Mercurial > repos > galaxyp > myrimatch
annotate myrimatch.xml @ 14:0f9b9855afda draft
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot commit e28e65d5554b851fa7880f0bfe32870524852276"
author | galaxyp |
---|---|
date | Fri, 12 Jun 2020 14:54:26 +0000 |
parents | 71967a735760 |
children |
rev | line source |
---|---|
4
e0584c24d0e7
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 2a4b1c0e842f356239c141ea7cad867d91607c6a
galaxyp
parents:
3
diff
changeset
|
1 <tool id="myrimatch" version="@VERSION@.0" name="MyriMatch"> |
0
cedaffdc5e40
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty
galaxyp
parents:
diff
changeset
|
2 <description>Identify peptides in tandem mass spectra.</description> |
4
e0584c24d0e7
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 2a4b1c0e842f356239c141ea7cad867d91607c6a
galaxyp
parents:
3
diff
changeset
|
3 <macros> |
e0584c24d0e7
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 2a4b1c0e842f356239c141ea7cad867d91607c6a
galaxyp
parents:
3
diff
changeset
|
4 <import>macros.xml</import> |
e0584c24d0e7
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 2a4b1c0e842f356239c141ea7cad867d91607c6a
galaxyp
parents:
3
diff
changeset
|
5 </macros> |
e0584c24d0e7
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 2a4b1c0e842f356239c141ea7cad867d91607c6a
galaxyp
parents:
3
diff
changeset
|
6 <expand macro="requirements" /> |
0
cedaffdc5e40
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty
galaxyp
parents:
diff
changeset
|
7 <stdio> |
cedaffdc5e40
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty
galaxyp
parents:
diff
changeset
|
8 <exit_code range="1:" level="fatal" description="Job Failed" /> |
cedaffdc5e40
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty
galaxyp
parents:
diff
changeset
|
9 <regex match="^Could not find the default configuration file.*$" |
cedaffdc5e40
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty
galaxyp
parents:
diff
changeset
|
10 source="both" |
cedaffdc5e40
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty
galaxyp
parents:
diff
changeset
|
11 level="warning" /> |
cedaffdc5e40
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty
galaxyp
parents:
diff
changeset
|
12 </stdio> |
cedaffdc5e40
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty
galaxyp
parents:
diff
changeset
|
13 <command> |
cedaffdc5e40
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty
galaxyp
parents:
diff
changeset
|
14 <![CDATA[ |
cedaffdc5e40
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty
galaxyp
parents:
diff
changeset
|
15 #set $db_name = $ProteinDatabase.display_name.replace(".fasta", "") + ".fasta" |
6
7ba6c7b12b30
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 9eee537ea6d1e33b21596390767e7701f95a67d3
galaxyp
parents:
4
diff
changeset
|
16 #if $OutputFormat.value == "mzIdentML" |
0
cedaffdc5e40
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty
galaxyp
parents:
diff
changeset
|
17 #set $output_ext="mzid" |
cedaffdc5e40
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty
galaxyp
parents:
diff
changeset
|
18 #else |
cedaffdc5e40
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty
galaxyp
parents:
diff
changeset
|
19 #set $output_ext="pepXML" |
cedaffdc5e40
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty
galaxyp
parents:
diff
changeset
|
20 #end if |
cedaffdc5e40
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty
galaxyp
parents:
diff
changeset
|
21 #set $input_name = $input.display_name |
cedaffdc5e40
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty
galaxyp
parents:
diff
changeset
|
22 #set $output_name = $input_name.split(".")[0] + "." + $output_ext |
cedaffdc5e40
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty
galaxyp
parents:
diff
changeset
|
23 |
cedaffdc5e40
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty
galaxyp
parents:
diff
changeset
|
24 #set $static_mods_str = "" |
cedaffdc5e40
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty
galaxyp
parents:
diff
changeset
|
25 #for $static_mod in $StaticMods |
cedaffdc5e40
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty
galaxyp
parents:
diff
changeset
|
26 #set $static_mods_str = $static_mods_str + " " + str($static_mod.aa) + " " + str($static_mod.mass) |
cedaffdc5e40
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty
galaxyp
parents:
diff
changeset
|
27 #end for |
3
c5e2f015165d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 23c80475d116664d179cd42a969b0b6bc33419ad
galaxyp
parents:
2
diff
changeset
|
28 #set $static_mods_str = $static_mods_str.lstrip() |
0
cedaffdc5e40
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty
galaxyp
parents:
diff
changeset
|
29 |
cedaffdc5e40
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty
galaxyp
parents:
diff
changeset
|
30 #set $dynamic_mods_str = "" |
cedaffdc5e40
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty
galaxyp
parents:
diff
changeset
|
31 #for $dynamic_mod in $DynamicMods |
cedaffdc5e40
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty
galaxyp
parents:
diff
changeset
|
32 #set $dynamic_mods_str = $dynamic_mods_str + " " + str($dynamic_mod.motif) + " * " + str($dynamic_mod.mass) |
cedaffdc5e40
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty
galaxyp
parents:
diff
changeset
|
33 #end for |
3
c5e2f015165d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 23c80475d116664d179cd42a969b0b6bc33419ad
galaxyp
parents:
2
diff
changeset
|
34 #set $dynamic_mods_str = $dynamic_mods_str.lstrip() |
0
cedaffdc5e40
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty
galaxyp
parents:
diff
changeset
|
35 |
cedaffdc5e40
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty
galaxyp
parents:
diff
changeset
|
36 ln -s '$input' '${input_name}' && |
cedaffdc5e40
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty
galaxyp
parents:
diff
changeset
|
37 ln -s '$ProteinDatabase' '${db_name}' && |
cedaffdc5e40
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty
galaxyp
parents:
diff
changeset
|
38 myrimatch -DecoyPrefix '${DecoyPrefix}' -cpus \${GALAXY_SLOTS:-1} |
cedaffdc5e40
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty
galaxyp
parents:
diff
changeset
|
39 -ProteinDatabase '${db_name}' |
cedaffdc5e40
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty
galaxyp
parents:
diff
changeset
|
40 -OutputFormat '${OutputFormat}' |
cedaffdc5e40
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty
galaxyp
parents:
diff
changeset
|
41 '${input_name}' |
cedaffdc5e40
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty
galaxyp
parents:
diff
changeset
|
42 -StaticMods '${static_mods_str}' |
cedaffdc5e40
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty
galaxyp
parents:
diff
changeset
|
43 -DynamicMods '${dynamic_mods_str}' |
cedaffdc5e40
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty
galaxyp
parents:
diff
changeset
|
44 -MaxDynamicMods $MaxDynamicMods |
cedaffdc5e40
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty
galaxyp
parents:
diff
changeset
|
45 -CleavageRules '${CleavageRules}' |
cedaffdc5e40
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty
galaxyp
parents:
diff
changeset
|
46 -MinTerminiCleavages $MinTerminiCleavages |
cedaffdc5e40
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty
galaxyp
parents:
diff
changeset
|
47 -MaxMissedCleavages $MaxMissedCleavages |
cedaffdc5e40
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty
galaxyp
parents:
diff
changeset
|
48 #set $precursor_type = $tolerance_options.precursor_tolerance.PrecursorMzToleranceRule |
cedaffdc5e40
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty
galaxyp
parents:
diff
changeset
|
49 -PrecursorMzToleranceRule '${tolerance_options.precursor_tolerance.PrecursorMzToleranceRule}' |
cedaffdc5e40
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty
galaxyp
parents:
diff
changeset
|
50 #if $tolerance_options.precursor_tolerance.PrecursorMzToleranceRule == "auto" or $tolerance_options.precursor_tolerance.PrecursorMzToleranceRule == "mono" |
cedaffdc5e40
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty
galaxyp
parents:
diff
changeset
|
51 -MonoPrecursorMzTolerance '${tolerance_options.precursor_tolerance.MonoPrecursorMzTolerance}${tolerance_options.precursor_tolerance.mono_precursor_mz_tolerance_units}' |
cedaffdc5e40
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty
galaxyp
parents:
diff
changeset
|
52 #end if |
cedaffdc5e40
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty
galaxyp
parents:
diff
changeset
|
53 #if $tolerance_options.precursor_tolerance.PrecursorMzToleranceRule == "auto" or $tolerance_options.precursor_tolerance.PrecursorMzToleranceRule == "avg" |
cedaffdc5e40
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty
galaxyp
parents:
diff
changeset
|
54 -AvgPrecursorMzTolerance '${tolerance_options.precursor_tolerance.AvgPrecursorMzTolerance}${tolerance_options.precursor_tolerance.avg_precursor_mz_tolerance_units}' |
cedaffdc5e40
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty
galaxyp
parents:
diff
changeset
|
55 #end if |
cedaffdc5e40
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty
galaxyp
parents:
diff
changeset
|
56 -FragmentMzTolerance '${tolerance_options.FragmentMzTolerance}${tolerance_options.fragment_mz_tolerance_units}' |
cedaffdc5e40
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty
galaxyp
parents:
diff
changeset
|
57 -UseSmartPlusThreeModel $advanced.UseSmartPlusThreeModel |
cedaffdc5e40
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty
galaxyp
parents:
diff
changeset
|
58 -MinPeptideLength $advanced.MinPeptideLength |
cedaffdc5e40
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty
galaxyp
parents:
diff
changeset
|
59 -MaxPeptideLength $advanced.MaxPeptideLength |
cedaffdc5e40
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty
galaxyp
parents:
diff
changeset
|
60 -NumChargeStates $advanced.NumChargeStates |
cedaffdc5e40
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty
galaxyp
parents:
diff
changeset
|
61 -MaxResultRank $advanced.MaxResultRank |
cedaffdc5e40
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty
galaxyp
parents:
diff
changeset
|
62 #set $set = str($advanced.MonoisotopeAdjustmentSet).replace("[[", "[").replace("]]","]") |
cedaffdc5e40
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty
galaxyp
parents:
diff
changeset
|
63 -MonoisotopeAdjustmentSet '$set' |
cedaffdc5e40
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty
galaxyp
parents:
diff
changeset
|
64 #if $advanced.MaxPeakCount |
cedaffdc5e40
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty
galaxyp
parents:
diff
changeset
|
65 -MaxPeakCount $advanced.MaxPeakCount |
cedaffdc5e40
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty
galaxyp
parents:
diff
changeset
|
66 #end if |
cedaffdc5e40
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty
galaxyp
parents:
diff
changeset
|
67 #if $advanced.fragmentation_rule.FragmentationAutoRule |
cedaffdc5e40
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty
galaxyp
parents:
diff
changeset
|
68 -FragmentationAutoRule false -FragmentationRule 'manual:${advanced.fragmentation_rule.FragmentationRule}' |
cedaffdc5e40
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty
galaxyp
parents:
diff
changeset
|
69 #end if |
cedaffdc5e40
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty
galaxyp
parents:
diff
changeset
|
70 && |
cedaffdc5e40
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty
galaxyp
parents:
diff
changeset
|
71 mv '$output_name' output |
cedaffdc5e40
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty
galaxyp
parents:
diff
changeset
|
72 ]]> |
cedaffdc5e40
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty
galaxyp
parents:
diff
changeset
|
73 </command> |
cedaffdc5e40
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty
galaxyp
parents:
diff
changeset
|
74 <inputs> |
3
c5e2f015165d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 23c80475d116664d179cd42a969b0b6bc33419ad
galaxyp
parents:
2
diff
changeset
|
75 <param name="input" type="data" format="mzml,mzxml,mgf,ms2,mz5" label="Input Raw MS File(s)"/> |
0
cedaffdc5e40
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty
galaxyp
parents:
diff
changeset
|
76 <param argument="-OutputFormat" type="select" label="Output Type" help="The file format to use for results of the search."> |
cedaffdc5e40
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty
galaxyp
parents:
diff
changeset
|
77 <option value="pepXML">pepXML</option> |
6
7ba6c7b12b30
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 9eee537ea6d1e33b21596390767e7701f95a67d3
galaxyp
parents:
4
diff
changeset
|
78 <option value="mzIdentML">mzIdentML</option> |
0
cedaffdc5e40
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty
galaxyp
parents:
diff
changeset
|
79 </param> |
cedaffdc5e40
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty
galaxyp
parents:
diff
changeset
|
80 <param argument="-ProteinDatabase" format="fasta" type="data" label="Protein Database" help="The FASTA protein database to search against. Only amino-acid type FASTA is supported." /> |
cedaffdc5e40
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty
galaxyp
parents:
diff
changeset
|
81 <param argument="-DecoyPrefix" type="text" label="Decoy Prefix" value="rev_" help="If the protein database contains accessions prefixed with this string, those proteins will be considered decoys. If there are no decoy protein, this prefix will be used to generate an automatic decoy for each target protein. Set this to an empty string to disable automatic decoys." /> |
cedaffdc5e40
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty
galaxyp
parents:
diff
changeset
|
82 <param argument="-CleavageRules" type="select" label="Cleavage Agent" help="The cleavage agent to generate in silico peptides from the protein database." > |
cedaffdc5e40
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty
galaxyp
parents:
diff
changeset
|
83 <option value="Trypsin/P">Trypsin/P (allows for cut after K or R)</option> |
cedaffdc5e40
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty
galaxyp
parents:
diff
changeset
|
84 <option value="Trypsin">Trypsin (normal trypsin cut, disallows cutting when the site is before a proline)</option> |
cedaffdc5e40
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty
galaxyp
parents:
diff
changeset
|
85 <option value="Chymotrypsin">Chymotrypsin (allows cut after F,Y,W,L. Disallows cutting before proline)</option> |
cedaffdc5e40
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty
galaxyp
parents:
diff
changeset
|
86 <option value="TrypChymo">TrypChymo (combines "Trypsin/P" and "Chymotrypsin" cleavage rules)</option> |
cedaffdc5e40
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty
galaxyp
parents:
diff
changeset
|
87 <option value="Lys-C">Lys-C</option> |
cedaffdc5e40
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty
galaxyp
parents:
diff
changeset
|
88 <option value="Lys-C/P">Lys-C/P (Lys-C, disallowing cutting before proline)</option> |
cedaffdc5e40
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty
galaxyp
parents:
diff
changeset
|
89 <option value="Asp-N">Asp-N</option> |
cedaffdc5e40
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty
galaxyp
parents:
diff
changeset
|
90 <option value="PepsinA">PepsinA (cuts right after F, L)</option> |
cedaffdc5e40
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty
galaxyp
parents:
diff
changeset
|
91 <option value="CNBr">CNBr (cyanogen bromide)</option> |
cedaffdc5e40
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty
galaxyp
parents:
diff
changeset
|
92 <option value="Formic_acid">Formic acid</option> |
13
71967a735760
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot commit 443a91ed5ca98c92635897f670b8f4efda51c78d
galaxyp
parents:
6
diff
changeset
|
93 <option value="Glu-C">Glu-C (glutamyl endopeptidase)</option> |
0
cedaffdc5e40
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty
galaxyp
parents:
diff
changeset
|
94 </param> |
cedaffdc5e40
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty
galaxyp
parents:
diff
changeset
|
95 <param argument="-MinTerminiCleavages" type="select" label="Cleavage Specificity" help="Controls which peptide termini must match the cleavage rules."> |
cedaffdc5e40
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty
galaxyp
parents:
diff
changeset
|
96 <option value="2">Fully specific (both termini match cleavage rules)</option> |
cedaffdc5e40
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty
galaxyp
parents:
diff
changeset
|
97 <option value="1" selected="true">Semi-specific (at least one terminus must match cleavage rules)</option> |
cedaffdc5e40
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty
galaxyp
parents:
diff
changeset
|
98 <option value="0">Non-specific (neither terminus is required to match cleavage rules)</option> |
cedaffdc5e40
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty
galaxyp
parents:
diff
changeset
|
99 </param> |
2
4bb0872e2b5f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 98f3323d4b92a4a3668788b3e1bad1a6529fd6df-dirty
galaxyp
parents:
0
diff
changeset
|
100 <param argument="-MaxMissedCleavages" type="integer" min="0" value="2" label="Maximum Missed Cleavages" help="Candidate peptides with more than this number of uncleaved cleavage sites will be skipped." /> |
3
c5e2f015165d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 23c80475d116664d179cd42a969b0b6bc33419ad
galaxyp
parents:
2
diff
changeset
|
101 <repeat name="StaticMods" title="Static Modifications" help="Modifications that are always applied to an amino acid. (-StaticMods)"> |
0
cedaffdc5e40
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty
galaxyp
parents:
diff
changeset
|
102 <param name="aa" type="text" label="Amino Acid"> |
cedaffdc5e40
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty
galaxyp
parents:
diff
changeset
|
103 <sanitizer><valid initial="string.ascii_uppercase"><remove value="B"/><remove value="J"/><remove value="O"/><remove value="Z"/></valid></sanitizer> |
cedaffdc5e40
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty
galaxyp
parents:
diff
changeset
|
104 </param> |
cedaffdc5e40
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty
galaxyp
parents:
diff
changeset
|
105 <param name="mass" type="float" label="Mass" value="0" /> |
cedaffdc5e40
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty
galaxyp
parents:
diff
changeset
|
106 </repeat> |
3
c5e2f015165d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 23c80475d116664d179cd42a969b0b6bc33419ad
galaxyp
parents:
2
diff
changeset
|
107 <repeat name="DynamicMods" title="Dynamic Modifications" help="Modifications that can either be present or absent on an amino acid. (-DynamicMods)"> |
0
cedaffdc5e40
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty
galaxyp
parents:
diff
changeset
|
108 <param name="motif" type="text" label="Amino Acid Motif"> |
cedaffdc5e40
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty
galaxyp
parents:
diff
changeset
|
109 <sanitizer> |
cedaffdc5e40
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty
galaxyp
parents:
diff
changeset
|
110 <valid initial="string.ascii_uppercase"> |
cedaffdc5e40
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty
galaxyp
parents:
diff
changeset
|
111 <remove value="B"/><remove value="J"/><remove value="O"/><remove value="Z"/> |
cedaffdc5e40
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty
galaxyp
parents:
diff
changeset
|
112 <add value="["/><add value="]"/> |
cedaffdc5e40
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty
galaxyp
parents:
diff
changeset
|
113 <add value="("/><add value=")"/> |
cedaffdc5e40
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty
galaxyp
parents:
diff
changeset
|
114 <add value="{"/><add value="}"/> |
cedaffdc5e40
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty
galaxyp
parents:
diff
changeset
|
115 <add value="."/> |
cedaffdc5e40
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty
galaxyp
parents:
diff
changeset
|
116 <add value="!"/> |
cedaffdc5e40
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty
galaxyp
parents:
diff
changeset
|
117 </valid> |
cedaffdc5e40
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty
galaxyp
parents:
diff
changeset
|
118 </sanitizer> |
cedaffdc5e40
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty
galaxyp
parents:
diff
changeset
|
119 </param> |
cedaffdc5e40
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty
galaxyp
parents:
diff
changeset
|
120 <param name="mass" type="float" label="Mass" value="0" /> |
cedaffdc5e40
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty
galaxyp
parents:
diff
changeset
|
121 </repeat> |
2
4bb0872e2b5f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 98f3323d4b92a4a3668788b3e1bad1a6529fd6df-dirty
galaxyp
parents:
0
diff
changeset
|
122 <param argument="-MaxDynamicMods" type="integer" min="0" value="4" label="Maximum Dynamic Mods" help="Candidate peptides with more than this number of dynamic modifications will be skipped." /> |
0
cedaffdc5e40
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty
galaxyp
parents:
diff
changeset
|
123 <section name="tolerance_options" title="M/Z Tolerance Options" expanded="True"> |
cedaffdc5e40
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty
galaxyp
parents:
diff
changeset
|
124 <conditional name="precursor_tolerance"> |
cedaffdc5e40
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty
galaxyp
parents:
diff
changeset
|
125 <param argument="-PrecursorMzToleranceRule" type="select" label="Precursor Mass Type" help="For data from Thermo instruments, using the 'auto' setting on a will automatically choose monoisotopic or average mass values, for other instruments monoisotopic or average should be chosen."> |
cedaffdc5e40
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty
galaxyp
parents:
diff
changeset
|
126 <option value="auto">Auto</option> |
cedaffdc5e40
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty
galaxyp
parents:
diff
changeset
|
127 <option value="avg">Average</option> |
cedaffdc5e40
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty
galaxyp
parents:
diff
changeset
|
128 <option value="mono">Monoisotopic</option> |
cedaffdc5e40
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty
galaxyp
parents:
diff
changeset
|
129 </param> |
cedaffdc5e40
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty
galaxyp
parents:
diff
changeset
|
130 <when value="auto"> |
2
4bb0872e2b5f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 98f3323d4b92a4a3668788b3e1bad1a6529fd6df-dirty
galaxyp
parents:
0
diff
changeset
|
131 <param argument="-MonoPrecursorMzTolerance" type="float" min="0.000001" value="10" label="Monoisotopic Precursor m/z Tolerance" help="This tolerance will be used for spectra that are determined to have monoisotopic precursors. MonoisotopeAdjustmentSet is applied to these." /> |
0
cedaffdc5e40
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty
galaxyp
parents:
diff
changeset
|
132 <param name="mono_precursor_mz_tolerance_units" type="select" label="Monoisotopic Precursor m/z Tolerance Units"> |
cedaffdc5e40
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty
galaxyp
parents:
diff
changeset
|
133 <option value="ppm">Parts per million</option> |
cedaffdc5e40
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty
galaxyp
parents:
diff
changeset
|
134 <option value="daltons">Daltons</option> |
cedaffdc5e40
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty
galaxyp
parents:
diff
changeset
|
135 </param> |
2
4bb0872e2b5f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 98f3323d4b92a4a3668788b3e1bad1a6529fd6df-dirty
galaxyp
parents:
0
diff
changeset
|
136 <param argument="-AvgPrecursorMzTolerance" type="float" min="0.000001" value="1.25" label="Average Precursor m/z Tolerance" help="This tolerance will be used for spectra that are determined to have average mass precursors. MonoisotopeAdjustmentSet is not applied to these." /> |
0
cedaffdc5e40
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty
galaxyp
parents:
diff
changeset
|
137 <param name="avg_precursor_mz_tolerance_units" type="select" label="Average Precursor m/z Tolerance Units"> |
cedaffdc5e40
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty
galaxyp
parents:
diff
changeset
|
138 <option value="ppm">Parts per million</option> |
cedaffdc5e40
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty
galaxyp
parents:
diff
changeset
|
139 <option value="daltons" selected="true">Daltons</option> |
cedaffdc5e40
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty
galaxyp
parents:
diff
changeset
|
140 </param> |
cedaffdc5e40
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty
galaxyp
parents:
diff
changeset
|
141 </when> |
cedaffdc5e40
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty
galaxyp
parents:
diff
changeset
|
142 <when value="avg"> |
2
4bb0872e2b5f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 98f3323d4b92a4a3668788b3e1bad1a6529fd6df-dirty
galaxyp
parents:
0
diff
changeset
|
143 <param argument="-AvgPrecursorMzTolerance" type="float" min="0.000001" value="1.25" label="Average Precursor m/z Tolerance" help="This tolerance will be used for all spectra, but MonoisotopeAdjustmentSet will never be applied." /> |
0
cedaffdc5e40
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty
galaxyp
parents:
diff
changeset
|
144 <param name="avg_precursor_mz_tolerance_units" type="select" label="Average Precursor m/z Tolerance Units"> |
cedaffdc5e40
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty
galaxyp
parents:
diff
changeset
|
145 <option value="ppm">Parts per million</option> |
cedaffdc5e40
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty
galaxyp
parents:
diff
changeset
|
146 <option value="daltons" selected="true">Daltons</option> |
cedaffdc5e40
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty
galaxyp
parents:
diff
changeset
|
147 </param> |
cedaffdc5e40
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty
galaxyp
parents:
diff
changeset
|
148 </when> |
cedaffdc5e40
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty
galaxyp
parents:
diff
changeset
|
149 <when value="mono"> |
2
4bb0872e2b5f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 98f3323d4b92a4a3668788b3e1bad1a6529fd6df-dirty
galaxyp
parents:
0
diff
changeset
|
150 <param argument="-MonoPrecursorMzTolerance" type="float" min="0.000001" value="10" label="Monoisotopic Precursor m/z Tolerance" help="This tolerance will be used for all spectra, and MonoisotopeAdjustmentSet is likewise applied to all spectra." /> |
0
cedaffdc5e40
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty
galaxyp
parents:
diff
changeset
|
151 <param name="mono_precursor_mz_tolerance_units" type="select" label="Monoisotopic Precursor m/z Tolerance Units"> |
cedaffdc5e40
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty
galaxyp
parents:
diff
changeset
|
152 <option value="ppm">Parts per million</option> |
cedaffdc5e40
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty
galaxyp
parents:
diff
changeset
|
153 <option value="daltons">Daltons</option> |
cedaffdc5e40
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty
galaxyp
parents:
diff
changeset
|
154 </param> |
cedaffdc5e40
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty
galaxyp
parents:
diff
changeset
|
155 </when> |
cedaffdc5e40
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty
galaxyp
parents:
diff
changeset
|
156 </conditional> |
2
4bb0872e2b5f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 98f3323d4b92a4a3668788b3e1bad1a6529fd6df-dirty
galaxyp
parents:
0
diff
changeset
|
157 <param argument="-FragmentMzTolerance" type="float" min="0.000001" value="0.5" label="Fragment m/z Tolerance" help="This tolerance is used for matching to fragment ions." /> |
0
cedaffdc5e40
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty
galaxyp
parents:
diff
changeset
|
158 <param name="fragment_mz_tolerance_units" type="select" label="Fragment m/z Tolerance Units"> |
cedaffdc5e40
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty
galaxyp
parents:
diff
changeset
|
159 <option value="ppm">Parts per million</option> |
cedaffdc5e40
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty
galaxyp
parents:
diff
changeset
|
160 <option value="daltons" selected="true">Daltons</option> |
cedaffdc5e40
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty
galaxyp
parents:
diff
changeset
|
161 </param> |
cedaffdc5e40
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty
galaxyp
parents:
diff
changeset
|
162 </section> |
cedaffdc5e40
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty
galaxyp
parents:
diff
changeset
|
163 <section name="advanced" title="Advanced Options" expanded="False"> |
2
4bb0872e2b5f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 98f3323d4b92a4a3668788b3e1bad1a6529fd6df-dirty
galaxyp
parents:
0
diff
changeset
|
164 <param argument="-MaxPeakCount" type="integer" min="10" value="" optional="true" label="Use Max Peaks" help="Filter out all but the specified number of peaks, keep empty to use all peaks." /> |
0
cedaffdc5e40
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty
galaxyp
parents:
diff
changeset
|
165 <conditional name="fragmentation_rule"> |
cedaffdc5e40
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty
galaxyp
parents:
diff
changeset
|
166 <param argument="-FragmentationAutoRule" type="boolean" label="Override Fragmentation Rule (Ion Series)" help="If the input file provides mass analyzer information (mzML, mzXML, mz5), MyriMatch can automatically choose the ion series to search on a scan-by-scan basis." /> |
cedaffdc5e40
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty
galaxyp
parents:
diff
changeset
|
167 <when value="false" /> |
cedaffdc5e40
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty
galaxyp
parents:
diff
changeset
|
168 <when value="true"> |
cedaffdc5e40
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty
galaxyp
parents:
diff
changeset
|
169 <param argument="-FragmentationRule" type="text" label="Fragmentation Rule" help="Specify as a comma-separated list of a, b, c, x, y, z, or z* (z+1), e.g. 'b,y,z'" /> |
cedaffdc5e40
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty
galaxyp
parents:
diff
changeset
|
170 </when> |
cedaffdc5e40
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty
galaxyp
parents:
diff
changeset
|
171 </conditional> |
2
4bb0872e2b5f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 98f3323d4b92a4a3668788b3e1bad1a6529fd6df-dirty
galaxyp
parents:
0
diff
changeset
|
172 <param argument="-MinPeptideLength" type="integer" min="3" value="5" label="Minimum Peptide Length" help="Candidate peptides shorter than this will not be compared against any spectrum." /> |
4bb0872e2b5f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 98f3323d4b92a4a3668788b3e1bad1a6529fd6df-dirty
galaxyp
parents:
0
diff
changeset
|
173 <param argument="-MaxPeptideLength" type="integer" min="3" value="75" label="Maximum Peptide Length" help="Candidate peptides longer than this will not be compared against any spectrum." /> |
0
cedaffdc5e40
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty
galaxyp
parents:
diff
changeset
|
174 <param argument="-UseSmartPlusThreeModel" type="boolean" truevalue="true" falsevalue="false" label="Use Smart Plus 3 Model" help="For +3 and higher precursors, the fragment ions predicted depend on the way this parameter is set. When this parameter is true, then for each peptide bond, an internal calculation is done to estimate the basicity of the b and y fragment sequence. When this parameter is false, however, ALL possible charge distributions for the fragment ions are generated for every peptide bond." checked="true" /> |
2
4bb0872e2b5f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 98f3323d4b92a4a3668788b3e1bad1a6529fd6df-dirty
galaxyp
parents:
0
diff
changeset
|
175 <param argument="-NumChargeStates" type="integer" min="1" value="3" label="Number of Charge States" help="For spectra with an ambiguous multiple charge state, it will be treated as any charge in the range: [+2,NumChargeStates]." /> |
4bb0872e2b5f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 98f3323d4b92a4a3668788b3e1bad1a6529fd6df-dirty
galaxyp
parents:
0
diff
changeset
|
176 <param argument="-MaxResultRank" type="integer" min="1" value="2" label="Maximum Result Rank" help="The maximum rank of a search result (results with the same score occupy the same rank)." /> |
0
cedaffdc5e40
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty
galaxyp
parents:
diff
changeset
|
177 <param argument="-MonoisotopeAdjustmentSet" type="text" value="[-1,2]" label="Monoisotope Adjustment Set" help="For monoisotopic precursors where the monoisotope may have been incorrectly assigned to a nearby isotope, this range of adjustments will be considered. Instead of trying a wide precursor tolerance for a spectrum, this tries multiple tight tolerances."> |
cedaffdc5e40
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty
galaxyp
parents:
diff
changeset
|
178 <sanitizer invalid_char=""><valid initial="string.digits"><add value="["/><add value="]"/><add value=","/><add value="-"/></valid><mapping initial="none"></mapping></sanitizer> |
cedaffdc5e40
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty
galaxyp
parents:
diff
changeset
|
179 </param> |
cedaffdc5e40
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty
galaxyp
parents:
diff
changeset
|
180 </section> |
cedaffdc5e40
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty
galaxyp
parents:
diff
changeset
|
181 </inputs> |
cedaffdc5e40
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty
galaxyp
parents:
diff
changeset
|
182 <outputs> |
cedaffdc5e40
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty
galaxyp
parents:
diff
changeset
|
183 <data format="raw_pepxml" name="output" from_work_dir="output"> |
cedaffdc5e40
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty
galaxyp
parents:
diff
changeset
|
184 <change_format> |
6
7ba6c7b12b30
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 9eee537ea6d1e33b21596390767e7701f95a67d3
galaxyp
parents:
4
diff
changeset
|
185 <when input="OutputFormat" value="mzIdentML" format="mzid" /> |
0
cedaffdc5e40
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty
galaxyp
parents:
diff
changeset
|
186 </change_format> |
cedaffdc5e40
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty
galaxyp
parents:
diff
changeset
|
187 </data> |
cedaffdc5e40
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty
galaxyp
parents:
diff
changeset
|
188 </outputs> |
cedaffdc5e40
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty
galaxyp
parents:
diff
changeset
|
189 <tests> |
cedaffdc5e40
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty
galaxyp
parents:
diff
changeset
|
190 <test> |
cedaffdc5e40
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty
galaxyp
parents:
diff
changeset
|
191 <param name="input" value="input/201208-378803.mzML" /> |
cedaffdc5e40
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty
galaxyp
parents:
diff
changeset
|
192 <param name="ProteinDatabase" value="input/cow.protein.PRG2012-subset.fasta" /> |
cedaffdc5e40
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty
galaxyp
parents:
diff
changeset
|
193 <param name="DecoyPrefix" value="XXX_" /> |
cedaffdc5e40
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty
galaxyp
parents:
diff
changeset
|
194 <param name="StaticMods_0|aa" value="C" /> |
cedaffdc5e40
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty
galaxyp
parents:
diff
changeset
|
195 <param name="StaticMods_0|mass" value="58.00548" /> |
cedaffdc5e40
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty
galaxyp
parents:
diff
changeset
|
196 <param name="DynamicMods_0|motif" value="M" /> |
cedaffdc5e40
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty
galaxyp
parents:
diff
changeset
|
197 <param name="DynamicMods_0|mass" value="15.9949" /> |
cedaffdc5e40
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty
galaxyp
parents:
diff
changeset
|
198 <param name="DynamicMods_1|motif" value="(Q" /> |
cedaffdc5e40
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty
galaxyp
parents:
diff
changeset
|
199 <param name="DynamicMods_1|mass" value="-17.026" /> |
cedaffdc5e40
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty
galaxyp
parents:
diff
changeset
|
200 <param name="DynamicMods_2|motif" value="[QN]" /> |
cedaffdc5e40
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty
galaxyp
parents:
diff
changeset
|
201 <param name="DynamicMods_2|mass" value="0.984016" /> |
cedaffdc5e40
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty
galaxyp
parents:
diff
changeset
|
202 <param name="PrecursorMzToleranceRule" value="mono" /> |
cedaffdc5e40
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty
galaxyp
parents:
diff
changeset
|
203 <param name="MonoPrecursorMzTolerance" value="50" /> |
cedaffdc5e40
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty
galaxyp
parents:
diff
changeset
|
204 <param name="MinTerminiCleavages" value="1" /> |
cedaffdc5e40
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty
galaxyp
parents:
diff
changeset
|
205 <param name="MaxMissedCleavages" value="2" /> |
cedaffdc5e40
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty
galaxyp
parents:
diff
changeset
|
206 <param name="MaxDynamicMods" value="2" /> |
cedaffdc5e40
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty
galaxyp
parents:
diff
changeset
|
207 <param name="NumChargeStates" value="5" /> |
cedaffdc5e40
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty
galaxyp
parents:
diff
changeset
|
208 <param name="MaxResultRank" value="3" /> |
cedaffdc5e40
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty
galaxyp
parents:
diff
changeset
|
209 <param name="MonoisotopeAdjustmentSet" value="[-1,2]" /> |
cedaffdc5e40
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty
galaxyp
parents:
diff
changeset
|
210 <param name="UseSmartPlusThreeModel" value="false" /> |
14
0f9b9855afda
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot commit e28e65d5554b851fa7880f0bfe32870524852276"
galaxyp
parents:
13
diff
changeset
|
211 <output name="output" file="201208-378803-mm.pepXML" lines_diff="9000" /> |
0
cedaffdc5e40
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty
galaxyp
parents:
diff
changeset
|
212 </test> |
cedaffdc5e40
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty
galaxyp
parents:
diff
changeset
|
213 <test> |
cedaffdc5e40
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty
galaxyp
parents:
diff
changeset
|
214 <param name="input" value="input/201208-378803.mzML" /> |
cedaffdc5e40
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty
galaxyp
parents:
diff
changeset
|
215 <param name="ProteinDatabase" value="input/cow.protein.PRG2012-subset.fasta" /> |
cedaffdc5e40
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty
galaxyp
parents:
diff
changeset
|
216 <param name="CleavageRules" value="Trypsin" /> |
cedaffdc5e40
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty
galaxyp
parents:
diff
changeset
|
217 <param name="DecoyPrefix" value="XXX_" /> |
cedaffdc5e40
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty
galaxyp
parents:
diff
changeset
|
218 <param name="PrecursorMzToleranceRule" value="mono" /> |
cedaffdc5e40
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty
galaxyp
parents:
diff
changeset
|
219 <param name="MonoPrecursorMzTolerance" value="15" /> |
cedaffdc5e40
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty
galaxyp
parents:
diff
changeset
|
220 <param name="MinTerminiCleavages" value="2" /> |
cedaffdc5e40
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty
galaxyp
parents:
diff
changeset
|
221 <param name="MaxMissedCleavages" value="4" /> |
cedaffdc5e40
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty
galaxyp
parents:
diff
changeset
|
222 <param name="NumChargeStates" value="3" /> |
cedaffdc5e40
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty
galaxyp
parents:
diff
changeset
|
223 <param name="MaxResultRank" value="1" /> |
cedaffdc5e40
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty
galaxyp
parents:
diff
changeset
|
224 <param name="MonoisotopeAdjustmentSet" value="0" /> |
14
0f9b9855afda
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot commit e28e65d5554b851fa7880f0bfe32870524852276"
galaxyp
parents:
13
diff
changeset
|
225 <output name="output" file="201208-378803-mm-15ppm-fully-tryptic.pepXML" lines_diff="200" /> |
0
cedaffdc5e40
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty
galaxyp
parents:
diff
changeset
|
226 </test> |
cedaffdc5e40
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty
galaxyp
parents:
diff
changeset
|
227 </tests> |
cedaffdc5e40
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty
galaxyp
parents:
diff
changeset
|
228 <help> |
cedaffdc5e40
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty
galaxyp
parents:
diff
changeset
|
229 <![CDATA[ |
cedaffdc5e40
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty
galaxyp
parents:
diff
changeset
|
230 **What it does** |
cedaffdc5e40
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty
galaxyp
parents:
diff
changeset
|
231 |
cedaffdc5e40
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty
galaxyp
parents:
diff
changeset
|
232 Performs protein identification via database search using MyriMatch. |
cedaffdc5e40
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty
galaxyp
parents:
diff
changeset
|
233 ]]> |
cedaffdc5e40
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty
galaxyp
parents:
diff
changeset
|
234 </help> |
cedaffdc5e40
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty
galaxyp
parents:
diff
changeset
|
235 <citations> |
cedaffdc5e40
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty
galaxyp
parents:
diff
changeset
|
236 <citation type="doi">10.1021/pr0604054</citation> |
cedaffdc5e40
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty
galaxyp
parents:
diff
changeset
|
237 <citation type="bibtex">@misc{toolsGalaxyP, author = {Chilton, J, Chambers MC, et al.}, title = {Galaxy Proteomics Tools}, publisher = {GitHub}, journal = {GitHub repository}, |
cedaffdc5e40
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty
galaxyp
parents:
diff
changeset
|
238 year = {2015}, url = {https://github.com/galaxyproteomics/tools-galaxyp}}</citation> <!-- TODO: fix substitution of commit ", commit = {$sha1$}" --> |
cedaffdc5e40
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty
galaxyp
parents:
diff
changeset
|
239 </citations> |
cedaffdc5e40
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty
galaxyp
parents:
diff
changeset
|
240 </tool> |