents: 4
diff changeset
671 <output name="psm_rank_txt">
3
d8962e547c9c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit ea7f4bae8a2ae72470b895476faf9a368496aa8d
galaxyp
parents: 2
diff changeset
672 <assert_contents>
d8962e547c9c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit ea7f4bae8a2ae72470b895476faf9a368496aa8d
galaxyp
parents: 2
diff changeset
673 <has_text text="AHSSMVGVNLPQK" />
d8962e547c9c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit ea7f4bae8a2ae72470b895476faf9a368496aa8d
galaxyp
parents: 2
diff changeset
674 <has_text text="6CPTAC_LUAD_W_BI_20180718_KL_f12:20286:3" />
6
01fd80b15053 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
galaxyp
parents: 5
diff changeset
675 <has_n_columns n="22" />
3
d8962e547c9c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit ea7f4bae8a2ae72470b895476faf9a368496aa8d
galaxyp
parents: 2
diff changeset
676 </assert_contents>
d8962e547c9c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit ea7f4bae8a2ae72470b895476faf9a368496aa8d
galaxyp
parents: 2
diff changeset
677 </output>
d8962e547c9c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit ea7f4bae8a2ae72470b895476faf9a368496aa8d
galaxyp
parents: 2
diff changeset
678 </test>
d8962e547c9c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit ea7f4bae8a2ae72470b895476faf9a368496aa8d
galaxyp
parents: 2
diff changeset
679
0
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
parents:
diff changeset
680 </tests>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
parents:
diff changeset
681 <help><![CDATA[
1
6b5ce9e2b0d0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 3f50a508dbb9050be48de5685cec9a82683d8457
galaxyp
parents: 0
diff changeset
682 **PepQuery2**
0
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
parents:
diff changeset
683
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
parents:
diff changeset
684 PepQuery_ is a universal targeted peptide search engine for identifying or validating known and novel peptides of interest in any local or publicly available mass spectrometry-based proteomics datasets.
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
parents:
diff changeset
685
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
parents:
diff changeset
686
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
parents:
diff changeset
687 PepQuery_ is a peptide-centric search engine for novel peptide identification and validation. Cancer genomics studies have identified a large number of genomic alterations that may lead to novel, cancer-specific protein sequences. Proteins resulted from these genomic alterations are attractive candidates for cancer biomarkers and therapeutic targets. The leading approach to proteomic validation of genomic alterations is to analyze tandem mass spectrometry (MS/MS) data using customized proteomics databases created from genomics data. Such analysis is time-consuming and requires thorough training and detailed knowledge in proteomics data analysis, leading to a gap between MS/MS data and the cancer genomics community. PepQuery does not require customized databases and allows quick and easy proteomic validation of genomic alterations.
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
parents:
diff changeset
688
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
parents:
diff changeset
689 PepQuery2 leverages a new MS/MS indexing approach and cloud storage to enable ultrafast, targeted identification of both novel and known peptides. PepQuery2 allows users to search more than one billion MS/MS data indexed in the PepQueryDB from any computers with internet access. It also supports direct analysis of user provided MS/MS data, any public datasets in PRIDE, MassIVE, jPOSTrepo and iProX, or Universal Spectrum Identifiers (USIs) from ProteomeXchange.
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
parents:
diff changeset
690
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
parents:
diff changeset
691 **Inputs**
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
parents:
diff changeset
692 - A sequence to match, one of the following:
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
parents:
diff changeset
693
1
6b5ce9e2b0d0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 3f50a508dbb9050be48de5685cec9a82683d8457
galaxyp
parents: 0
diff changeset
694 - A peptide string (or strings separated by commas)
6b5ce9e2b0d0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 3f50a508dbb9050be48de5685cec9a82683d8457
galaxyp
parents: 0
diff changeset
695 - A history dataset with a list of peptides
0
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
parents:
diff changeset
696 - A protein string or a history dataset with a protein fasta
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
parents:
diff changeset
697 - A DNA string that is at least 60 base pairs in length
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
parents:
diff changeset
698
1
6b5ce9e2b0d0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 3f50a508dbb9050be48de5685cec9a82683d8457
galaxyp
parents: 0
diff changeset
699
6b5ce9e2b0d0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 3f50a508dbb9050be48de5685cec9a82683d8457
galaxyp
parents: 0
diff changeset
700 - MS/MS data used for identification, one of the following:
6b5ce9e2b0d0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 3f50a508dbb9050be48de5685cec9a82683d8457
galaxyp
parents: 0
diff changeset
701
6b5ce9e2b0d0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 3f50a508dbb9050be48de5685cec9a82683d8457
galaxyp
parents: 0
diff changeset
702 - Mass Spectrometry history datasets in MGF, mzML, or mzXML format
6b5ce9e2b0d0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 3f50a508dbb9050be48de5685cec9a82683d8457
galaxyp
parents: 0
diff changeset
703 - An Indexed MS/MS dataset (from previous PepQuery2 run or from **PepQuery2 index** tool.)
6b5ce9e2b0d0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 3f50a508dbb9050be48de5685cec9a82683d8457
galaxyp
parents: 0
diff changeset
704 - PepQueryDB dataset IDs
6b5ce9e2b0d0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 3f50a508dbb9050be48de5685cec9a82683d8457
galaxyp
parents: 0
diff changeset
705
6b5ce9e2b0d0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 3f50a508dbb9050be48de5685cec9a82683d8457
galaxyp
parents: 0
diff changeset
706 ..
0
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
parents:
diff changeset
707
1
6b5ce9e2b0d0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 3f50a508dbb9050be48de5685cec9a82683d8457
galaxyp
parents: 0
diff changeset
708 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.
6b5ce9e2b0d0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 3f50a508dbb9050be48de5685cec9a82683d8457
galaxyp
parents: 0
diff changeset
709
6b5ce9e2b0d0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 3f50a508dbb9050be48de5685cec9a82683d8457
galaxyp
parents: 0
diff changeset
710
0
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
parents:
diff changeset
711 - Dataset IDs from public proteomics data repositories: PRIDE, MassIVE, jPOSTrepo and iProX
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
parents:
diff changeset
712
1
6b5ce9e2b0d0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 3f50a508dbb9050be48de5685cec9a82683d8457
galaxyp
parents: 0
diff changeset
713 ..
6b5ce9e2b0d0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 3f50a508dbb9050be48de5685cec9a82683d8457
galaxyp
parents: 0
diff changeset
714
6b5ce9e2b0d0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 3f50a508dbb9050be48de5685cec9a82683d8457
galaxyp
parents: 0
diff changeset
715 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
6b5ce9e2b0d0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 3f50a508dbb9050be48de5685cec9a82683d8457
galaxyp
parents: 0
diff changeset
716
0
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
parents:
diff changeset
717 - A reference protein fasta database, novel peptides matching a reference sequence will be excluded.
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
parents:
diff changeset
718
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
parents:
diff changeset
719 - A protein fasta file
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
parents:
diff changeset
720 - The ID for a public reference protein database from RefSeq, GENCODE, Ensembl or UniProt.
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
parents:
diff changeset
721
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
parents:
diff changeset
722
1
6b5ce9e2b0d0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 3f50a508dbb9050be48de5685cec9a82683d8457
galaxyp
parents: 0
diff changeset
723 **Options**
6b5ce9e2b0d0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 3f50a508dbb9050be48de5685cec9a82683d8457
galaxyp
parents: 0
diff changeset
724
6b5ce9e2b0d0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 3f50a508dbb9050be48de5685cec9a82683d8457
galaxyp
parents: 0
diff changeset
725 - MS/MS searching parameter set name
6b5ce9e2b0d0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 3f50a508dbb9050be48de5685cec9a82683d8457
galaxyp
parents: 0
diff changeset
726
6b5ce9e2b0d0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 3f50a508dbb9050be48de5685cec9a82683d8457
galaxyp
parents: 0
diff changeset
727 ..
6b5ce9e2b0d0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 3f50a508dbb9050be48de5685cec9a82683d8457
galaxyp
parents: 0
diff changeset
728
6b5ce9e2b0d0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 3f50a508dbb9050be48de5685cec9a82683d8457
galaxyp
parents: 0
diff changeset
729 Setting a *parameter set name* will change defaults for various options, These may be overridden by manually setting the option.
6b5ce9e2b0d0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 3f50a508dbb9050be48de5685cec9a82683d8457
galaxyp
parents: 0
diff changeset
730 The **PepQuery2 Show Sets** tool *PepQuery Predefined Parameter Sets* will list those available along with the option values that will be set.
6b5ce9e2b0d0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 3f50a508dbb9050be48de5685cec9a82683d8457
galaxyp
parents: 0
diff changeset
731 The **PepQuery2 Show Sets** tool *PepQuery Datasets* column *parameter_set* column for each PepQueryDB dataset.
6b5ce9e2b0d0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 3f50a508dbb9050be48de5685cec9a82683d8457
galaxyp
parents: 0
diff changeset
732
6b5ce9e2b0d0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 3f50a508dbb9050be48de5685cec9a82683d8457
galaxyp
parents: 0
diff changeset
733
6b5ce9e2b0d0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 3f50a508dbb9050be48de5685cec9a82683d8457
galaxyp
parents: 0
diff changeset
734 - Override default options
6b5ce9e2b0d0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 3f50a508dbb9050be48de5685cec9a82683d8457
galaxyp
parents: 0
diff changeset
735
6b5ce9e2b0d0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 3f50a508dbb9050be48de5685cec9a82683d8457
galaxyp
parents: 0
diff changeset
736 ..
6b5ce9e2b0d0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 3f50a508dbb9050be48de5685cec9a82683d8457
galaxyp
parents: 0
diff changeset
737
6b5ce9e2b0d0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 3f50a508dbb9050be48de5685cec9a82683d8457
galaxyp
parents: 0
diff changeset
738 Values for modifications are provided in a select list.
6b5ce9e2b0d0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 3f50a508dbb9050be48de5685cec9a82683d8457
galaxyp
parents: 0
diff changeset
739 The **PepQuery2 Show Sets** tool *PepQuery Modifications* lists all available modifications.
6b5ce9e2b0d0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 3f50a508dbb9050be48de5685cec9a82683d8457
galaxyp
parents: 0
diff changeset
740
0
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
parents:
diff changeset
741 **Outputs**
4
29e6417b913c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit b7f27d4872020b09656a2f53d667217b762fa202
galaxyp
parents: 3
diff changeset
742 - Log.txt:
29e6417b913c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit b7f27d4872020b09656a2f53d667217b762fa202
galaxyp
parents: 3
diff changeset
743
29e6417b913c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit b7f27d4872020b09656a2f53d667217b762fa202
galaxyp
parents: 3
diff changeset
744 - Logging output from PepQuery2
29e6417b913c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit b7f27d4872020b09656a2f53d667217b762fa202
galaxyp
parents: 3
diff changeset
745 - When searching for *novel* peptides ignored peptide have a log message similar to:
29e6417b913c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit b7f27d4872020b09656a2f53d667217b762fa202
galaxyp
parents: 3
diff changeset
746
29e6417b913c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit b7f27d4872020b09656a2f53d667217b762fa202
galaxyp
parents: 3
diff changeset
747 - Ignore peptide (reason: exist in reference database): *PEPTIDE*
29e6417b913c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit b7f27d4872020b09656a2f53d667217b762fa202
galaxyp
parents: 3
diff changeset
748
29e6417b913c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit b7f27d4872020b09656a2f53d667217b762fa202
galaxyp
parents: 3
diff changeset
749 - When searching for *known* proteins, ignored protein have a log message similar to:
29e6417b913c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit b7f27d4872020b09656a2f53d667217b762fa202
galaxyp
parents: 3
diff changeset
750
29e6417b913c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit b7f27d4872020b09656a2f53d667217b762fa202
galaxyp
parents: 3
diff changeset
751 - Target protein is not present in database *DATABASE_NAME*: *PROTEIN_NAME*, ignored!
29e6417b913c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit b7f27d4872020b09656a2f53d667217b762fa202
galaxyp
parents: 3
diff changeset
752
0
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
parents:
diff changeset
753 - Parameters:
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
parents:
diff changeset
754
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
parents:
diff changeset
755 - parameters used in the search
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
parents:
diff changeset
756
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
parents:
diff changeset
757 - PSM - tabular with columns:
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
parents:
diff changeset
758
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
parents:
diff changeset
759 - peptide modification n spectrum_title charge exp_mass ppm pep_mass mz score n_db total_db n_random total_random pvalue
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
parents:
diff changeset
760
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
parents:
diff changeset
761 - PSM Rank - tabular with columns:
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
parents:
diff changeset
762
4
29e6417b913c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit b7f27d4872020b09656a2f53d667217b762fa202
galaxyp
parents: 3
diff changeset
763 - 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
0
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
parents:
diff changeset
764
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
parents:
diff changeset
765 - An MGF with the best matching spectrums
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
parents:
diff changeset
766
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
parents:
diff changeset
767 - Detail - tabular with columns:
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
parents:
diff changeset
768
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
parents:
diff changeset
769 - spectrum_title peptide modification pep_mass score
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
parents:
diff changeset
770
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
parents:
diff changeset
771 - PSM annotation - tabular with columns:
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
parents:
diff changeset
772
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
parents:
diff changeset
773 - peptide Query calc_mr observed_mz charge pepSeq m_label m_mz m_intensity mz intensity
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
parents:
diff changeset
774
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
parents:
diff changeset
775 - PTM - tabular with columns:
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
parents:
diff changeset
776
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
parents:
diff changeset
777 - spectrum_title peptide charge exp_mass pep_mass tol_ppm tol_da isotope_error modification score
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
parents:
diff changeset
778
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
parents:
diff changeset
779 - PTM Detail - tabular with columns:
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
parents:
diff changeset
780
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
parents:
diff changeset
781 - peptide modification n spectrum_title charge exp_mass tol_ppm tol_da isotope_error pep_mass mz score n_db total_db n_random total_random pvalue rank ptm_spectrum_title ptm_peptide ptm_charge ptm_exp_mass ptm_pep_mass ptm_tol_ppm ptm_tol_da ptm_isotope_error ptm_modification ptm_score
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
parents:
diff changeset
782
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
parents:
diff changeset
783 - An Indexed MS/MS dataset *when MS/MS data is MGF, mzML, or mzXML history datasets*
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
parents:
diff changeset
784
4
29e6417b913c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit b7f27d4872020b09656a2f53d667217b762fa202
galaxyp
parents: 3
diff changeset
785
0
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
parents:
diff changeset
786 .. _PepQuery: http://pepquery.org/document.html
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
parents:
diff changeset
787
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
parents:
diff changeset
788 ]]></help>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
parents:
diff changeset
789 <expand macro="citations" />
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
parents:
diff changeset
790 </tool>