Mercurial > repos > galaxyp > pepquery

annotate pepquery.xml @ 1:9b5989900a87 draft

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/pepquery commit 542fee4158c3dbd0c5ad8cd7e97b77f55982e0bf"
author galaxyp
date Fri, 17 Jul 2020 21:05:11 +0000
parents 851dcf14ee3a
children 36716331fb7a
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
851dcf14ee3a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
1 <tool id="pepquery" name="PepQuery" version="@VERSION@.0">
851dcf14ee3a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
2 <description>Peptide-centric search engine for novel peptide identification and validation.</description>
851dcf14ee3a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
3 <macros>
851dcf14ee3a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
4 <import>macros.xml</import>
851dcf14ee3a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
5 </macros>
851dcf14ee3a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
6 <requirements>
851dcf14ee3a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
7 <requirement type="package" version="@VERSION@">pepquery</requirement>
851dcf14ee3a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
8 </requirements>
851dcf14ee3a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
9 <stdio>
851dcf14ee3a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
10 <exit_code range="1:" level="fatal" description="Failed" />
851dcf14ee3a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
11 <regex match="Exception"
851dcf14ee3a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
12 source="stderr"
851dcf14ee3a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
13 level="fatal"
851dcf14ee3a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
14 description="java Exception" />
851dcf14ee3a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
15 </stdio>
851dcf14ee3a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
16 <command><![CDATA[
851dcf14ee3a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
17 #import re
851dcf14ee3a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
18 #set $spectrum_file = $re.sub('\s','_',$re.sub('[.][^.]*$','',$req_inputs.spectrum_file.display_name.split('/')[-1])) + ".mgf"
851dcf14ee3a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
19 #set $db_file = $re.sub('\s','_',$re.sub('[.][^.]*$','',$req_inputs.db_file.display_name.split('/')[-1])) + ".fa"
851dcf14ee3a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
20 ln -s '$req_inputs.spectrum_file' '$spectrum_file' &&
851dcf14ee3a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
21 ln -s '$req_inputs.db_file' '$db_file' &&
851dcf14ee3a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
22 pepquery
851dcf14ee3a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
23 -ms '$spectrum_file'
851dcf14ee3a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
24 -db '$db_file'
851dcf14ee3a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
25 #if $req_inputs.input_type.input_type_selector == 'peptide'
851dcf14ee3a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
26 -pep '$req_inputs.input_type.multiple.input'
851dcf14ee3a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
27 #else
851dcf14ee3a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
28 -t '$req_inputs.input_type.input_type_selector'
851dcf14ee3a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
29 #if int(str($req_inputs.input_type.input_type_selector)) == 1
851dcf14ee3a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
30 -i '$req_inputs.input_type.multiple.input'
851dcf14ee3a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
31 #else
851dcf14ee3a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
32 -i '$req_inputs.input_type.input'
851dcf14ee3a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
33 #if int(str($req_inputs.input_type.input_type_selector)) == 2
851dcf14ee3a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
34 #if $req_inputs.input_type.frame == 'None'
851dcf14ee3a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
35 -f '0'
851dcf14ee3a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
36 #else
851dcf14ee3a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
37 -f '$req_inputs.input_type.frame'
851dcf14ee3a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
38 #end if
851dcf14ee3a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
39 #else
851dcf14ee3a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
40 -anno '$req_inputs.input_type.anno'
851dcf14ee3a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
41 #end if
851dcf14ee3a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
42 #end if
851dcf14ee3a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
43 #end if
1
9b5989900a87 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 542fee4158c3dbd0c5ad8cd7e97b77f55982e0bf"
galaxyp
parents: 0
diff changeset
44 -indexType $req_inputs.indexType
0
851dcf14ee3a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
45 #if $modifications.fixed_mod
851dcf14ee3a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
46 -fixMod '$modifications.fixed_mod'
851dcf14ee3a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
47 #end if
851dcf14ee3a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
48 #if $modifications.var_mod
851dcf14ee3a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
49 -varMod '$modifications.var_mod'
851dcf14ee3a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
50 #end if
851dcf14ee3a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
51 -maxVar '$modifications.max_mods'
851dcf14ee3a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
52 $modifications.unmodified
851dcf14ee3a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
53 $modifications.aa
851dcf14ee3a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
54 -tol '$ms_params.tolerance_params.precursor_tolerance'
851dcf14ee3a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
55 -tolu '$ms_params.tolerance_params.precursor_unit'
851dcf14ee3a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
56 -itol '$ms_params.tolerance_params.tolerance'
851dcf14ee3a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
57 -e '$ms_params.digestion.enzyme'
851dcf14ee3a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
58 -fragmentMethod '$ms_params.search.frag_method'
851dcf14ee3a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
59 -m '$ms_params.search.scoring_method'
851dcf14ee3a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
60 -maxCharge '$ms_params.search.max_charge'
851dcf14ee3a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
61 -minCharge '$ms_params.search.min_charge'
851dcf14ee3a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
62 -minPeaks '$ms_params.search.min_peaks'
851dcf14ee3a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
63 -minScore '$ms_params.search.min_score'
851dcf14ee3a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
64 -maxLength '$ms_params.search.max_length'
851dcf14ee3a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
65 -n '$ms_params.search.num_random_peptides'
851dcf14ee3a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
66 -o pepquery_output
851dcf14ee3a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
67 | sed 's/No valid peptide/Error: No valid peptide/' | tee >(cat 1>&2)
851dcf14ee3a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
68 #if $report_spectrum_file:
851dcf14ee3a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
69 && for f in pepquery_output/psm.txt pepquery_output/psm_annotation.txt pepquery_output/detail.txt pepquery_output/psm_rank.txt; do if [ -e \${f} ]; then cp \${f} \${f}.orig; awk 'BEGIN{FS="\t"; OFS="\t"; stc = 0;}; NR==1{for (i = 1; i <= NF; i++) {if (\$i == "spectrum_title") stc = i;}}; NR==1{if (stc>0){\$stc = "spectrum_file" FS \$stc}; print}; NR>1{if (stc>0){\$stc = "$spectrum_file" FS \$stc}; print}' \${f}.orig > \${f};fi;done
851dcf14ee3a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
70 #end if
851dcf14ee3a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
71 ]]>
851dcf14ee3a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
72 </command>
851dcf14ee3a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
73 <inputs>
851dcf14ee3a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
74 <section name="req_inputs" title="Input Data" expanded="true">
851dcf14ee3a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
75 <conditional name="input_type">
851dcf14ee3a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
76 <param name="input_type_selector" type="select" label="Input Type" argument="-t" help="" >
851dcf14ee3a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
77 <option value="peptide">peptide</option>
851dcf14ee3a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
78 <option value="1">protein</option>
851dcf14ee3a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
79 <option value="2">DNA (translate to protein sequences)</option>
851dcf14ee3a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
80 <!-- these are not working with pepquery version 1.3
851dcf14ee3a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
81 <option value="3">VCF (translate to protein sequences)</option>
851dcf14ee3a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
82 <option value="4">BED (translate to protein sequences)</option>
851dcf14ee3a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
83 <option value="5">GTF (translate to protein sequences)</option>
851dcf14ee3a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
84 -->
851dcf14ee3a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
85 </param>
851dcf14ee3a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
86 <when value="peptide">
851dcf14ee3a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
87 <conditional name="multiple">
851dcf14ee3a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
88 <param name="peptide_input_selector" type="select" label="Peptides?">
851dcf14ee3a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
89 <option value="multiple">Peptide list from your history</option>
851dcf14ee3a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
90 <option value="single">Single peptide entered as text</option>
851dcf14ee3a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
91 </param>
851dcf14ee3a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
92 <when value="multiple">
851dcf14ee3a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
93 <param name="input" type="data" format="txt" label="Peptide Sequences (.txt)" argument="-pep" help="Peptide sequence file containing peptides which you want to search (no column header, 1 peptide per line)." />
851dcf14ee3a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
94 </when>
851dcf14ee3a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
95 <when value="single">
851dcf14ee3a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
96 <param name="input" type="text" label="Peptide Sequence" argument="-pep" help="Peptide sequence which you want to search">
851dcf14ee3a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
97 <validator type="regex" message="Must be AA letters">^[AC-IK-NP-TV-Yac-ik-np-tv-y]+$</validator>
851dcf14ee3a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
98 </param>
851dcf14ee3a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
99 </when>
851dcf14ee3a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
100 </conditional>
851dcf14ee3a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
101 </when>
851dcf14ee3a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
102 <when value="1">
851dcf14ee3a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
103 <conditional name="multiple">
851dcf14ee3a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
104 <param name="protein_input_selector" type="select" label="Proteins?">
851dcf14ee3a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
105 <option value="multiple">Protein fasta from your history</option>
851dcf14ee3a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
106 <option value="single">Single protein entered as text</option>
851dcf14ee3a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
107 </param>
851dcf14ee3a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
108 <when value="multiple">
851dcf14ee3a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
109 <param name="input" type="data" format="fasta" label="Protein Sequences (.txt)" argument="-i" help="Protein fasta file containing proteins which you want to search." />
851dcf14ee3a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
110 </when>
851dcf14ee3a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
111 <when value="single">
851dcf14ee3a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
112 <param name="input" type="text" label="Protein Sequence" argument="-i" help="Protein sequence which you want to search">
851dcf14ee3a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
113 <validator type="regex" message="Must be AA letters">^[AC-IK-NP-TV-Yac-ik-np-tv-y]+$</validator>
851dcf14ee3a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
114 </param>
851dcf14ee3a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
115 </when>
851dcf14ee3a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
116 </conditional>
851dcf14ee3a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
117 </when>
851dcf14ee3a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
118 <when value="2">
851dcf14ee3a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
119 <param name="input" type="text" label="DNA Sequence (at least 60 bp)" argument="-i" help="DNA sequence which you want to search">
851dcf14ee3a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
120 <validator type="regex" message="Must be at least 60bp">^[acgtuAGCTU]{60}[acgtuAGCTU]*$</validator>
851dcf14ee3a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
121 </param>
851dcf14ee3a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
122 <param name="frame" type="select" label="Frame(s) for DNA translation" argument="-f" multiple="true" help="The frame(s) to translate DNA sequence to protein. Selecting nothing (default) keeps the longest frame">
851dcf14ee3a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
123 <option value="1">1</option>
851dcf14ee3a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
124 <option value="2">2</option>
851dcf14ee3a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
125 <option value="3">3</option>
851dcf14ee3a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
126 <option value="4">4</option>
851dcf14ee3a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
127 <option value="5">5</option>
851dcf14ee3a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
128 <option value="6">6</option>
851dcf14ee3a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
129 </param>
851dcf14ee3a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
130 </when>
851dcf14ee3a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
131 <!-- these are not working with pepquery version 1.3
851dcf14ee3a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
132 <when value="3">
851dcf14ee3a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
133 <param name="input" type="data" format="vcf" label="VCF File" argument="-i" help="" />
851dcf14ee3a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
134 <param name="anno" type="data_collection" label="Annotation Files" argument="-anno" help="Annotation files for the VCF file. Please follow preparation instructions here: http://bioconductor.org/packages/devel/bioc/html/PGA.html" />
851dcf14ee3a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
135 </when>
851dcf14ee3a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
136 <when value="4">
851dcf14ee3a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
137 <param name="input" type="data" format="bed" label="BED File" argument="-i" help="" />
851dcf14ee3a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
138 <param name="anno" type="data_collection" label="Annotation Files" argument="-anno" help="Annotation files for the BED file. Please follow preparation instructions here: http://bioconductor.org/packages/devel/bioc/html/PGA.html" />
851dcf14ee3a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
139 </when>
851dcf14ee3a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
140 <when value="5">
851dcf14ee3a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
141 <param name="input" type="data" format="gtf" label="GTF File" argument="-i" help="" />
851dcf14ee3a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
142 <param name="anno" type="data_collection" label="Annotation Files" argument="-anno" help="Annotation files for the GTF file. Please follow preparation instructions here: http://bioconductor.org/packages/devel/bioc/html/PGA.html" />
851dcf14ee3a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
143 </when>
851dcf14ee3a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
144 -->
851dcf14ee3a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
145 </conditional>
851dcf14ee3a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
146 <param name="db_file" type="data" format="fasta" label="Protein Reference Database File" argument="-db" help="an input sequence that matches a reference will be ignored." />
851dcf14ee3a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
147 <param name="spectrum_file" type="data" format="mgf" label="Spectrum File" argument="-ms" help="Spectrum file used for identification, mgf format" />
1
9b5989900a87 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 542fee4158c3dbd0c5ad8cd7e97b77f55982e0bf"
galaxyp
parents: 0
diff changeset
148 <param name="indexType" type="select" label="Report Spectrum Scan as" argument="-indexType" help="" >
9b5989900a87 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 542fee4158c3dbd0c5ad8cd7e97b77f55982e0bf"
galaxyp
parents: 0
diff changeset
149 <option value="1" selected="true">index (1-based) in MGF</option>
9b5989900a87 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 542fee4158c3dbd0c5ad8cd7e97b77f55982e0bf"
galaxyp
parents: 0
diff changeset
150 <option value="2">spectrum title in MGF</option>
9b5989900a87 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 542fee4158c3dbd0c5ad8cd7e97b77f55982e0bf"
galaxyp
parents: 0
diff changeset
151 </param>
0
851dcf14ee3a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
152 </section>
851dcf14ee3a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
153 <section name="modifications" title="Modifications" expanded="false">
851dcf14ee3a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
154 <param name="fixed_mod" type="select" label="Fixed modification(s)" multiple="true" argument="-fixMod" help="Fixed modification">
851dcf14ee3a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
155 <option value="6" selected="true">Carbamidomethylation of C (57.02146372057) modaa</option>
851dcf14ee3a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
156 <option value="117">Oxidation of M (15.99491461956) modaa</option>
851dcf14ee3a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
157 <expand macro="modifications" />
851dcf14ee3a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
158 </param>
851dcf14ee3a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
159 <param name="var_mod" type="select" label="Variable modification(s)" multiple="true" argument="-varMod" help="Variable modification" >
851dcf14ee3a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
160 <option value="117" selected="true">Oxidation of M (15.99491461956) modaa</option>
851dcf14ee3a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
161 <option value="6">Carbamidomethylation of C (57.02146372057) modaa</option>
851dcf14ee3a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
162 <expand macro="modifications" />
851dcf14ee3a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
163 </param>
851dcf14ee3a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
164 <param name="max_mods" type="integer" label="Max Modifications" value="3" argument="-maxVar" help="Max number of variable modifications" />
851dcf14ee3a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
165 <param name="unmodified" type="boolean" truevalue="-um" falsevalue="" checked="false" label="Unmodified?" argument="-um" help="Validation with unrestricted modification searching" />
851dcf14ee3a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
166 <param name="aa" type="boolean" truevalue="-aa" falsevalue="" checked="false" label="Consider amino acid substitution modifications?" argument="-aa" help="Whether or not to consider aa substitution modifications when perform modification filtering." />
851dcf14ee3a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
167 </section>
851dcf14ee3a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
168 <section name="ms_params" title="Mass spectrometer" expanded="false">
851dcf14ee3a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
169 <section name="tolerance_params" title="Tolerance" expanded="true">
851dcf14ee3a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
170 <param name="precursor_tolerance" type="integer" value="10" label="Precursor Tolerance" argument="-tol" 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." />
851dcf14ee3a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
171 <param name="precursor_unit" type="select" label="Precursor Unit" argument="-tolu" help="The unit of precursor ion m/z tolerance">
851dcf14ee3a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
172 <option value="ppm" selected="true">ppm</option>
851dcf14ee3a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
173 <option value="Da">Da</option>
851dcf14ee3a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
174 </param>
851dcf14ee3a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
175 <param name="tolerance" type="float" value="0.6" label="Tolerance" argument="-itol" help="Error window for MS/MS fragment ion mass values in Da unit." />
851dcf14ee3a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
176 </section>
851dcf14ee3a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
177 <section name="digestion" title="Digestion" expanded="false">
851dcf14ee3a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
178 <param name="enzyme" type="select" label="Enzyme" argument="-e" help="Enzyme used for protein digestion" >
851dcf14ee3a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
179 <option value="0">Non enzyme</option>
851dcf14ee3a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
180 <option value="1" selected="true">Trypsin</option>
851dcf14ee3a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
181 <option value="2">Trypsin (no P rule)</option>
851dcf14ee3a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
182 <option value="3">Arg-C</option>
851dcf14ee3a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
183 <option value="4">Arg-C (no P rule)</option>
851dcf14ee3a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
184 <option value="5">Arg-N</option>
851dcf14ee3a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
185 <option value="6">Glu-C</option>
851dcf14ee3a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
186 <option value="7">Lys-C</option>
851dcf14ee3a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
187 </param>
851dcf14ee3a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
188 <param name="max_missed_cleavages" type="integer" value="2" label="Max Missed Cleavages" argument="-c" help="The max missed cleavages" />
851dcf14ee3a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
189 </section>
851dcf14ee3a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
190 <section name="search" title="PSM" expanded="false">
851dcf14ee3a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
191 <param name="frag_method" type="select" label="Fragmentation Method" argument="-fragmentMethod">
851dcf14ee3a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
192 <option value="1" selected="true">CID/HCD</option>
851dcf14ee3a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
193 <option value="2">ETD</option>
851dcf14ee3a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
194 </param>
851dcf14ee3a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
195 <param name="scoring_method" type="select" label="Scoring Method" argument="-m">
851dcf14ee3a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
196 <option value="1" selected="true">HyperScore</option>
851dcf14ee3a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
197 <option value="2">MVH</option>
851dcf14ee3a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
198 </param>
851dcf14ee3a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
199 <param name="max_charge" type="integer" value="3" label="Max Charge" argument="-maxCharge" help="The maximum charge to consider if the charge state is not available" />
851dcf14ee3a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
200 <param name="min_charge" type="integer" value="2" label="Minimum Charge" argument="-minCharge" help="The minimum charge to consider if the charge state is not available" />
851dcf14ee3a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
201 <param name="min_peaks" type="integer" value="10" label="Minimum Peaks" argument="-minPeaks" help="Min peaks in spectrum" />
851dcf14ee3a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
202 <param name="min_score" type="integer" value="12" label="Minimum Score" argument="-minScore" help="Minimum score to consider for peptide searching" />
851dcf14ee3a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
203 <param name="max_length" type="integer" value="45" label="Maximum length of peptide" argument="-maxLength" help="The maximum length of peptide to consider." />
851dcf14ee3a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
204 <param name="num_random_peptides" type="integer" value="1000" label="Number of Random Peptides" argument="-n" help="The number of random peptides" />
851dcf14ee3a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
205 </section>
851dcf14ee3a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
206 </section>
851dcf14ee3a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
207 <param name="report_spectrum_file" type="boolean" truevalue="spectrum_file," falsevalue="" checked="false" label="Add spectrum_file column" help="Add a spectrum_file column before the spectrum_title column. Useful for combining pepquery outputs." />
851dcf14ee3a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
208 </inputs>
851dcf14ee3a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
209 <outputs>
851dcf14ee3a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
210 <data format="tabular" name="psm_annotation" from_work_dir="pepquery_output/psm_annotation.txt" label="${tool.name} on ${on_string}: PSM Annotation">
851dcf14ee3a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
211 <actions>
851dcf14ee3a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
212 <action name="comment_lines" type="metadata" default="1" />
851dcf14ee3a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
213 <action name="column_names" type="metadata" default="peptide,Query,calc_mr,observed_mz,charge,pepSeq,m_label,m_mz,m_intensity,mz,intensity" />
851dcf14ee3a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
214 </actions>
851dcf14ee3a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
215 </data>
851dcf14ee3a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
216 <data format="tabular" name="detail" from_work_dir="pepquery_output/detail.txt" label="${tool.name} on ${on_string}: Detail">
851dcf14ee3a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
217 <actions>
851dcf14ee3a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
218 <action name="comment_lines" type="metadata" default="1" />
851dcf14ee3a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
219 <action name="column_names" type="metadata" default="${report_spectrum_file}spectrum_title,peptide,modification,pep_mass,score" />
851dcf14ee3a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
220 </actions>
851dcf14ee3a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
221 </data>
851dcf14ee3a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
222 <data format="tabular" name="psm" from_work_dir="pepquery_output/psm.txt" label="${tool.name} on ${on_string}: PSM">
851dcf14ee3a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
223 <actions>
851dcf14ee3a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
224 <action name="comment_lines" type="metadata" default="1" />
851dcf14ee3a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
225 <action name="column_names" type="metadata" default="peptide,modification,n,${report_spectrum_file}spectrum_title,charge,exp_mass,ppm,pep_mass,mz,score,n_db,total_db,n_random,total_random,pvalue" />
851dcf14ee3a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
226 </actions>
851dcf14ee3a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
227 </data>
851dcf14ee3a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
228 <data format="tabular" name="psm_rank_txt" from_work_dir="pepquery_output/psm_rank.txt" label="${tool.name} on ${on_string}: PSM Rank (txt)">
851dcf14ee3a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
229 <actions>
851dcf14ee3a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
230 <action name="comment_lines" type="metadata" default="1" />
851dcf14ee3a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
231 <action name="column_names" type="metadata" default="peptide,modification,n,${report_spectrum_file}spectrum_title,charge,exp_mass,ppm,pep_mass,mz,score,n_db,total_db,n_random,total_random,pvalue,rank,n_ptm" />
851dcf14ee3a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
232 </actions>
851dcf14ee3a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
233 </data>
851dcf14ee3a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
234 <data format="mgf" name="psm_rank_mgf" from_work_dir="pepquery_output/psm_rank.mgf" label="${tool.name} on ${on_string}: PSM Rank (mgf)"/>
851dcf14ee3a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
235 </outputs>
851dcf14ee3a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
236 <tests>
851dcf14ee3a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
237 <test>
851dcf14ee3a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
238 <section name="req_inputs">
851dcf14ee3a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
239 <conditional name="input_type">
851dcf14ee3a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
240 <param name="input_type_selector" value="peptide"/>
851dcf14ee3a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
241 <conditional name="multiple">
851dcf14ee3a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
242 <param name="peptide_input_selector" value="single" />
851dcf14ee3a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
243 <param name="input" value="ELGSSDLTAR"/>
851dcf14ee3a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
244 </conditional>
851dcf14ee3a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
245 </conditional>
851dcf14ee3a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
246 <param name="db_file" ftype="fasta" value="Uniprot.fasta"/>
851dcf14ee3a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
247 <param name="spectrum_file" ftype="mgf" value="iTRAQ_f4.mgf"/>
851dcf14ee3a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
248 </section>
851dcf14ee3a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
249 <section name="modifications">
851dcf14ee3a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
250 <param name="fixed_mod" value="6,103,157"/>
851dcf14ee3a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
251 <param name="var_mod" value="117"/>
851dcf14ee3a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
252 <param name="max_mods" value="3"/>
851dcf14ee3a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
253 <param name="unmodified" value="False"/>
851dcf14ee3a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
254 <param name="aa" value="True"/>
851dcf14ee3a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
255 </section>
851dcf14ee3a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
256 <section name="ms_params">
851dcf14ee3a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
257 <section name="tolerance_params">
851dcf14ee3a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
258 <param name="precursor_tolerance" value="10"/>
851dcf14ee3a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
259 <param name="precursor_unit" value="ppm"/>
851dcf14ee3a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
260 <param name="tolerance" value="0.6"/>
851dcf14ee3a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
261 </section>
851dcf14ee3a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
262 <section name="digestion">
851dcf14ee3a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
263 <param name="enzyme" value="0"/>
851dcf14ee3a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
264 <param name="max_missed_cleavages" value="2"/>
851dcf14ee3a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
265 </section>
851dcf14ee3a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
266 <section name="search">
851dcf14ee3a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
267 <param name="frag_method" value="1"/>
851dcf14ee3a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
268 <param name="scoring_method" value="1"/>
851dcf14ee3a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
269 <param name="max_charge" value="3"/>
851dcf14ee3a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
270 <param name="min_charge" value="2"/>
851dcf14ee3a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
271 <param name="min_peaks" value="10"/>
851dcf14ee3a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
272 <param name="min_score" value="12"/>
851dcf14ee3a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
273 <param name="max_length" value="45"/>
851dcf14ee3a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
274 <param name="num_random_peptides" value="1000"/>
851dcf14ee3a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
275 </section>
851dcf14ee3a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
276 </section>
851dcf14ee3a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
277 <param name="report_spectrum_file" value="true"/>
851dcf14ee3a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
278 <output name="psm_rank_txt">
851dcf14ee3a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
279 <assert_contents>
851dcf14ee3a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
280 <has_text text="ELGSSDLTAR" />
851dcf14ee3a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
281 </assert_contents>
851dcf14ee3a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
282 </output>
851dcf14ee3a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
283 </test>
851dcf14ee3a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
284
851dcf14ee3a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
285 <test>
851dcf14ee3a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
286 <section name="req_inputs">
851dcf14ee3a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
287 <conditional name="input_type">
851dcf14ee3a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
288 <param name="input_type_selector" value="peptide"/>
851dcf14ee3a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
289 <conditional name="multiple">
851dcf14ee3a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
290 <param name="peptide_input_selector" value="multiple" />
851dcf14ee3a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
291 <param name="input" ftype="tabular" value="novel_peptides"/>
851dcf14ee3a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
292 </conditional>
851dcf14ee3a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
293 </conditional>
851dcf14ee3a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
294 <param name="db_file" ftype="fasta" value="Uniprot.fasta"/>
851dcf14ee3a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
295 <param name="spectrum_file" ftype="mgf" value="iTRAQ_f4.mgf"/>
851dcf14ee3a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
296 </section>
851dcf14ee3a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
297 <section name="modifications">
851dcf14ee3a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
298 <param name="fixed_mod" value="6,103,157"/>
851dcf14ee3a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
299 <param name="var_mod" value="117"/>
851dcf14ee3a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
300 <param name="max_mods" value="3"/>
851dcf14ee3a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
301 <param name="unmodified" value="False"/>
851dcf14ee3a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
302 <param name="aa" value="True"/>
851dcf14ee3a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
303 </section>
851dcf14ee3a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
304 <section name="ms_params">
851dcf14ee3a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
305 <section name="tolerance_params">
851dcf14ee3a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
306 <param name="precursor_tolerance" value="10"/>
851dcf14ee3a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
307 <param name="precursor_unit" value="ppm"/>
851dcf14ee3a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
308 <param name="tolerance" value="0.6"/>
851dcf14ee3a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
309 </section>
851dcf14ee3a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
310 <section name="digestion">
851dcf14ee3a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
311 <param name="enzyme" value="0"/>
851dcf14ee3a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
312 <param name="max_missed_cleavages" value="2"/>
851dcf14ee3a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
313 </section>
851dcf14ee3a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
314 <section name="search">
851dcf14ee3a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
315 <param name="frag_method" value="1"/>
851dcf14ee3a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
316 <param name="scoring_method" value="1"/>
851dcf14ee3a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
317 <param name="max_charge" value="3"/>
851dcf14ee3a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
318 <param name="min_charge" value="2"/>
851dcf14ee3a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
319 <param name="min_peaks" value="10"/>
851dcf14ee3a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
320 <param name="min_score" value="12"/>
851dcf14ee3a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
321 <param name="max_length" value="45"/>
851dcf14ee3a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
322 <param name="num_random_peptides" value="1000"/>
851dcf14ee3a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
323 </section>
851dcf14ee3a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
324 </section>
851dcf14ee3a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
325 <param name="report_spectrum_file" value="true"/>
851dcf14ee3a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
326 <output name="psm_rank_txt">
851dcf14ee3a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
327 <assert_contents>
851dcf14ee3a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
328 <has_text text="ELGSSDLTAR" />
851dcf14ee3a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
329 <has_text text="SPYREFTDHLVK" />
851dcf14ee3a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
330 </assert_contents>
851dcf14ee3a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
331 </output>
851dcf14ee3a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
332 </test>
851dcf14ee3a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
333
851dcf14ee3a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
334 <test>
851dcf14ee3a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
335 <section name="req_inputs">
851dcf14ee3a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
336 <conditional name="input_type">
851dcf14ee3a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
337 <param name="input_type_selector" value="1"/>
851dcf14ee3a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
338 <conditional name="multiple">
851dcf14ee3a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
339 <param name="protein_input_selector" value="multiple" />
851dcf14ee3a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
340 <param name="input" ftype="fasta" value="novel_proteins.fa"/>
851dcf14ee3a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
341 </conditional>
851dcf14ee3a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
342 </conditional>
851dcf14ee3a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
343 <param name="db_file" ftype="fasta" value="Uniprot.fasta"/>
851dcf14ee3a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
344 <param name="spectrum_file" ftype="mgf" value="iTRAQ_f4.mgf"/>
851dcf14ee3a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
345 </section>
851dcf14ee3a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
346 <section name="modifications">
851dcf14ee3a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
347 <param name="fixed_mod" value="6,103,157"/>
851dcf14ee3a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
348 <param name="var_mod" value="117"/>
851dcf14ee3a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
349 <param name="max_mods" value="3"/>
851dcf14ee3a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
350 <param name="unmodified" value="False"/>
851dcf14ee3a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
351 <param name="aa" value="True"/>
851dcf14ee3a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
352 </section>
851dcf14ee3a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
353 <section name="ms_params">
851dcf14ee3a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
354 <section name="tolerance_params">
851dcf14ee3a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
355 <param name="precursor_tolerance" value="10"/>
851dcf14ee3a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
356 <param name="precursor_unit" value="ppm"/>
851dcf14ee3a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
357 <param name="tolerance" value="0.6"/>
851dcf14ee3a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
358 </section>
851dcf14ee3a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
359 <section name="digestion">
851dcf14ee3a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
360 <param name="enzyme" value="0"/>
851dcf14ee3a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
361 <param name="max_missed_cleavages" value="2"/>
851dcf14ee3a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
362 </section>
851dcf14ee3a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
363 <section name="search">
851dcf14ee3a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
364 <param name="frag_method" value="1"/>
851dcf14ee3a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
365 <param name="scoring_method" value="1"/>
851dcf14ee3a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
366 <param name="max_charge" value="3"/>
851dcf14ee3a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
367 <param name="min_charge" value="2"/>
851dcf14ee3a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
368 <param name="min_peaks" value="10"/>
851dcf14ee3a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
369 <param name="min_score" value="12"/>
851dcf14ee3a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
370 <param name="max_length" value="45"/>
851dcf14ee3a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
371 <param name="num_random_peptides" value="1000"/>
851dcf14ee3a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
372 </section>
851dcf14ee3a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
373 </section>
851dcf14ee3a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
374 <param name="report_spectrum_file" value="true"/>
851dcf14ee3a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
375 <output name="psm_rank_txt">
851dcf14ee3a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
376 <assert_contents>
851dcf14ee3a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
377 <has_text text="ELGSSDLTAR" />
851dcf14ee3a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
378 <has_text text="SPYREFTDHLVK" />
851dcf14ee3a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
379 </assert_contents>
851dcf14ee3a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
380 </output>
851dcf14ee3a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
381 </test>
851dcf14ee3a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
382
851dcf14ee3a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
383 <test>
851dcf14ee3a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
384 <section name="req_inputs">
851dcf14ee3a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
385 <conditional name="input_type">
851dcf14ee3a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
386 <param name="input_type_selector" value="2"/>
851dcf14ee3a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
387 <param name="input" value="gaactgggcagcagcgatctgaccgcgcgcagcccgtatcgcgaatttaccgatcatctggtgaaa"/>
851dcf14ee3a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
388 </conditional>
851dcf14ee3a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
389 <param name="db_file" ftype="fasta" value="Uniprot.fasta"/>
851dcf14ee3a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
390 <param name="spectrum_file" ftype="mgf" value="iTRAQ_f4.mgf"/>
851dcf14ee3a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
391 </section>
851dcf14ee3a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
392 <section name="modifications">
851dcf14ee3a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
393 <param name="fixed_mod" value="6,103,157"/>
851dcf14ee3a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
394 <param name="var_mod" value="117"/>
851dcf14ee3a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
395 <param name="max_mods" value="3"/>
851dcf14ee3a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
396 <param name="unmodified" value="False"/>
851dcf14ee3a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
397 <param name="aa" value="True"/>
851dcf14ee3a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
398 </section>
851dcf14ee3a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
399 <section name="ms_params">
851dcf14ee3a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
400 <section name="tolerance_params">
851dcf14ee3a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
401 <param name="precursor_tolerance" value="10"/>
851dcf14ee3a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
402 <param name="precursor_unit" value="ppm"/>
851dcf14ee3a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
403 <param name="tolerance" value="0.6"/>
851dcf14ee3a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
404 </section>
851dcf14ee3a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
405 <section name="digestion">
851dcf14ee3a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
406 <param name="enzyme" value="0"/>
851dcf14ee3a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
407 <param name="max_missed_cleavages" value="2"/>
851dcf14ee3a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
408 </section>
851dcf14ee3a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
409 <section name="search">
851dcf14ee3a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
410 <param name="frag_method" value="1"/>
851dcf14ee3a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
411 <param name="scoring_method" value="1"/>
851dcf14ee3a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
412 <param name="max_charge" value="3"/>
851dcf14ee3a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
413 <param name="min_charge" value="2"/>
851dcf14ee3a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
414 <param name="min_peaks" value="10"/>
851dcf14ee3a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
415 <param name="min_score" value="12"/>
851dcf14ee3a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
416 <param name="max_length" value="45"/>
851dcf14ee3a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
417 <param name="num_random_peptides" value="1000"/>
851dcf14ee3a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
418 </section>
851dcf14ee3a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
419 </section>
851dcf14ee3a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
420 <param name="report_spectrum_file" value="true"/>
851dcf14ee3a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
421 <output name="psm_rank_txt">
851dcf14ee3a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
422 <assert_contents>
851dcf14ee3a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
423 <has_text text="ELGSSDLTAR" />
851dcf14ee3a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
424 </assert_contents>
851dcf14ee3a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
425 </output>
851dcf14ee3a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
426 </test>
851dcf14ee3a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
427
851dcf14ee3a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
428 </tests>
851dcf14ee3a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
429 <help><![CDATA[
851dcf14ee3a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
430 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.
851dcf14ee3a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
431
851dcf14ee3a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
432 **Inputs**
851dcf14ee3a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
433 - A sequence to match, one of the following:
851dcf14ee3a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
434
851dcf14ee3a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
435 - A peptide string or a history dataset with a list of peptides
851dcf14ee3a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
436 - A protein string or a history dataset with a protein fasta
851dcf14ee3a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
437 - A DNA string that is at least 60 base pairs in length
851dcf14ee3a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
438
851dcf14ee3a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
439 - A mass spectrometry MGF file
851dcf14ee3a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
440 - A reference protein fasta database, peptides matching a reference sequence will be excluded.
851dcf14ee3a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
441
851dcf14ee3a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
442 **Outputs**
851dcf14ee3a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
443 - PSM annotation - tabular with columns:
851dcf14ee3a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
444 peptide Query calc_mr observed_mz charge pepSeq m_label m_mz m_intensity mz intensity
851dcf14ee3a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
445 - Detail - tabular with columns:
851dcf14ee3a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
446 *report_spectrum_file* spectrum_title peptide modification pep_mass score
851dcf14ee3a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
447 - PSM - tabular with columns:
851dcf14ee3a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
448 peptide modification n *report_spectrum_file* spectrum_title charge exp_mass ppm pep_mass mz score n_db total_db n_random total_random pvalue
851dcf14ee3a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
449 - PSM Rank - tabular with columns:
851dcf14ee3a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
450 peptide modification n *report_spectrum_file* spectrum_title charge exp_mass ppm pep_mass mz score n_db total_db n_random total_random pvalue rank *n_ptm*
851dcf14ee3a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
451 - An MGF with the best matching spectrums
851dcf14ee3a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
452
851dcf14ee3a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
453 The *report_spectrum_file* is an optional field that can be added.
851dcf14ee3a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
454 The *n_ptm* field is added when using unrestricted modification searching (-um).
851dcf14ee3a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
455
851dcf14ee3a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
456
851dcf14ee3a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
457 ]]></help>
851dcf14ee3a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
458 <citations>
851dcf14ee3a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
459 <citation type="doi">10.1101/gr.235028.118</citation>
851dcf14ee3a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
460 </citations>
851dcf14ee3a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff changeset
461 </tool>